diff --git a/head/abstracts.tex b/head/abstracts.tex index 98319f1..50563b0 100644 --- a/head/abstracts.tex +++ b/head/abstracts.tex @@ -1,72 +1,72 @@ %\begingroup %\let\cleardoublepage\clearpage % English abstract \cleardoublepage \chapter*{Abstract} \markboth{Abstract}{Abstract} \addcontentsline{toc}{chapter}{Abstract (English/Français/Deutsch)} % adds an entry to the table of contents % put your text here -Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the needed information that the organism will ever need, from its development to a mature individual to environment specific responses. Since all these instructions are not needed at the same time, the gene expression needs to be regulated. +Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the necessary information that the organism will ever need, from its development to a mature individual to environment specific responses. Since all these instructions are not needed at the same time, the gene expression needs to be regulated. -Eukaryotic genomes are stored inside nuclei as chromatin. The chromatin is the association of DNA with dedicated storage proteins - the histones - and the necessary machinery to regulate and express genes. +Eukaryotic genomes are stored inside nuclei as chromatin. The chromatin is the association of DNA with dedicated storage proteins - the histones - and the necessary machinery to regulate and express genes (RNA polymerases or RNAPs). -In the nuclei, histones are assembled into octamers around which ~148bp of DNA are wrapped. This structure is known as the nucleosome. The repetition of nucleosomes along the genome allows to drastically compact the genome, eventually allowing to fit it inside the nuclei. However, this come at the cost of rendering the DNA sequence inaccessible to DNA readers, such as the transcriptional machinery and transcription factors (TFs). +In the nuclei, histones are assembled into octamers around which are wrapped ~148bp of DNA. This structure is known as the nucleosome. The repetition of nucleosomes along the genome allows to drastically compact the genome, eventually allowing to fit it inside the nucleus. However, this comes at the cost of rendering the DNA sequence inaccessible to DNA readers, such as the RNAPs and transcription factors (TFs). -TFs are a class of proteins that have the remarkable property of recognizing and binding specific DNA sequences. More striking, each TF can recognize a multitude of different - but similar - DNA sequences providing TF with a wide sequence specificity range. Eventually, this allows the cell to recruit TFs at dedicated locations in the genome called regulatory elements (RE). +TFs are a class of proteins that have the remarkable property of recognizing and binding specific DNA sequences. More striking, each TF can recognize a multitude of different - but similar - DNA sequences providing TFs with a wide sequence specificity range. Eventually, this allows the cell to recruit TFs at dedicated locations in the genome called regulatory elements (REs). -The action of TF at RE is crucial to gene expression. Indeed, TFs are involved in many processes such the opening of the chromatin structure or the recruitment of the transcriptional machinery. However if TFs can influence the chromatin structure, the reverse is also true as histones impede TFs binding on DNA. Thus the regulation of gene relies on a subtle and complex interaction between the chromatin and TFs. +The action of TFs at REs is crucial to gene expression. Indeed, TFs are involved in many processes such as the opening of the chromatin structure or the recruitment of RNAPs. However if TFs can influence the chromatin structure, the opposite is also true as histones impede TF binding on DNA. Thus the regulation of genes relies on a subtle and complex crosstalk between the chromatin and TFs. -To better understand how TF and chromatin interact together to regulate gene expression, I lead several projects prospecting TF binding specificity and the chromatin structure at REs in human. +To better understand how TFs and chromatin interact together to regulate gene expression, I lead several projects prospecting TF binding specificity and the chromatin structure at REs in human. -First, I used ENCODE next generation sequencing (NGS) data to explore how TF binding influences the nearby nucleosome organization and the propensity of some TFs to bind together. The results suggest that regular nucleosome arrays are found near all TFs. It also points out two special cases. When CTCF binds with the cohesin complex, they seem to drive the nucleosome organization, which is a unique feature among all TFs investigates. Additionally I present evidences suggesting that EBF1 is a pioneer factor - a special class of TFs able to bind nucleosome. +First, I used ENCODE next generation sequencing (NGS) data to explore how TF binding influences the nearby nucleosome organization and the propensity of some TFs to bind together. The results suggest that regular nucleosome arrays are found near all TFs. They also point out two special cases. When CTCF binds with the cohesin complex, it seems to drive the nucleosome organization, which is a unique feature among all TFs investigates. Additionally I present evidence supporting that EBF1 is a pioneer factor - a special class of TFs able to bind nucleosome. -Second, I developed several unsupervised clustering algorithms and software to partition genomic regions according to NGS data and/or on their DNA sequences. These methods allow to discover important trends, for instance different nucleosome architectures . I illustrated the usefulness of these methods for the study of chromatin accessibility data and the identification of REs. +Secondly, I developed several clustering algorithms and software to partition genomic regions according to NGS data and/or on their DNA sequences. These methods allow to discover important trends, for instance different nucleosome architectures . I illustrated the usefulness of these methods for the study of chromatin accessibility data and the identification of REs. -Third, I participated to the assessment SMiLE-seq, a new microfluidic device that generates TF specificity data. The creation of TF specificity models and their comparison with other publicly available models demonstrated the value of SMiLE-seq to study TF specificity. +Thirdly, I participated to the assessment SMiLE-seq, a new microfluidic device that generates TF specificity data. The creation of TF specificity models and their comparison with other publicly available models demonstrated the value of SMiLE-seq to study TF specificity. -Finally, I participated in the development of a software that predicts TF binding sites. A careful benchmarking suggested that this software is - at the time of writing - the best available software in terms of speed while showing other other performances similar to its competitors. +Finally, I participated in the development of a software that predicts TF binding sites. A careful benchmarking suggested that this software is - at the time of writing - the best available software in terms of speed while showing other performances similar to its competitors. % German abstract % \begin{otherlanguage}{german} % \cleardoublepage % \chapter*{Zusammenfassung} % \markboth{Zusammenfassung}{Zusammenfassung} % % put your text here % \lipsum[1-2] % \end{otherlanguage} % French abstract \begin{otherlanguage}{french} \cleardoublepage \chapter*{Résumé} \markboth{Résumé}{Résumé} Tout organisme vivant contient un jeu d'instructions encodé sous la forme de gènes dans son ADN. Ces instructions contiennent toutes les informations nécessaires à la vie de l'organisme en question, de son développement à l'adaptation à des conditions environnementales spécifiques. Étant donné que ces instructions ne sont pas toutes nécessaires en même temps, l'expression des gènes doit être régulée. Chez les eucaryotes, le génome est stocké dans dans le noyau sous forme de chromatine. La chromatine est l'association de l'ADN, de protéines dédiées au stockage de celui-ci et de toute la machinerie nécessaire à la régulation et à l'expression des gènes. -Dans le noyau, les histones sont assemblés en octamères autour desquels s'enroule 148pb d'ADN et forme le nucleosome. La répétition de nucleosomes le long du génome permet de compacter fortement le génome et d’être contenu dans le noyau. Cependant, cela se fait au prix de rendre certaines séquences d’ADN inaccessibles aux facteurs lisant l’ADN tels que la machinerie de transcription ou les facteurs de transcription (FTs). +Dans le noyau, les histones sont assemblés en octamères autour desquels s'enroulent 148pb d'ADN et forment le nucleosome. La répétition de nucleosomes le long du génome permet de le compacter fortement et d’être contenu dans le noyau. Cependant, cela se fait au prix de rendre certaines séquences d’ADN inaccessibles aux facteurs le lisant tels que la machinerie de transcription (les ARNs polymerases ou ARNPs) ou les facteurs de transcription (FTs). -Les FTs sont une classe de protéine qui possèdent la remarquable capacité de pouvoir reconnaître et lier spécifiquement certaines séquences d’ADN. Plus encore, chaque FT est capable de reconnaître une multitude de séquences différentes – mais similaires – étendant d’autant plus la spécifique de reconnaissance. Cela permet à la cellule de recruter certains FTs à des endroits précis dans le génome appelés éléments régulateurs (ERs). +Les FTs forment une classe de protéines qui possède la remarquable capacité de pouvoir reconnaître et lier spécifiquement certaines séquences d’ADN. Plus encore, chaque FT est capable de reconnaître une multitude de séquences différentes – mais similaires – étendant d’autant plus la spécificité de reconnaissance. Cela permet à la cellule de recruter certains FTs à des endroits précis du génome appelés éléments régulateurs (ERs). -Le rôle des FTs au niveau des REs est cruciale pour l’expression des gènes. En effet, les FTs sont nécessaires pour plusieurs processus tels que la décompaction locale de la chromatine ou le recrutement de la machinerie transcriptionnelle. Cependant, si les FTs sont capables d’influer sur la structure de la chromatine, l’inverse est aussi vrai. Les histones sont capables d’empêcher la liaison des FTs sur l’ADN. La régulation de l’expression des gènes s’appuie donc sur un phénomène subtile et complexe d’interaction entre la chromatine et les FTs. +Le rôle des FTs au niveau des REs est crucial pour l’expression des gènes. En effet, les FTs sont nécessaires pour plusieurs processus tels que la décompaction locale de la chromatine ou le recrutement de la machinerie transcriptionnelle. Cependant, si les FTs sont capables d’influer sur la structure de la chromatine, l’inverse est aussi vrai. Les histones sont capables d’empêcher la liaison des FTs à l’ADN. La régulation de l’expression des gènes s’appuie donc sur un phénomène subtile et complexe d’interactions entre la chromatine et les FTs. Afin de mieux comprendre ces interactions et comment elles participent à la régulation de l’expression des gènes, j’ai conduits plusieurs projets ayant pour sujet la spécificité des FTs et la structure de la chromatine dans les ERs. Premièrement, j’ai utilisé les données de séquençage à haut débit (SAD) générées par ENCODE afin d’explorer comment la liaison des FTs à l’ADN influence l’organisation des nucleosomes proches ainsi que la tendance de certains FTs à s’associer. Les résultats suggèrent que des agencements de nucléosomes réguliers se trouvent autour des sites de liaison de tous les FTs. Cependant, seule l’association entre CTCF et la cohésine semble capable d’influencer cette organisation. De plus, d’autres observations suggèrent fortement que le FT EBF1 est un facteur pionnier – une classe de FTs spéciaux capables de lier les nucléosomes. -Deuxièmement, j’ai développé plusieurs algorithmes et sofwares de clustering non-supervisés permettant de grouper les régions du génome en fonction de données SAD et/ou de leur séquence ADN. Ces méthodes permettent d’identifier des tendances, par exemple différentes organisation des nucléosomes. J’ai illustré l’utilisé de ces méthodes au travers de l’étude de l’accessibilité de la chromatine et de l’identification d’ERs. +Deuxièmement, j’ai développé plusieurs algorithmes et sofwares de clustering permettant de grouper les régions du génome en fonction de données SAD et/ou de leur séquence ADN. Ces méthodes permettent d’identifier des tendances, par exemple différentes organisation des nucléosomes. J’ai illustré l’utilité de ces méthodes au travers de l’étude de l’accessibilité de la chromatine et de l’identification d’ERs. -Troisièmement, j’ai participé à l’évaluation du SmiLE-seq, une nouvelle plateforme microfluidique permettant de générer des données sur la spécificité des FTs. La mise au point de modèles de spécificité et leur comparaison avec d’autres modèles disponibles a permis de démontrer la valeur du SMiLE-seq pour les études de spécificité des FTs. +Troisièmement, j’ai participé à l’évaluation du SMiLE-seq, une nouvelle plateforme microfluidique permettant de générer des données sur la spécificité des FTs. La mise au point de modèles de spécificité et leur comparaison avec d’autres modèles disponibles a permis de démontrer la valeur du SMiLE-seq pour les études de spécificité des FTs. -Finalement, j’ai participé au développement et à l’évaluation d’un software prédisant régions liées par un FT, le long d’un génome. Le processus d’évaluation suggère que ce software est actuellement – au moment de la rédaction – le meilleur en terme de rapidité tout présentant d’autres performances similaires à ses compétiteurs. +Finalement, j’ai participé au développement et à l’évaluation d’un software prédisant les régions liées par un FT, le long d’un génome. Le processus d’évaluation suggère que ce software est actuellement – au moment de la rédaction – le meilleur en terme de rapidité tout en présentant d’autres performances similaires à ses compétiteurs. \end{otherlanguage} %\endgroup %\vfill diff --git a/main/ch_atac-seq.aux b/main/ch_atac-seq.aux index 3829ca0..f8ce2bc 100644 --- a/main/ch_atac-seq.aux +++ b/main/ch_atac-seq.aux @@ -1,142 +1,144 @@ \relax \providecommand\hyper@newdestlabel[2]{} \citation{neph_expansive_2012} \citation{berest_quantification_2018} \citation{grossman_positional_2018} -\@writefile{toc}{\contentsline {chapter}{\numberline {7}Chromatin accessibility of monocytes}{83}{chapter.7}} +\@writefile{toc}{\contentsline {chapter}{\numberline {7}Chromatin accessibility of monocytes}{85}{chapter.7}} \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} \@writefile{loa}{\addvspace {10\p@ }} -\newlabel{atac_seq}{{7}{83}{Chromatin accessibility of monocytes}{chapter.7}{}} -\@writefile{chapter}{\contentsline {toc}{Chromatin accessibility of monocytes}{83}{chapter.7}} -\@writefile{toc}{\contentsline {section}{\numberline {7.1}Monitoring TF binding}{83}{section.7.1}} +\newlabel{atac_seq}{{7}{85}{Chromatin accessibility of monocytes}{chapter.7}{}} +\@writefile{chapter}{\contentsline {toc}{Chromatin accessibility of monocytes}{85}{chapter.7}} +\@writefile{toc}{\contentsline {section}{\numberline {7.1}Monitoring TF binding}{85}{section.7.1}} \citation{angerer_single_2017} -\@writefile{toc}{\contentsline {section}{\numberline {7.2}The advent of single cell DGF}{84}{section.7.2}} -\@writefile{toc}{\contentsline {section}{\numberline {7.3}Open issues}{84}{section.7.3}} -\@writefile{toc}{\contentsline {section}{\numberline {7.4}Data}{84}{section.7.4}} +\@writefile{toc}{\contentsline {section}{\numberline {7.2}The advent of single cell DGF}{86}{section.7.2}} +\@writefile{toc}{\contentsline {section}{\numberline {7.3}Open issues}{86}{section.7.3}} +\@writefile{toc}{\contentsline {section}{\numberline {7.4}Data}{86}{section.7.4}} \citation{hon_chromasig:_2008} \citation{nielsen_catchprofiles:_2012} \citation{kundaje_ubiquitous_2012} \citation{nair_probabilistic_2014} \citation{groux_spar-k:_2019} \citation{nair_probabilistic_2014} \citation{nair_probabilistic_2014} \citation{nair_probabilistic_2014} \citation{lawrence_expectation_1990} \citation{bailey_fitting_1994} -\@writefile{toc}{\contentsline {section}{\numberline {7.5}Identifying over-represented signals}{85}{section.7.5}} -\@writefile{toc}{\contentsline {subsection}{\numberline {7.5.1}ChIPPartitioning algorithm}{85}{subsection.7.5.1}} -\@writefile{toc}{\contentsline {subsection}{\numberline {7.5.2}EMSequence algorithm}{85}{subsection.7.5.2}} -\@writefile{lof}{\contentsline {figure}{\numberline {7.1}{\ignorespaces \textbf {Illustration of the expectation-maximization algorithms} \textbf {A} illustration of ChIPPartitioning, an algorithm dedicated to the discovery of over-represented chromatin patterns, as described in \citep {nair_probabilistic_2014}. \textbf {B} illustration of EMSequence, an algorithm to discover over-represented DNA motifs. 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I present the basements of a computational framework to analyse chromatin organization around TF binding sites from ATAC-seq data. As a matter of fact, the results presented here are quite preliminary. However, in the best case, this may shape a basis for other projects. % Because reporting these results, even if incomplete, is at least useless and at most useful to the scientific community, there is no reason not to present them. \section{Monitoring TF binding} -As discusses above (see section \ref{intro_dgf}), DGF assays are able to highlight active regulatory elements from an entire genome, at once. However, this comes with the price of an information loss. First, even if we can identify active loci likely to be bound by TFs, we have no direct idea about the identities of the TFs bound. Second, we have no idea about the function of those regions. These regions may act as transcriptional activator or repressor. This activity is ultimately bared by the TF and other complexes bound. Thus delineating a region function necessitate to identify the TFs bound here. +As discussed above (see section \ref{intro_dgf}), DGF assays are able to highlight active regulatory elements from an entire genome, at once. However, this comes with the price of an information loss. First, even if we can identify active loci likely to be bound by TFs, we have no direct idea about the identities of the TFs bound. Second, we have no idea about the function of those regions. These regions may act as transcriptional activator or repressor. This activity is ultimately bared by the TF and other complexes bound. Thus delineating a region function necessitate to identify the TFs bound here. -This task, even if difficult, can be undertaken by implementing dedicated strategies. First, it is possible to collect evidences about the identity of TF likely to bind at a given location through a motif analysis. TFs can bind DNA directly through their own DNA binding domain or indirectly, through an interaction with at least on other partner TF which binds DNA directly \citep{neph_expansive_2012}. For a given TF, direct binding events can be detected by monitoring the presence of a binding motif if a specificity model is available. Thus a footprint baring a motif is likely to reflect a direct binding event. However, this method has two important limitations : related TF often share a common DNA specificity. For indirect binding, however, nothing can be done to detect such events. Also, evidences about the presence of biggest complexes can be collected by studying the size of the footprint. Large complexes should leave large footprints. This approach, even if limited is able to pinpoint a handful of candidate TFs. +This task, even if difficult, can be undertaken by implementing dedicated strategies. First, it is possible to collect evidences about the identity of TF likely to bind at a given location through a motif analysis. TFs can bind DNA directly through their own DNA binding domain or indirectly, through an interaction with at least one other partner TF which binds DNA directly \citep{neph_expansive_2012}. For a given TF, direct binding events can be detected by monitoring the presence of a binding motif if a specificity model is available. Thus a footprint baring a motif is likely to reflect a direct binding event. However, this method has two important limitations : i) related TF often share a common DNA specificity and ii) this does not detect indirect binding events. However, evidences about the presence of biggest complexes can be collected by studying the size of the footprint. Large complexes should leave large footprints. This approach, even if limited is able to pinpoint a handful of candidate TFs. Second, deciphering the functions of the regulatory elements can be undertaken by looking at the footprint produced by a given factor. Indeed, previous studies have showed that activator and repressor TFs tend to produce different types of footprints \citep{berest_quantification_2018}. Also, the spatial positioning of TF motif within the footprint seemed to be linked with the factor functions \citep{grossman_positional_2018}. For instance, factors associated with the regulation of transcription tend to have a motif in the middle of the footprint whereas factors known to interact with chromatin remodeling factors tend to have a footprint at the edge of the footprint, in contact with the surrounding nucleosomes. \section{The advent of single cell DGF} Recently, the advent of single-cell (sc) sequencing technologies have been a real game changer in the field of life science. These technological advances allowed to measure gene expression and chromatin accessibility (scATAC-seq) at a yet unprecedented resolution. As bulk sequencing was providing an average overview of what was going on, single-cell sequencing allows to monitor what is happening in each cell of a population. This advance had a profound impact on genomics for two reasons. -First, for the really first time, the heterogeneity of a cell population became accessible and could be studied at the chromatin, transcriptional and protein levels. Second, the possibility of collecting high dimensionality data from tenth of thousands of individual cells allows genomics to fully enter in the modern big data era, making commonly used machine learning methods usable as the number of parameters to estimate in the models became smaller than the number of individuals in the data \citep{angerer_single_2017}. +First, for the really first time, the heterogeneity of a cell population became accessible and could be studied at the chromatin, transcriptional and protein levels. Second, the possibility of collecting high dimensionality data from tenth of thousands of individual cells allows genomics to fully enter in the modern big data era, making commonly used machine learning methods usable as the number of parameters to estimate in the models became smaller than the number of individuals, in this case cells, in the data \citep{angerer_single_2017}. % \section{A quick overview of scATAC-seq data analysis} % So far, most of the single cell technologies are targeted at measuring gene expression through scRNA-seq. Naturally, dedicated algorithms and computational methods have been developed to analyze these data. Currently, the most common types of analyses made are i) data projections and dimensionality reduction such as principal component analysis (PCA), t-stochastic distributed neighbours embedding (t-SNE) or uniform manifold approximation and projection (UMAP) and ii) cell population detection by clustering the cells based on the expression of genes \citep{fan_characterizing_2016, kiselev_sc3:_2017}, by reconstructing gene regulation network \citep{aibar_scenic:_2017} or by identifying cellular states based on the accessible region motif content \citep{gonzalez-blas_cistopic:_2019}. In all cases, the use of scATAC-seq data is to determined whether a region is accessible or not. The downstream analyses characterizes the accessible region using i) the number of reads mapping in these regions as a measure of the accessibility or ii) the sequence content within these accessible regions to determine regulatory topics. % \section{Open questions} % \begin{figure}[!htbp] % \begin{center} % \includegraphics[scale=0.5]{images/ch_atac-seq/pipeline.png} % \captionof{figure}{\textbf{framework to identify chromatin organization and use them to annotate cellular state :} the scATAC-seq data available in each individual cell are aggregated and used a if it was a bulk sequencing experiment. Regions of interest are listed using peak calling on the the bulk data. The read densities in these regions (center of the peaks +/- a given offset) are measured. The regions are then clustered based on their signal shape to identify different chromatin architectures and create a catalog. These chromatin signatures can then be used to annotate each region of interest in each cell, based on the signal resemblance. The information can be stored as a matrix (M) that can be used for downstream analyses, such as sub-population identification.} % \label{atac_seq_pipeline} % \end{center} % \end{figure} % All these methods have shown good performances to identify know and new cell populations [REFERENCES]. However, some issues remains open. First, none of these methods uses DGF data to identify different types of footprints or chromatin architecture, in terms of signal shape, at the single cell level. Second, ATAC-seq measures chromatin accessibility but also provides information about the nucleosome occupancy at accessible genomic regions \citep{buenrostro_transposition_2013}. Thus counting the number of reads mapping at a given loci is, indeed, an indication of accessibility but it does use only a small fraction of the available information. Finally, to date, no study has tried to determine whether what is observed at the bulk level can also be seen at the individual cell level and whether this can be used to infer the molecular state of the cells. % In this project, I designed and developed the basements of a computational framework to construct a catalog of prototypical chromatin architectures from single-cell data that can later on be used to annotate individual regions, in single cell. Such a method can be useful to determine cellular molecular state and to group cells accordingly. The entire pipeline is illustrate in Figure \ref{atac_seq_pipeline}. \section{Open issues} I identified two interesting question with regard to ATAC-seq data. First, in the previous chapters, I studied how chromatin is organized in the vicinity of TF binding sites using a pretty standard combination of ChIP-seq, DNase-seq and MNase-seq data. However, I wanted to asses to what extend the same could be done from ATAC-seq data which are cheaper and easier to produce. Second, I wonder to what extent single-cell data could be pooled together and used as a bulk sequencing experiment. \section{Data} To this end, I choose to work with a publicly available sc-ATAC-seq dataset from 5'000 human blood monocytes from a healthy donor. These data have been produced by 10xGenomics (\url{https://www.10xgenomics.com}). % 10xGenomics is one of the most promising and fast growing company specialized in sequencing technologies in the San Francisco Bay area \citep{hepler_10x_2018}. The core activity is to sell sequencing technologies and data analysis softwares to public and private entities. To advertise their products, 10xGenomics offer a free access to several high quality single cell datasets. 10xGenomics is a company active in the field of sequencing technologies and data analysis softwares. To demonstrate the capabilities of their sequencing and bioinformatics analysis technologies, 10xGenomics offer a free access to several high quality single cell datasets together with their analysis results. Thus pre-processing steps such as mapping, cell demultiplexing, sequencing adapters trimming, quality control checks have already been performed. Thus working with these data require minimum handling. Additionally, some downstream analyses such as peak calling or clustering have already been performed. For these reasons, their datasets offer all the conditions to be used as a standard to develop and benchmark new analyses methods. -Hg19 mapped reads were downloaded in bam format as well as and the corresponding peaks called on the aggregated data. +Hg19 mapped reads were downloaded in bam format as well as the corresponding peaks called on the aggregated data. \section{Identifying over-represented signals} -The study of signal shape (distribution) has been a quite active field for bulk sequencing experiments during the last decade. Dedicated algorithms \citep{hon_chromasig:_2008} \citep{nielsen_catchprofiles:_2012} \citep{kundaje_ubiquitous_2012} \citep{nair_probabilistic_2014} \citep{groux_spar-k:_2019} have been developed to cluster genomic regions based on their distribution of reads, which reflects their function. The major issue faced where i) to assess whether two regions had the same signal, they had to be properly aligned, ii) even if the regions were properly aligned, they had to be properly oriented and iii) the signal may be sparse due to an different sequencing depth. - +The study of signal shape (distribution) has been a quite active field for bulk sequencing experiments during the last decade. Dedicated algorithms \citep{hon_chromasig:_2008} \citep{nielsen_catchprofiles:_2012} \citep{kundaje_ubiquitous_2012} \citep{nair_probabilistic_2014} \citep{groux_spar-k:_2019} have been developed to cluster genomic regions based on their distribution of reads. The major issue faced where i) to assess whether two regions are similar in terms of sequencing signal, they have to be properly aligned and ii) oriented and iii) there may be region-specific sequencing depth differences. Nonetheless, these algorithms allow to capture important trends in the data and to collect evidence about the underlying biological mechanisms at play. \subsection{ChIPPartitioning algorithm} ChIPPartitioning is an algorithm that has been developed by \cite{nair_probabilistic_2014} to classify regions based on their sequencing profiles and to identify archetypical sequencing densities (or models). Because the algorithm is already presented details in section \ref{encode_peaks_chippartitioning}, it will not be discussed further here. Nonetheless, the reader is invited to read the above mentioned section in order to properly understand the points discussed below. % Most of the above mentioned algorithms and softwares deal with some of these issues. However, ChIPPartitioning \citep{nair_probabilistic_2014} (see section \ref{encode_peaks_chippartitioning}) is really interesting. It is a probabilistic partitioning method that softly clusters a sets of genomic regions represented as a vector of counts corresponding to the number of reads (ChIP-seq, DNase-seq) along them. The regions clustered based on their signal shape resemblance. To ensure proper comparisons between the regions, the algorithm allows to offset one region compare to the other to retrieve a similar signal at different offsets and to flip the signal orientation. Finally, it has been demonstrated to be really robust to sparse data. % This algorithm models the signal over a region of length $L$ has having being sampled from a mixture of $K$ signal models, using $L$ independent Poisson distributions. The number of reads sequenced over this region is then the result of this sampling process. The entire set of regions is assumed to have been generated from a mixture of $K$ different signal models (classes). Each class is represented by a vector of $L' \le L$ values that represent the expected number of reads at each position for that class. These values are thus the Poisson distribution parameters. % In order to discover the $K$ different chromatin signatures in the data, the algorithm proceed to a maximum likelihood estimation of the Poisson distribution parameters using an expectation-maximization (EM) framework. Given a set of $K$ models, the likelihoods of each region given each class is computed. A posterior probability of each class given each region can, in turn, be computed. These probabilities can be interpreted as a soft clustering. The parameters of the classes are updated using a weighted aggregation of the signal. Since each region is computed a probability to belong to each class, it participates to the update of all the classes, with different weights. % If the length of the chromatin signature searched $L' | cut -d ',' -f 1" where is the downloaded file. %genome The hg19 genome sequence was downloaded from the Ensembl ftp at \url{ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/}. Chromosome 1, 2, ..., 22, X and Y sequences were downloaded in fasta format and concatenated together. The sequence headers were then formatted to fit a "chr" format where is 1, 2, ..., 22, X or Y as in the bed file containing the peaks. % repeat mask The list of repeated elements for hg19 was downloaded from USCS Genome Browser Table Browser (\url{http://genome.ucsc.edu/cgi-bin/hgTables}). The parameters were set as follows : i) clade to mammal, ii) genome to human, iii) assembly to hg19, iv) group to repeat, v) track to repeatMasker. Finally all the regions that were not mapped to chromosome 1 to 22, M, X or Y were filtered out. \subsection{Data post-processing} % reads The reads that did not have a proper barcode were filtered out using "python3.6 filter\_bam.py -i --tag CB --values -o " where is the bam file containing the reads, the file containing the barcodes created with the above grep command and is the output bam file. filter\_bam.py is a in-house developed python program for this project. % peaks The peak name field was modified such that the values corresponding to a chromosome name followed a "chrN" format using "sed -E s/\^{}\textbackslash([0-9XY])/chr\textbackslash\textbackslash1/". Then only the peaks mapping to chromosome contigs were selected using "grep -E \^{}chr". The peaks that had at least 30\% overlap with any repeated element were filtered out using "bedtools substract -A -f 0.3 -a -b " where and are the peak and repeat files in bed format, from the bedtools suite \citep{quinlan_bedtools:_2010}. Finally, the peaks were sortede by position using "sort -K 1,1V -k2,2n -k3,3n". \subsection{Model extension} \label{atac_seq_method_model_ext} Let's assume that we have partitioned a read density matrix $R$ of dimensions $NxL$ using $K$ classes, a shifting freedom $S$ and with flipping. The posterior matrix probability $P$ has dimensions $NxKxSx2$ and the $K$ models have a length of $L'=L-S+1$. Extending the models is obtained by computing a larger matrix $R^{ext}$ of dimensions $NxL''$ where $L''=L+E$. In this case $E$ is the extra number of columns to add. Care should be taken to construct $R^{ext}$ by adding exactly $E/2$ columns one each side of $R$ such that $R$ is contained in the central part of $R^{ext}$. Once $R^{ext}$ has been constructed, the model update step (equation 11 in \cite{nair_probabilistic_2014}) can be applied on it using the posterior probability matrix $P$. This will results in the creation of $K$ models of length $L''-S+1$. The $K$ original models will be contained in the central part of the $K$ extended models. Extending a sequence model is done using exactly the same procedure with the exception that equation \ref{atac_seq_emseq_update_model_shift_flip} should be used to compute the models. The read and sequence model extension procedures are implemented in C++ in the ReadModelExtender and SequenceModelExtender programs. \subsection{Extracting data assigned to a class} -The difference between hard and soft clustering (such as ChIPPartitioning) methods is that in soft clustering "the output is a membership function, so each pattern can belong to more than one group with varying degrees of membership" \citep{dalton_clustering_2009}, while in hard clustering each pattern is assigned to only one group. In the former case, isolating all regions assigned to a class $X$, creating a matrix of read density and re-running the clustering method on this matrix is straightforward and would do the trick. In the latter case, this is also possible but requires to account for the specificity described above. -Let's assume that a first matrix $R$ of dimensions $NxL$ containing $N$ regions of length $L$ has been partitioned in $K$ classes by ChIPPartitioning, with shifting freedom $S -o " where is the bam file containing the di-nucleosome fragments and is the output bam file containing the the reads corresponding to the fragments cut in two. "split\_in\_two.py" is a in-house developed python program for this projet. This file was then sorted using "samtools sort " from the samtools suite \citep{li_sequence_2009}. The sorted file was then merged with the mono-nucleosome fragments using "samtools sort " where is the bam file containing the mono-nucleosome fragments and is the sorted bam file containing the di-nucleosome fragments split in two. Finally, the open chromatin fragment and nucleosome fragment bam files were indexed using "samtools index " where is the bam file to sort. \subsection{Simulated sequences} 2'000 synthetic DNA sequences of 100bp long were simulated. Two equiprobable classes were created and each sequence was assign to either of the two classes. Each class was defined by a 8bp sequence motif (Figure \ref{suppl_atac_seq_emseq_best_motifs}). Each sequence had exactly one motif occurrence, anywhere in the sequence (with a uniform probability), on either strand (equiprobable). The motif sequence was sampled using the corresponding class model. Finally, the bases outside the sequence were sampled using a mono-nucleotide model with 0.25 probability for each base. \subsection{Binding site prediction} \label{atac_seq_method_pwmscan} The hg19 genome was scanned on both strands using PWMScan \citep{ambrosini_pwmscan:_2018} from its web interface (\url{https://ccg.epfl.ch/pwmtools/pwmscan.php}) to predict the binding sites of CTCF, EBF1, myc and SP1 using PWMs from the JASPAR 2018 collection \citep{khan_jaspar_2018} (MA0139.1 CTCF, MA0154.3 EBF1, MA0147.3 MYC and MA0079.3 SP1 respectively). The reference position was set to 10, 7, 6 and 6 respectively and the threshold was set to a pvalue of $1^{-6}$ for all TFs excepted for SP1 for which a pvalue of $1^{-7}$ was used. Non-overlapping matches option was enabled. \subsection{Realignment using JASPAR motifs} % peaks and repeat masking The peaks were filtered for repeated elements. The peaks that had at least 30\% overlap with any repeated element were filtered out using "bedtools substract -A -f 0.3 -a -b " where and are the peak and repeat files in bed format, from the bedtools suite \citep{quinlan_bedtools:_2010}. % matrix creation 70'642 DNA sequences of 1'0001bp corresponding to the central position of each peak +/-500bp were extracted and used to create a sequence matrix using "SequenceMatrixCreator --bed --fasta --from -500 --to 500" where is the bed file containing the repeat filtered peaks and is a fasta file containing chromosome 1, 2, ..., 22, X and Y sequences of the hg19 genome assembly. The corresponding open chromatin and nucleosome sequencing read density matrices were created using "CorrelationMatrixCreator --bed --bam --bai --from -500 --to 500 --binSize 1 --method read\_atac" and "CorrelationMatrixCreator --bed --bam --bai --from -500 --to 500 --binSize 1 --method fragment\_center". and are the bam file containing the ATAC-seq reads, as provided by 10xGenomics and the corresponding bam index file. The bin size of 1b ensured that the read density matrix regions exactly correspond the sequence matrix regions. % PWMs A total of 23 binding models were downloaded from the motif clustering of JASPAR \citep{castro-mondragon_rsat_2017}. Briefly, the motif clustering is made of a forest of trees (each tree is a cluster in which the leaves are the individual TF binding models. Internal nodes binding models are also available. As a matter of fact, they represent a consensus over multiple individual TF binding models. In order to i) have models representing the binding specificity of the TFs of interest and ii) widen the analysis to other TFs if they were sufficiently related to one of the TFs of interest in terms of specificity, I manually selected binding motifs, in the different motif trees, that would fit these requirements. The downloaded models were : \begin{table}[H] \begin{center} \begin{tabular}{ |l|l|p{90mm}|l| } \hline \multicolumn{4}{|c|}{Binding models downloaded} \\ \hline Cluster ID & Node ID & TFs covered & Name \\ \hline 1 & 74 & ARID3b, LHX3 & LHX3 \\ 2 & 12 & ESRRG, NR4A1, ESRRB, NR2F2 & NR4A1 \\ 3 & 23 & FOSL1::JUNB, FOSL1::JUN, FOS::JUND, \newline FOSL2::JUN, FOS::JUNB, JDP2, NFE2, FOSL1, FOS, JUND, FOSL2, JUNB, JUN::JUNB, FOSL1::JUND, FOS::JUN, FOSL2::JUND, FOSB::JUNB, FOSL2::JUNB, BATF::JUN, JUN & AP1 \\ 3 & 24 & NFE2L2, BACH1::MAFK, MAF::NFE2, BACH2 & NFE2 \\ 4 & 22 & max::myc, MXI1, myc, mycn & myc \\ 4 & 30 & ARNT, AHR::ARNT & AHR \\ 4 & 31 & HIF1A, HES5, HES7 & HIF1A \\ 5 & 20 & CEBPA, CEBPG, CEBPD, CEBPB, CEBPE & CEBP \\ 7 & 13 & SPIC, SPI1 & PU.1 \\ 7 & 17 & ELF5, ELF3, EHF, ELF1, ELF4 & ELF \\ 19 & 2 & NFAT5,NFATC1,NFATC3 & NFAT \\ 20 & 4 & MEF2C,MEF2B,MEF2A,MEF2D & MEF2 \\ 21 & 5 & GATA3, GATA5, GATA4, GATA6, GATA1, GATA2 & GATA \\ 28 & 13 & EGR2, EGR4, EGR1, EGR3 & EGR \\ 28 & 14 & KLF4,KLF1,KLF9 & KLF \\ 31 & 4 & IRF7, IRF9, IRF4, IRF8, IRF5 & IRF4 \\ 31 & 5 & STAT1::STAT2, IRF2 & IRF2 \\ 32 & STAT6 & STAT6 & STAT6 \\ 33 & 1 & SOX3, SOX6 & SOX \\ 38 & 3 & RUNX1, RUNX2, RUNX3 & RUNX \\ 39 & 1 & E2F3, E2F2 & E2F \\ 48 & CTCF & CTCF & CTCF \\ 66 & 1 & FOXH1 & FOXH1 \\ \hline \end{tabular} \captionof{table} { \textbf{TF binding models} from JASPAR matrix clustering. Each model can be retrieved within JASPAR matrix clustering (\url{http://jaspar2018.genereg.net/matrix-clusters/vertebrates/?detail=true}) using the cluster and node ID. "TFs covered" refers to all TF which models are children of the given node. "Name" refers to the label this model is referred to in the text and figures.} \label{atac_seq_motif_table} \end{center} \end{table} All the binding models were downloaded as LFMs, in JASPAR format and were then converted into LPMs. % partitioning The DNA sequence matrix was partitioned into 23 classes using EMSequence with the model initialized using the 23 LPMs from JASPAR using "EMSequence --seq --class 23 --motifs --shift 971 --flip --iter 1 --seed --out " where is a text file containing the sequence matrix created by SequenceMatrixCreator, ,...,LPM23> is a coma separated list of 23 files containing the 23 JASPAR LPMs, a randomly generated seed and the output file containing the probability matrix. This resulted in the creation of 23 31bp sequence models from which the corresponding read models (open chromatin and nucleosome) were computed using "ProbToModel --read --prob " where is the file containing the read density matrix created using CorrelationMatrixCreator and is the file containing the probability matrix returned by EMSequence. These models were then extended of 1000bp leading to the creation of 1031bp models that are displayed in Figures \ref{suppl_atac_seq_23class} and \ref{atac_seq_23class}. The sequence models were extended using "SequenceModelExtender --bed --fasta --prob --from -500 --to 500 --ext 1000" where the values of the --bed, --fasta, --from and --to option were the values used for the creation of the sequence matrix using SequenceMatrixCreator and is the probability matrix file returned by EMSequence. The read models were extended using "ReadModelExtender --bed --bam --bai --prob --from -500 --to 500 --ext 1000 --binSize 1 --method " where the value of the --bed, --bam, --bai, --from, --to, --binSize and --method options were the values used for the creation of the read density matrices (open chromatin and nucleosomes) using CorrelationMatrixCreator and is the probability matrix file returned by EMSequence. \subsection{Per TF sub-classes} For each of the 23 classes, a sequence matrix, an open chromatin read density matrix and a nucleosome read density matrix were created, correponding to each class signal. The sequence matrix was created using "ClassSequenceDataCreator --bed --fasta --prob --from -500 --to 500 --k --out " where the values of the --bed, --fasta, --from and --to option were the values used for the creation of the sequence matrix using SequenceMatrixCreator, is the probability matrix file returned by EMSequence, the number of the class to extract and the output file. The read density matrices were created using ""ClassReadDataCreator --bed --bam --bai --prob --from -500 --to 500 --binSize 1 --method " where the value of the --bed, --bam, --bai, --from, --to, --binSize and --method options were the values used for the creation of the read density matrices (open chromatin and nucleosomes) using CorrelationMatrixCreator and is the probability matrix file returned by EMSequence. The rows with no signal (0) in the open chromatin read density matrix were listed using "WhichNullRows --mat " where is the matrix created using ClassReadDataCreator. The partitioning was performed on the open chromatin signal using ChIPPartitiong using "EMRead --read --iter 20 --class --shift 1 --filter --seed --filter --out " where is the file containing the open chromatin read density matrix created using ClassReadDataCreator, is the number of classes from 1 to 10, the file created by WhichNullRows, a randomly generated seed and is the output file containing the probability matrix. No shifting nor flipping was used because the previous step of TF motif instance alignment already solved it. 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The CTCF peaklist used as reference to assess CTCF presence was CTCF.Sydh (in red), the two RAD21 peaklists are RAD21.Haib and RAD21.Sydh respectively (in blue), the SMC3 peaklist is SMC3.Sydh (in green), the YY1 peaklist is YY1.Haib (in orange) and the ZNF143 peaklist is ZNF143.Sydh (in violet). \textbf {B} Venn diagrams showing the proportion of peaks for each TF with i) an instance of its own motif, ii) a CTCF.Sydh peak within 100bp, iii) both or iv) neither of them. RAD21 and SMC3 are not represented as there is no PWM available to describe their sequence specificity. \textbf {C} ChIPPartitioning classification with shift and flip of MNase patterns +/- 1kb of YY1.Haib peaks using 10bp bins. YY1 peaks with (upper row) and without (lower row) a CTCF peak within 100bp. Two classes were used to account for "typical" and "non-typical" looking MNase patterns. 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The presence of SMC3 only, RAD21 only and SMC3 and RAD21 together are indicated in violet, blue and orange respectively. \textbf {B} The proportion of peaks (in green), in each subgroup, having a TSS within a 1kb.\relax }}{39}{figure.caption.19}} -\newlabel{encode_peaks_ctcf_ndr}{{3.5}{39}{\textbf {Nucleosome free region at CTCF binding sites} \textbf {a} The length are represented as boxplots. The CTCF binding sites are divided into subgroups according to additional presence of SCM3, RAD21, YY1 or ZNF143. The number of binding sites in each subgroup is indicated in red above the boxplots. The presence of SMC3 only, RAD21 only and SMC3 and RAD21 together are indicated in violet, blue and orange respectively. \textbf {B} The proportion of peaks (in green), in each subgroup, having a TSS within a 1kb.\relax }{figure.caption.19}{}} +\@writefile{toc}{\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{39}{section.3.4}} +\newlabel{encode_peaks_section_ctcf_rad21_smc3_yy1_znf143}{{3.4}{39}{The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{section.3.4}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces \textbf { Colocalization with CTCF peaks in GM12878 cells : } \textbf {A} Proportion of peaks for different TFs having a CTCF peak within 10bp, 50bp and 100bp. The colours indicate different TFs. The CTCF peaklist used as reference to assess CTCF presence was CTCF.Sydh (in red), the two RAD21 peaklists are RAD21.Haib and RAD21.Sydh respectively (in blue), the SMC3 peaklist is SMC3.Sydh (in green), the YY1 peaklist is YY1.Haib (in orange) and the ZNF143 peaklist is ZNF143.Sydh (in violet). \textbf {B} Venn diagrams showing the proportion of peaks for each TF with i) an instance of its own motif, ii) a CTCF.Sydh peak within 100bp, iii) both or iv) neither of them. RAD21 and SMC3 are not represented as there is no PWM available to describe their sequence specificity. \textbf {C} ChIPPartitioning classification with shift and flip of MNase patterns +/- 1kb of YY1.Haib peaks using 10bp bins. YY1 peaks with (upper row) and without (lower row) a CTCF peak within 100bp. Two classes were used to account for "typical" and "non-typical" looking MNase patterns. DNaseI (blue), TSS density (violet) and sequence conservation (green) were overlaid according to MNase classification (taking into account both shift and flip). The number at the upper right corner of each plot indicate the overall class probability. The number of YY1 peaks is slightly smaller than in B) because peaks showing no MNase reads were not included in the classification analysis. Peaklists are named using the TF together with the laboratory which produced the data.\relax }}{40}{figure.caption.18}} +\newlabel{encode_peaks_colocalization_ctcf}{{3.4}{40}{\textbf { Colocalization with CTCF peaks in GM12878 cells : } \textbf {A} Proportion of peaks for different TFs having a CTCF peak within 10bp, 50bp and 100bp. The colours indicate different TFs. The CTCF peaklist used as reference to assess CTCF presence was CTCF.Sydh (in red), the two RAD21 peaklists are RAD21.Haib and RAD21.Sydh respectively (in blue), the SMC3 peaklist is SMC3.Sydh (in green), the YY1 peaklist is YY1.Haib (in orange) and the ZNF143 peaklist is ZNF143.Sydh (in violet). \textbf {B} Venn diagrams showing the proportion of peaks for each TF with i) an instance of its own motif, ii) a CTCF.Sydh peak within 100bp, iii) both or iv) neither of them. RAD21 and SMC3 are not represented as there is no PWM available to describe their sequence specificity. \textbf {C} ChIPPartitioning classification with shift and flip of MNase patterns +/- 1kb of YY1.Haib peaks using 10bp bins. YY1 peaks with (upper row) and without (lower row) a CTCF peak within 100bp. Two classes were used to account for "typical" and "non-typical" looking MNase patterns. DNaseI (blue), TSS density (violet) and sequence conservation (green) were overlaid according to MNase classification (taking into account both shift and flip). The number at the upper right corner of each plot indicate the overall class probability. The number of YY1 peaks is slightly smaller than in B) because peaks showing no MNase reads were not included in the classification analysis. Peaklists are named using the TF together with the laboratory which produced the data.\relax }{figure.caption.18}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces \textbf {Nucleosome free region at CTCF binding sites} \textbf {a} The length are represented as boxplots. The CTCF binding sites are divided into subgroups according to additional presence of SCM3, RAD21, YY1 or ZNF143. The number of binding sites in each subgroup is indicated in red above the boxplots. 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The presence of SMC3 only, RAD21 only and SMC3 and RAD21 together are indicated in violet, blue and orange respectively. \textbf {B} The proportion of peaks (in green), in each subgroup, having a TSS within a 1kb.\relax }{figure.caption.19}{}} \citation{stedman_cohesins_2008} \citation{losada_cohesin_2014} \citation{donohoe_identification_2007} \citation{bailey_znf143_2015} \citation{ong_ctcf:_2014,ghirlando_ctcf:_2016} \citation{wang_sequence_2012,neph_expansive_2012,consortium_integrated_2012,guo_high_2012} \citation{chatr-aryamontri_biogrid_2017} \citation{wang_sequence_2012,neph_expansive_2012,consortium_integrated_2012,guo_high_2012} \citation{chatr-aryamontri_biogrid_2017} \citation{ghirlando_ctcf:_2016} \citation{ong_ctcf:_2014} -\@writefile{toc}{\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{41}{section.3.5}} -\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces \textbf {CTCF motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The CTCF dataset ORs are too high to be represented in this plot. \textbf {B} Density of CTCF motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif. The absence of CTCF motif within the first 70bp around CTCF binding sites is explained by the peak processing (see section \ref {encode_peaks_methods_data}).\relax }}{42}{figure.caption.20}} -\newlabel{encode_peaks_ctcf_association}{{3.6}{42}{\textbf {CTCF motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The CTCF dataset ORs are too high to be represented in this plot. \textbf {B} Density of CTCF motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif. The absence of CTCF motif within the first 70bp around CTCF binding sites is explained by the peak processing (see section \ref {encode_peaks_methods_data}).\relax }{figure.caption.20}{}} -\@writefile{lot}{\contentsline {table}{\numberline {3.1}{\ignorespaces \textbf {Identified associations : } Details of all the TF associations identified, as well as the possible molecular mechanisms explaining them. The columns 'TF${_A}$' and 'TF${_B}$' refer to the TF involved in the association, 'Motif.ass.' to whether both motif are associated together ('positive') or repel each other ('negative'), as measured by the Fisher test, 'Type' to the proposed interaction mechanism between both TFs, 'Binder' to the TF binding DNA in case of an indirect co-binding, the value 'both' means that both tethering complexes may exist, 'Reported' to whether this interaction has already been reported in one of the following study \cite {wang_sequence_2012, neph_expansive_2012, consortium_integrated_2012, guo_high_2012} and 'Validated' to whether this physical association is experimentally validated and reported in BioGRID v.3.4.145 \citep {chatr-aryamontri_biogrid_2017}.\relax }}{43}{table.caption.21}} -\newlabel{encode_peaks_association_table}{{3.1}{43}{\textbf {Identified associations : } Details of all the TF associations identified, as well as the possible molecular mechanisms explaining them. The columns 'TF${_A}$' and 'TF${_B}$' refer to the TF involved in the association, 'Motif.ass.' to whether both motif are associated together ('positive') or repel each other ('negative'), as measured by the Fisher test, 'Type' to the proposed interaction mechanism between both TFs, 'Binder' to the TF binding DNA in case of an indirect co-binding, the value 'both' means that both tethering complexes may exist, 'Reported' to whether this interaction has already been reported in one of the following study \cite {wang_sequence_2012, neph_expansive_2012, consortium_integrated_2012, guo_high_2012} and 'Validated' to whether this physical association is experimentally validated and reported in BioGRID v.3.4.145 \citep {chatr-aryamontri_biogrid_2017}.\relax }{table.caption.21}{}} +\@writefile{toc}{\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{43}{section.3.5}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces \textbf {CTCF motif association} measured around the binding sites of different TFs. 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The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif. The absence of CTCF motif within the first 70bp around CTCF binding sites is explained by the peak processing (see section \ref {encode_peaks_methods_data}).\relax }}{44}{figure.caption.20}} +\newlabel{encode_peaks_ctcf_association}{{3.6}{44}{\textbf {CTCF motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The CTCF dataset ORs are too high to be represented in this plot. \textbf {B} Density of CTCF motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif. The absence of CTCF motif within the first 70bp around CTCF binding sites is explained by the peak processing (see section \ref {encode_peaks_methods_data}).\relax }{figure.caption.20}{}} +\@writefile{lot}{\contentsline {table}{\numberline {3.1}{\ignorespaces \textbf {Identified associations : } Details of all the TF associations identified, as well as the possible molecular mechanisms explaining them. The columns 'TF${_A}$' and 'TF${_B}$' refer to the TF involved in the association, 'Motif.ass.' to whether both motif are associated together ('positive') or repel each other ('negative'), as measured by the Fisher test, 'Type' to the proposed interaction mechanism between both TFs, 'Binder' to the TF binding DNA in case of an indirect co-binding, the value 'both' means that both tethering complexes may exist, 'Reported' to whether this interaction has already been reported in one of the following study \cite {wang_sequence_2012, neph_expansive_2012, consortium_integrated_2012, guo_high_2012} and 'Validated' to whether this physical association is experimentally validated and reported in BioGRID v.3.4.145 \citep {chatr-aryamontri_biogrid_2017}.\relax }}{45}{table.caption.21}} +\newlabel{encode_peaks_association_table}{{3.1}{45}{\textbf {Identified associations : } Details of all the TF associations identified, as well as the possible molecular mechanisms explaining them. 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The dyad distributions have been measured from two independent datasets : i) MNase-seq data released by the ENCODE Consortium (in red) and by Gaffney et al. (in blue) \citep {gaffney_controls_2012}. \textbf {B} Dinucleotide frequencies around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. \textbf {C} Motif frequency around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.\relax }}{46}{figure.caption.22}} -\newlabel{encode_peaks_ebf1}{{3.7}{46}{\textbf {EBF1 binding sites} stand on the edge of a nucleosome. \textbf {A} Nucleosome dyad distributions around the EBF1 binding sites (from the Haib dataset). The dyad distributions have been measured from two independent datasets : i) MNase-seq data released by the ENCODE Consortium (in red) and by Gaffney et al. (in blue) \citep {gaffney_controls_2012}. \textbf {B} Dinucleotide frequencies around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. \textbf {C} Motif frequency around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.\relax }{figure.caption.22}{}} +\@writefile{toc}{\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{47}{section.3.6}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.7}{\ignorespaces \textbf {EBF1 binding sites} stand on the edge of a nucleosome. \textbf {A} Nucleosome dyad distributions around the EBF1 binding sites (from the Haib dataset). The dyad distributions have been measured from two independent datasets : i) MNase-seq data released by the ENCODE Consortium (in red) and by Gaffney et al. (in blue) \citep {gaffney_controls_2012}. \textbf {B} Dinucleotide frequencies around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. \textbf {C} Motif frequency around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.\relax }}{48}{figure.caption.22}} +\newlabel{encode_peaks_ebf1}{{3.7}{48}{\textbf {EBF1 binding sites} stand on the edge of a nucleosome. \textbf {A} Nucleosome dyad distributions around the EBF1 binding sites (from the Haib dataset). The dyad distributions have been measured from two independent datasets : i) MNase-seq data released by the ENCODE Consortium (in red) and by Gaffney et al. (in blue) \citep {gaffney_controls_2012}. \textbf {B} Dinucleotide frequencies around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. \textbf {C} Motif frequency around the nucleosome dyads from the Gaffney dataset that have an EBF1 binding site within 100bp. 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index 8601c11..6915dc3 100644 --- a/main/ch_introduction.aux +++ b/main/ch_introduction.aux @@ -1,214 +1,215 @@ \relax \providecommand\hyper@newdestlabel[2]{} \citation{mcginty_robert_k._and_tan_song_fundamentals_2014} \citation{mcginty_robert_k._and_tan_song_fundamentals_2014} \@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}} \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} \@writefile{loa}{\addvspace {10\p@ }} \newlabel{intro}{{1}{1}{Introduction}{chapter.1}{}} \@writefile{toc}{\contentsline {chapter}{Introduction}{1}{chapter.1}} \@writefile{toc}{\contentsline {section}{\numberline {1.1}About chromatin}{1}{section.1.1}} \newlabel{intro_about_chromatin}{{1.1}{1}{About chromatin}{section.1.1}{}} \citation{kouzarides_chromatin_2007} \citation{henikoff_histone_2015} \citation{mcginty_robert_k._and_tan_song_fundamentals_2014} \citation{weirauch_methods_2011} \@writefile{toc}{\contentsline {subsection}{\numberline {1.1.1}The 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The NCP is made of a four hetero-dimers histone octamer around which 146-148 DNA bp wraps. The histone tails protrude out of the nucleosome core particle and are accessible to other factors, unlike the inner part of the histone octamer. \textbf {B} The chromatin structure. Inside eukaryotes, DNA is wrapped around histones cores forming nucleosomes. Nucleosomes can then be organized into higher-level helical-like structure, compacting the DNA. The ultimate compaction state is reached at mitosis meta-phase, when the mitotic chromosomes are visible. Figure and legend taken and modified from \cite {mcginty_robert_k._and_tan_song_fundamentals_2014}.\relax }}{3}{figure.caption.5}} \providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}} \newlabel{intro_chromatin}{{1.1}{3}{\textbf {A} Top view of a nucleosome core particle displayed as a ribbon representation on the left and space filling representation on the right. The NCP is made of a four hetero-dimers histone octamer around which 146-148 DNA bp wraps. The histone tails protrude out of the nucleosome core particle and are accessible to other factors, unlike the inner part of the histone octamer. \textbf {B} The chromatin structure. Inside eukaryotes, DNA is wrapped around histones cores forming nucleosomes. Nucleosomes can then be organized into higher-level helical-like structure, compacting the DNA. The ultimate compaction state is reached at mitosis meta-phase, when the mitotic chromosomes are visible. Figure and legend taken and modified from \cite {mcginty_robert_k._and_tan_song_fundamentals_2014}.\relax }{figure.caption.5}{}} \citation{langst_chromatin_2015} \citation{kouzarides_chromatin_2007,hyun_writing_2017} \citation{zhou_charting_2011,hyun_writing_2017} \citation{hyun_writing_2017} \citation{jiang_nucleosome_2009} \citation{jiang_nucleosome_2009} \citation{kubik_nucleosome_2015} \citation{west_nucleosomal_2014} \citation{schones_dynamic_2008,gaffney_controls_2012} \citation{gaffney_controls_2012} \citation{fu_insulator_2008} \citation{jiang_nucleosome_2009} \@writefile{toc}{\contentsline {subsection}{\numberline {1.1.3}About nucleosome positioning}{4}{subsection.1.1.3}} \@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces \textbf {Nucleosome positioning} \textbf {A} Activated gene transcription start site (TSS) region. The nucleosomes located immediately downstream of the TSS show a strong positioning. The positioning of the first nucleosome can be influence by sequence preferences. Eventually the phasing is propagated to neighboring nucleosomes through statistical positioning. The nucleosome array is not anymore visible as the nucleosomes become fuzzily positioned among the cells. \textbf {B} Influence of the rotational positioning on the sequence accessibility. Left, a sequence (indicated by the black \IeC {\textquoteleft }rungs\IeC {\textquoteright } on the DNA helix) has its major groove facing toward the nucleosome outside and is accessible. Center, a 5bp rotation of the nucleosome hides the sequence as its major groove is now facing the histone octamer. Right, another 5bp rotation makes the sequence accessible again. Both images are taken and adapted from \citep {jiang_nucleosome_2009}.\relax }}{5}{figure.caption.6}} \newlabel{intro_nucleosome_positioning}{{1.2}{5}{\textbf {Nucleosome positioning} \textbf {A} Activated gene transcription start site (TSS) region. The nucleosomes located immediately downstream of the TSS show a strong positioning. The positioning of the first nucleosome can be influence by sequence preferences. Eventually the phasing is propagated to neighboring nucleosomes through statistical positioning. The nucleosome array is not anymore visible as the nucleosomes become fuzzily positioned among the cells. \textbf {B} Influence of the rotational positioning on the sequence accessibility. Left, a sequence (indicated by the black ‘rungs’ on the DNA helix) has its major groove facing toward the nucleosome outside and is accessible. Center, a 5bp rotation of the nucleosome hides the sequence as its major groove is now facing the histone octamer. Right, another 5bp rotation makes the sequence accessible again. Both images are taken and adapted from \citep {jiang_nucleosome_2009}.\relax }{figure.caption.6}{}} \citation{dreos_influence_2016} \citation{jiang_nucleosome_2009} \citation{jiang_nucleosome_2009} \citation{trifonov_cracking_2011} \citation{wingender_tfclass:_2013} \citation{weirauch_methods_2011} \citation{latchman_transcription_1997} \citation{latchman_transcription_1997} \citation{field_methods_2011} \citation{weirauch_methods_2011} \@writefile{toc}{\contentsline {section}{\numberline {1.2}About transcription factors}{7}{section.1.2}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.2.1}TF co-binding}{7}{subsection.1.2.1}} \newlabel{intro_tf_cobinding}{{1.2.1}{7}{TF co-binding}{subsection.1.2.1}{}} \citation{field_methods_2011,heinz_selection_2015} \citation{heinz_simple_2010} \@writefile{lof}{\contentsline {figure}{\numberline {1.3}{\ignorespaces \textbf {Possible interaction scenarios between TFs} \textbf {A} Direct co-binding. The TFs dimerize and bind together on DNA. \textbf {B} Indirect co-binding. Both TF dimerize but only one binds the DNA, the other (the blue) is the tethering factor. \textbf {C} Independent co-binding. Both TF bind in close vicinity but without forming a complex. Both TFs may not be necessarily bound at the same time. \textbf {D} Interference. Both motifs partially or totally overlap each other.\relax }}{8}{figure.caption.7}} \newlabel{intro_tf_association}{{1.3}{8}{\textbf {Possible interaction scenarios between TFs} \textbf {A} Direct co-binding. The TFs dimerize and bind together on DNA. \textbf {B} Indirect co-binding. Both TF dimerize but only one binds the DNA, the other (the blue) is the tethering factor. \textbf {C} Independent co-binding. Both TF bind in close vicinity but without forming a complex. Both TFs may not be necessarily bound at the same time. \textbf {D} Interference. Both motifs partially or totally overlap each other.\relax }{figure.caption.7}{}} \citation{von_bakel_methods_2011} \citation{von_bakel_methods_2011} \citation{von_bakel_methods_2011} \citation{von_bakel_methods_2011} \citation{von_bakel_methods_2011} \citation{field_methods_2011} \@writefile{toc}{\contentsline {section}{\numberline {1.3}Gene regulation in a nutshell}{9}{section.1.3}} \newlabel{intro_gene_regulation}{{1.3}{9}{Gene regulation in a nutshell}{section.1.3}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.1}The chromatin barrier}{9}{subsection.1.3.1}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.2}TFs cooperative binding}{9}{subsection.1.3.2}} \citation{zaret_pioneer_2011,iwafuchi-doi_pioneer_2014} \citation{cirillo_opening_2002} \citation{cirillo_opening_2002} \citation{zaret_pioneer_2011} \citation{soufi_pioneer_2015} \citation{heinz_simple_2010} \citation{takahashi_induction_2006} \citation{cairns_logic_2009} \citation{lenhard_metazoan_2012} \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.3}Pioneer TFs}{10}{subsection.1.3.3}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.4}Regulatory elements}{10}{subsection.1.3.4}} \citation{heinz_selection_2015} \citation{heinz_selection_2015} \citation{heinz_selection_2015} \citation{heinz_selection_2015} \citation{zhou_charting_2011} \citation{boller_pioneering_2016,heinz_simple_2010} \citation{hagman_early_2005,kurotaki_transcriptional_2017} \citation{bonev_organization_2016} \citation{bonev_organization_2016} \citation{ong_ctcf:_2014} \citation{ghirlando_ctcf:_2016} \citation{stedman_cohesins_2008} \citation{losada_cohesin_2014} \citation{losada_cohesin_2014,bonev_organization_2016} \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.5}The genome goes 3D}{11}{subsection.1.3.5}} \citation{voong_genome-wide_2017} \citation{voong_genome-wide_2017} \citation{jiang_nucleosome_2009} \citation{schones_dynamic_2008} \citation{schones_dynamic_2008,gaffney_controls_2012,west_nucleosomal_2014,kubik_nucleosome_2015} \@writefile{toc}{\contentsline {section}{\numberline {1.4}Measuring chromatin features}{12}{section.1.4}} \newlabel{measuring_chromatin_features}{{1.4}{12}{Measuring chromatin features}{section.1.4}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.4.1}Measuring nucleosome occupancy}{12}{subsection.1.4.1}} \citation{voong_genome-wide_2017} \citation{kubik_nucleosome_2015} \citation{jin_h3.3/h2a.z_2009} \citation{vierstra_genomic_2016,klemm_chromatin_2019} \citation{vierstra_genomic_2016,klemm_chromatin_2019} \citation{tsompana_chromatin_2014,vierstra_genomic_2016} \citation{neph_expansive_2012} \citation{adey_rapid_2010,buenrostro_transposition_2013} \citation{herrera_characterization_1994} \citation{adey_rapid_2010,buenrostro_transposition_2013} \citation{adey_rapid_2010} \@writefile{toc}{\contentsline {subsection}{\numberline {1.4.2}Digital footprinting}{13}{subsection.1.4.2}} \newlabel{intro_dgf}{{1.4.2}{13}{Digital footprinting}{subsection.1.4.2}{}} \@writefile{lof}{\contentsline {figure}{\numberline {1.4}{\ignorespaces \textbf {Digital footprinting :} \textbf {A} DNase-seq uses the endonuclease DNase to cleave DNA within accessible chromatin. Endonuclease cleavage is greatly attenuated at the protein-bound loci (the red crosses denote cleavage blockade). Accessible library fragments are generated by barcoding each cleavage site independently after restriction digestion (single cut) or as proximal cleavage pairs (double cut). \textbf {B} Assay for transposase-accessible chromatin using sequencing (ATAC-seq) uses a hyperactive transposase (Tn5) to simultaneously cleave and ligate adaptors to accessible DNA. \textbf {C} The purified DNA fragments are then subjected to massively parallel sequencing and mapped to the reference genome to generate a digital readout of per-nucleotide insertion (DNaseI nick or Tn5 transposition event) genome-wide. Figure and legend taken and adapted from \citep {vierstra_genomic_2016, klemm_chromatin_2019}.\relax }}{14}{figure.caption.8}} \newlabel{intro_figure_dgf}{{1.4}{14}{\textbf {Digital footprinting :} \textbf {A} DNase-seq uses the endonuclease DNase to cleave DNA within accessible chromatin. Endonuclease cleavage is greatly attenuated at the protein-bound loci (the red crosses denote cleavage blockade). Accessible library fragments are generated by barcoding each cleavage site independently after restriction digestion (single cut) or as proximal cleavage pairs (double cut). \textbf {B} Assay for transposase-accessible chromatin using sequencing (ATAC-seq) uses a hyperactive transposase (Tn5) to simultaneously cleave and ligate adaptors to accessible DNA. \textbf {C} The purified DNA fragments are then subjected to massively parallel sequencing and mapped to the reference genome to generate a digital readout of per-nucleotide insertion (DNaseI nick or Tn5 transposition event) genome-wide. Figure and legend taken and adapted from \citep {vierstra_genomic_2016, klemm_chromatin_2019}.\relax }{figure.caption.8}{}} \citation{vierstra_genomic_2016} \citation{barski_high-resolution_2007} \citation{odom_methods_2011} \citation{barski_high-resolution_2007,robertson_genome-wide_2007} \citation{jothi_genome-wide_2008} \@writefile{toc}{\contentsline {subsection}{\numberline {1.4.3}Measuring TF binding in vivo}{15}{subsection.1.4.3}} \citation{stormo_determining_2010} \citation{maerkl_systems_2007,geertz_massively_2012} \citation{tuerk_systematic_1990} \citation{roulet_high-throughput_2002,zhao_inferring_2009,jolma_multiplexed_2010} \citation{stormo_determining_2010} \citation{bulyk_exploring_2001,mukherjee_rapid_2004,berger_compact_2006} \citation{berger_universal_2009} \@writefile{toc}{\contentsline {subsection}{\numberline {1.4.4}Measuring TF binding in vitro}{16}{subsection.1.4.4}} \@writefile{toc}{\contentsline {section}{\numberline {1.5}Modeling sequence specificity}{17}{section.1.5}} \newlabel{intro_specificity_modeling}{{1.5}{17}{Modeling sequence specificity}{section.1.5}{}} \@writefile{toc}{\contentsline {subsubsection}{The physics approach to PWMs}{17}{section.1.5}} \newlabel{intro_ka}{{1.1}{17}{The physics approach to PWMs}{equation.1.5.1}{}} \newlabel{intro_delta_free_energy}{{1.2}{17}{The physics approach to PWMs}{equation.1.5.2}{}} \citation{man_non-independence_2001,bulyk_nucleotides_2002} \citation{benos_additivity_2002,zhao_quantitative_2011} \citation{stormo_specificity_1998} \citation{schneider_information_1986} \citation{berg_selection_1988} \@writefile{toc}{\contentsline {subsubsection}{The statistical mechanic approach to PWMs}{18}{equation.1.5.2}} \citation{stormo_specificity_1998} \citation{stormo_identifying_1989} \citation{schneider_information_1986} \citation{hertz_identification_1990} \citation{lawrence_expectation_1990} \citation{bailey_fitting_1994} \citation{kulakovskiy_hocomoco:_2016} \citation{kulakovskiy_hocomoco:_2016} -\citation{schneider_sequence_1990} \newlabel{intro_eq_pwm_berg}{{1.3}{19}{The statistical mechanic approach to PWMs}{equation.1.5.3}{}} \newlabel{intro_eq_pwm_stormo}{{1.4}{19}{The statistical mechanic approach to PWMs}{equation.1.5.4}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.5.1}Aligning binding sites}{19}{subsection.1.5.1}} \newlabel{intro_aligning_binding_sites}{{1.5.1}{19}{Aligning binding sites}{subsection.1.5.1}{}} -\@writefile{toc}{\contentsline {subsection}{\numberline {1.5.2}Platitudes}{19}{subsection.1.5.2}} +\citation{schneider_sequence_1990} \citation{khan_jaspar_2018} \citation{kulakovskiy_hocomoco:_2018} \citation{weirauch_determination_2014} \@writefile{lof}{\contentsline {figure}{\numberline {1.5}{\ignorespaces \textbf {Position weight matrix : } \textbf {A} Human JunD (JUND\textunderscore HUMAN.H10MO) PWM from the HOCOMOCO version 10 collection \cite {kulakovskiy_hocomoco:_2016}. \textbf {B} Corresponding PWM logo. The palindromic nature of the recognized motif is explained by the fact that JunD belongs to the basic helix-loop-helix family. As such, it is obligated to hetero- or homo-dimerize with another member of its family to bind DNA. Both \textbf {A} and \textbf {B} were taken from http://ccg.vital-it.ch/ssa/oprof.php\relax }}{20}{figure.caption.9}} \newlabel{intro_pwm_logo}{{1.5}{20}{\textbf {Position weight matrix : } \textbf {A} Human JunD (JUND\textunderscore HUMAN.H10MO) PWM from the HOCOMOCO version 10 collection \cite {kulakovskiy_hocomoco:_2016}. \textbf {B} Corresponding PWM logo. The palindromic nature of the recognized motif is explained by the fact that JunD belongs to the basic helix-loop-helix family. As such, it is obligated to hetero- or homo-dimerize with another member of its family to bind DNA. Both \textbf {A} and \textbf {B} were taken from http://ccg.vital-it.ch/ssa/oprof.php\relax }{figure.caption.9}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.5.2}Platitudes}{20}{subsection.1.5.2}} \@writefile{toc}{\contentsline {subsection}{\numberline {1.5.3}Predicting binding sites}{20}{subsection.1.5.3}} -\newlabel{intro_eq_score_pwm}{{1.5}{20}{Predicting binding sites}{equation.1.5.5}{}} \@writefile{lof}{\contentsline {figure}{\numberline {1.6}{\ignorespaces \textbf {Signal comparison} between two regions $r_{1}$ and $r_{2}$ bearing a nucleosome array, measured by MNase-seq, at their beginning and ending edges. The bars indicate the density of sequencing reads stacked at each position. \textbf {A} The regions are compared position-wise, as they are, which results in a strong dissimilarity as the arrays are not aligned. \textbf {B} Performing the comparison after flipping $r_{2}$ result in both regions being highly similar. \textbf {C} A shorter stretch of signal of length $L' < L$ from $r_{1}$, highlighted in red and corresponding to the array, is searched in $r_{2}$. In this case, because a highly ressembling strech of signal, in red, can be found in $r_{2}$, both regions are considered highly similar.\relax }}{21}{figure.caption.10}} \newlabel{intro_figure_comparison}{{1.6}{21}{\textbf {Signal comparison} between two regions $r_{1}$ and $r_{2}$ bearing a nucleosome array, measured by MNase-seq, at their beginning and ending edges. The bars indicate the density of sequencing reads stacked at each position. \textbf {A} The regions are compared position-wise, as they are, which results in a strong dissimilarity as the arrays are not aligned. \textbf {B} Performing the comparison after flipping $r_{2}$ result in both regions being highly similar. \textbf {C} A shorter stretch of signal of length $L' < L$ from $r_{1}$, highlighted in red and corresponding to the array, is searched in $r_{2}$. 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Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 7--8 [] [] ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.9 T ranscription factors (TFs) are a class of nuclear proteins that can bin... You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Missing character: There is no T in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 9--10 [] [] ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.11 T he results reported in this work can be sub-divided in two sub-topics.... You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 11--12 [] [] ! Undefined control sequence. l.13 \section {About chromatin} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.13 \section{A bout chromatin} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 13--15 [] [] ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.16 I n eukaryotes, the DNA is stored in the nucleus. Each human cell contai... You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no U in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no O in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 16--17 [] [] ! Undefined control sequence. l.18 \subsection {The chromatin structure} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.18 \subsection{T he chromatin structure} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 18--20 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.21 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.22 \begin{center} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. Overfull \hbox (20.0pt too wide) in paragraph at lines 22--22 [] [] ! Undefined control sequence. l.23 \includegraphics [scale=0.3]{images/ch_introduction/chromatin.png} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.23 \includegraphics[scale=0.3]{images/ch_ introduction/chromatin.png} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. LaTeX Font Info: External font `cmex10' loaded for size (Font) <7> on input line 23. LaTeX Font Info: External font `cmex10' loaded for size (Font) <5> on input line 23. ! Extra }, or forgotten $. l.23 ...0.3]{images/ch_introduction/chromatin.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.24 \captionof {figure}{\textbf{A} Top view of a nucleosome core particle d... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \citation{mcginty_robert_k._and_tan_song_fundamentals_2014} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.24 ..._robert_k._and_tan_song_fundamentals_2014} .} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `mcginty_robert_k._and_tan_song_fundamentals_2014' on p age undefined on input line 24. ! LaTeX Error: Command \end{center} invalid in math mode. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.26 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.26 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.26 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! Missing $ inserted. $ l.26 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Missing } inserted. } l.26 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{document} ended by \end{figure}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27 \end{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (3244.11751pt too wide) in paragraph at lines 23--28 []\OML/cmm/m/it/10 ntroduction=chromatin:png[][][]$ [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no 6 in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no 8 in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...nce `intro_chromatin' on page \thepage \space undefined\on@line . l.30 ..."nucleosome", Figure \ref{intro_chromatin} A). The DNA is kept wrappe... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_chromatin' on page undefined on input line 30. Missing character: There is no A in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 30--31 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 30--31 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! ! Undefined control sequence. l.32 ...-translational modifications (PTMs) \citep {kouzarides_chromatin_2007}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no k in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Missing $ inserted. $ l.32 ...al modifications (PTMs) \citep{kouzarides_ chromatin_2007}. I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.32 ...s (PTMs) \citep{kouzarides_chromatin_2007} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.33 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 32--33 [] [] Overfull \hbox (68.8605pt too wide) in paragraph at lines 32--33 []\OML/cmm/m/it/10 hromatin[]\OT1/cmr/m/n/10 007\OML/cmm/m/it/10 :$ [] Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.34 ...ons, to fulfill dedicated functions \citep {henikoff_histone_2015}. H... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! ! Missing $ inserted. $ l.34 ...lfill dedicated functions \citep{henikoff_ histone_2015}. However, th... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.34 ...ed functions \citep{henikoff_histone_2015} . However, this topic is o... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.35 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 34--35 [] [] Overfull \hbox (269.63649pt too wide) in paragraph at lines 34--35 []\OML/cmm/m/it/10 istone[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 :However; thisto picisoutsidethescopeofthiswork:$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...nce `intro_chromatin' on page \thepage \space undefined\on@line . l.37 ... 30-nm fiber (Figure \ref{intro_chromatin} B). Eventually, higher ord... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_chromatin' on page undefined on input line 37. Missing character: There is no B in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! ! Undefined control sequence. l.37 ...reasing the genome compaction level \citep { mcginty_robert_k._and_ta... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no m in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! ! Missing $ inserted. $ l.37 ...e genome compaction level \citep{ mcginty_ robert_k._and_tan_song_fun... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.37 ..._robert_k._and_tan_song_fundamentals_2014} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.38 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 37--38 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 37--38 [] [] Overfull \hbox (170.93892pt too wide) in paragraph at lines 37--38 []\OML/cmm/m/it/10 obert[]:[]nd[]an[]ong[]undamentals[]\OT1/cmr/m/n/10 014\OML/ cmm/m/it/10 :$ [] Missing character: There is no I in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.40 ...s the linker DNA remains accessible \citep {weirauch_methods_2011}. T... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.40 ...er DNA remains accessible \citep{weirauch_ methods_2011}. Thus storin... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.40 ...s accessible \citep{weirauch_methods_2011} . Thus storing the genome ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.41 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 40--41 [] [] Overfull \hbox (1542.22885pt too wide) in paragraph at lines 40--41 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Thusstoringtheg enomeimpedesitsreadability:BecausetranscribinggenesisallaboutreadingtheDNAtempl ate; thestateofthechromatineventuallyimpactgeneexpression:Consequently; thecell facesasituationwhereitneedstokeeponlytheimmediatelyusefulgenomicregionsreadable whilekeepingtheabilitytoopen=closeotherregionsondemand:$ [] ! Undefined control sequence. l.42 \subsection {The chromatin is dynamic} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 42--45 [] [] Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Undefined control sequence. l.47 ...ach fulfilling a different function \citep {langst_chromatin_2015}. S... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! ! Missing $ inserted. $ l.47 ...illing a different function \citep{langst_ chromatin_2015}. SWI/SNF m... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.47 ...ent function \citep{langst_chromatin_2015} . SWI/SNF members can slid... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.48 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 47--48 [] [] Overfull \hbox (2096.66978pt too wide) in paragraph at lines 47--48 []\OML/cmm/m/it/10 hromatin[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 :SWI=SNFmember scanslideand=ortoevictnucleosomesfromDNAandarelinkedwithchromatinopening:ISWIme mberstendtorecognizeunmodifiedH\OT1/cmr/m/n/10 4\OML/cmm/m/it/10 histoneandcata lyzenucleosomespacingandchromatincompaction:CHDmembersarelesswellfunctionallych aracterizedbutbearchromodomainsthatallowsthemtorecognizehistonemethylation:Fina lly; INO\OT1/cmr/m/n/10 80\OML/cmm/m/it/10 membersseemtobeabletoslideandevictnu cleosomesandseemstobeinvolvedinDNArepairandreplication:$ [] Missing character: There is no H in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! ! Undefined control sequence. l.50 ...d proteins (referred to as readers) \citep {kouzarides_chromatin_2007... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no k in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Missing $ inserted. $ l.50 ...referred to as readers) \citep{kouzarides_ chromatin_2007,hyun_writin... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.50 ...uzarides_chromatin_2007,hyun_writing_2017} . This allows histone PTMs... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.50 ... transcribed genes and at enhancers \citep {zhou_charting_2011,hyun_w... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.50 ...ber of the CHD chromatin remodelers \citep {hyun_writing_2017}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.51 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 50--51 [] [] Overfull \hbox (639.79309pt too wide) in paragraph at lines 50--51 []\OML/cmm/m/it/10 hromatin[]\OT1/cmr/m/n/10 007\OML/cmm/m/it/10 ; hyun[]riting []\OT1/cmr/m/n/10 017\OML/cmm/m/it/10 :ThisallowshistonePTMstobeusedtorecruitsp ecificfactorsatgivengenomiclocation:Forinstance; H\OT1/cmr/m/n/10 3\OML/cmm/m/i t/10 lysine\OT1/cmr/m/n/10 4\OML/cmm/m/it/10 di \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1095.38593pt too wide) in paragraph at lines 50--51 \OML/cmm/m/it/10 methylation\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 3\OML/cmm/m/it/10 K\OT1/cmr/m/n/10 4\OML/cmm/m/it/10 me\OT1/cmr/m/n/10 2)\OML/c mm/m/it/10 hasbeenshowntobeenrichedatthepromotersofactivelytranscribedgenesanda tenhancers[]andtobespecificallyrecognizedbyCHD\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 ; amemberoftheCHDchromatinremodelers[]:$ [] ! Undefined control sequence. l.52 \subsection {About nucleosome positioning} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 52--54 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.55 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (20.0pt too wide) in paragraph at lines 56--56 [] [] ! Undefined control sequence. l.57 \includegraphics [scale=0.2]{images/ch_introduction/nucleosome_position... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.57 \includegraphics[scale=0.2]{images/ch_ introduction/nucleosome_position... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.57 ...h_introduction/nucleosome_positioning.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.58 \captionof {figure}{\textbf{Nucleosome positioning} \textbf{A} Activate... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.58 ...h images are taken and adapted from \citep {jiang_nucleosome_2009}.} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! LaTeX Error: Command \end{center} invalid in math mode. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.60 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.60 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.60 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! Missing $ inserted. $ l.60 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ˜ in font cmr10! Missing character: There is no â in font cmr10! Missing character: There is no € in font cmr10! Missing character: There is no ™ in font cmr10! ! Missing } inserted. } l.60 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{document} ended by \end{figure}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.61 \end{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (4006.2901pt too wide) in paragraph at lines 57--62 []\OML/cmm/m/it/10 ntroduction=nucleosome[]ositioning:png[][][]$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! ! Undefined control sequence. l.63 ...y in many species, such as in yeast \citep {kubik_nucleosome_2015}, m... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no k in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! ! Missing $ inserted. $ l.63 ...ny species, such as in yeast \citep{kubik_ nucleosome_2015}, mouse \c... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.63 ... as in yeast \citep{kubik_nucleosome_2015} , mouse \citep{west_nucleo... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.63 ...citep{kubik_nucleosome_2015}, mouse \citep {west_nucleosomal_2014} or... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.63 ...tep{west_nucleosomal_2014} or human \citep {schones_dynamic_2008, gaf... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.64 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 63--64 [] [] Overfull \hbox (432.49097pt too wide) in paragraph at lines 63--64 []\OML/cmm/m/it/10 ucleosome[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 ; mouse[]orhu man[]:$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...cleosome_positioning' on page \thepage \space undefined\on@line . l.66 ... Figure \ref{intro_nucleosome_positioning} A). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_nucleosome_positioning' on page undefined on i nput line 66. Missing character: There is no A in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 66--67 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 66--67 [] [] Missing character: There is no N in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.69 ...n occur throughout the human genome \citep {gaffney_controls_2012}. H... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! ! Missing $ inserted. $ l.69 ...hroughout the human genome \citep{gaffney_ controls_2012}. However, t... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.69 ...human genome \citep{gaffney_controls_2012} . However, there are regio... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.69 ...binding factor (CTCF) binding sites \citep {fu_insulator_2008}. It ha... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.69 ...red to as "statistical positioning" \citep {jiang_nucleosome_2009}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.70 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 69--70 [] [] Overfull \hbox (402.2777pt too wide) in paragraph at lines 69--70 []\OML/cmm/m/it/10 ontrols[]\OT1/cmr/m/n/10 012\OML/cmm/m/it/10 :However; there areregionswheretheyareenriched; forinstanceattheCCCTC \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (3321.06728pt too wide) in paragraph at lines 69--70 \OML/cmm/m/it/10 bindingfactor\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 CTCF\OT1/cmr/m/ n/10 )\OML/cmm/m/it/10 bindingsites[]:Ithasbeenproposedthatthearraysresultedfro mthenucleosomesorganizingwithrespecttoabarrier\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 oranchor\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 :Inthiscase; thebarrierwouldbeCTCF:T heregulararrayorganizationhasbeenproposedtobepropagatedfarfromtheiranchorsbecau setheimmediatelyflankingnucleosomepositionsareconstrainedbythebarrier:Inturn; t hesenucleosomesbecomeabarrierforthefollowingones; andsoone; eventuallyformingth earray:However; becausethedegreeofconstraindiminishesateachnewnucleosome; thenu cleosomesarenotsufficientlyphasedanymorethroughoutthecellpopulation:Theybecomef uzzyandthesignalbluroutatsomepoint:Thisphenomenonisreferredtoas\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 statisticalpositioning\OT1/cmr/m/n/10 "[]\OML/cmm/m/it/10 :$ [] Missing character: There is no A in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Undefined control sequence. l.72 ... driving the nucleosome positioning \citep {dreos_influence_2016}. To... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! ! Missing $ inserted. $ l.72 ...g the nucleosome positioning \citep{dreos_ influence_2016}. To wrap a... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.72 ...e positioning \citep{dreos_influence_2016} . To wrap around the histo... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.72 ...r and the minor groove respectively \citep {jiang_nucleosome_2009}. H... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. ...cleosome_positioning' on page \thepage \space undefined\on@line . l.72 ... Figure \ref{intro_nucleosome_positioning} B). Consequently, dinucleo... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_nucleosome_positioning' on page undefined on i nput line 72. ! Undefined control sequence. l.72 ...rred to as "rotational positioning" \citep {jiang_nucleosome_2009}. I... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.72 ...ng sequence matching these criteria \citep {trifonov_cracking_2011}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.73 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 72--73 [] [] Overfull \hbox (511.0338pt too wide) in paragraph at lines 72--73 []\OML/cmm/m/it/10 nfluence[]\OT1/cmr/m/n/10 016\OML/cmm/m/it/10 :Towraparoundt hehistoneoctamertheDNAshouldbecurved; whichrequiressomeflexibility:WW\OT1/cmr/m /n/10 (\OML/cmm/m/it/10 W \OT1/cmr/m/n/10 = [] Overfull \hbox (74.68404pt too wide) in paragraph at lines 72--73 \OML/cmm/m/it/10 A=T\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 andSS\OT1/cmr/m/n/10 (\OM L/cmm/m/it/10 S \OT1/cmr/m/n/10 = [] Overfull \hbox (4913.41797pt too wide) in paragraph at lines 72--73 \OML/cmm/m/it/10 C=G\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 dinucleotideshavebeenshow ntocurvetheDNAbyextendingthemajorandtheminorgrooverespectively[]:However; becau sethemajorandminorgroovesprecessaroundtheDNAhelixaxis; eachgroovealternativelyf acesthenucleosomecenter\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 thehistoneoctamer\OT1/ cmr/m/n/10 )\OML/cmm/m/it/10 andthenucleosomeoutside\OT1/cmr/m/n/10 (\OML/cmm/m /it/10 theoppositedirection\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 every []\OT1/cmr/m /n/10 5\OML/cmm/m/it/10 bp\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 thustheDNAhelixperi odicityis []\OT1/cmr/m/n/10 10\OML/cmm/m/it/10 :\OT1/cmr/m/n/10 4\OML/cmm/m/it/ 10 bp; seeFigure[]B\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 :Consequently; dinucleotid esfavoringDNAflexibilityarerequiredtooccuratdifferentlocationsaroundthenucleoso me; accordingtotheireffectontheDNAhelixstructure:Forinstance; stretchingthemajo rgrooveneedstooccurwhenitisfacingthenucleosomeoutside; toforcetheadjacentDNAseg menttobecurvedtoward\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 around\OT1/cmr/m/n/10 )\O ML/cmm/m/it/10 thenucleosomecenter:Ifanucleosomeisboundtoafavorablesequence; th enextmostlikelyfavorablebindingsitesarelocated\OT1/cmr/m/n/10 10\OML/cmm/m/it/1 0 bpupstreamordownstream:Thesecorrespondtothelocationsatwhichallthedinucleotide swillreacquirethesameorientationwithrespecttothehistoneoctamer:Thisisreferredto as\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 rotationalpositioning\OT1/cmr/m/n/10 "[]\OM L/cmm/m/it/10 :In\OT1/cmr/m/n/10 2011\OML/cmm/m/it/10 ; TrifonovidentifiedtheYR RRRRYYYYYR\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 whereR \OT1/cmr/m/n/10 = [] Overfull \hbox (55.99446pt too wide) in paragraph at lines 72--73 \OML/cmm/m/it/10 A=GandY \OT1/cmr/m/n/10 = [] Overfull \hbox (755.25165pt too wide) in paragraph at lines 72--73 \OML/cmm/m/it/10 C=T\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 consensussequencetobeanuc leosomepositioningsequencematchingthesecriteria[]:Thefirstandlastpositionsindic atethecyclicnatureofthispattern:$ [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...cleosome_positioning' on page \thepage \space undefined\on@line . l.74 ...(Figure \ref{intro_nucleosome_positioning} B). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_nucleosome_positioning' on page undefined on i nput line 74. Missing character: There is no B in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 74--75 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 74--75 [] [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 76--77 [] [] ! Undefined control sequence. l.79 \section {About transcription factors} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 79--83 [] [] Missing character: There is no T in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no O in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 85--86 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.88 ...ce the case in the TFclass database \citep {wingender_tfclass:_2013}.... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! ! Missing $ inserted. $ l.88 ... in the TFclass database \citep{wingender_ tfclass:_2013}. In metazoa... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.88 ...s database \citep{wingender_tfclass:_2013} . In metazoans, TFs have b... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.88 ...he helix-turn-helix TFs and iv) the $\beta $ scaffold TFs. Each type ... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.88 ...ferent DNA structures and sequences \citep {weirauch_methods_2011}. O... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.88 ... structures and sequences \citep{weirauch_ methods_2011}. Of further ... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.88 ...nd sequences \citep{weirauch_methods_2011} . Of further importance, a... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.89 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 88--89 [] [] Overfull \hbox (41.70375pt too wide) in paragraph at lines 88--89 []\OML/cmm/m/it/10 fclass \OT1/cmr/m/n/10 :[] [] Overfull \hbox (283.5305pt too wide) in paragraph at lines 88--89 \OT1/cmr/m/n/10 013\OML/cmm/m/it/10 :Inmetazoans; TFshavebeengroupedintofourdis tinctsuper \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (45.00838pt too wide) in paragraph at lines 88--89 \OML/cmm/m/it/10 families \OT1/cmr/m/n/10 : [] Overfull \hbox (280.01956pt too wide) in paragraph at lines 88--89 \OML/cmm/m/it/10 i\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 thebasicdomainTFs; ii\OT1/c mr/m/n/10 )\OML/cmm/m/it/10 thezinccoordinatedTFs; iii\OT1/cmr/m/n/10 )\OML/cmm /m/it/10 thehelix \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (27.90521pt too wide) in paragraph at lines 88--89 \OML/cmm/m/it/10 turn \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (91.74455pt too wide) in paragraph at lines 88--89 \OML/cmm/m/it/10 helixTFsandiv\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 the$$^^L$ [] Overfull \hbox (691.7635pt too wide) in paragraph at lines 88--89 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Offurtherimport ance; asingleDBDisabletorecognizedifferentyetsimilarsequences:Becausethesequenc edifferenceshaveanimpactontheTF \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (844.23714pt too wide) in paragraph at lines 88--89 \OML/cmm/m/it/10 proteininteractioninterface; eachsequenceisboundwithadifferent affinity:Biologically; havinghighandlowaffinitybindingsitesmaybeusefultotunethe intensityofoneTFactiononagivengene:$ [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! ! Undefined control sequence. l.91 ...on the co-regulators it can recruit \citep {latchman_transcription_19... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.91 ...regulators it can recruit \citep{latchman_ transcription_1997}. I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.91 ...ecruit \citep{latchman_transcription_1997} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.92 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 91--92 [] [] Overfull \hbox (82.04904pt too wide) in paragraph at lines 91--92 []\OML/cmm/m/it/10 ranscription[]\OT1/cmr/m/n/10 997\OML/cmm/m/it/10 :$ [] Missing character: There is no U in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.93 ...e the TF recruitement on the genome \citep {latchman_transcription_19... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.93 ...ecruitement on the genome \citep{latchman_ transcription_1997}. I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.93 ...genome \citep{latchman_transcription_1997} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.94 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 93--94 [] [] Overfull \hbox (82.04904pt too wide) in paragraph at lines 93--94 []\OML/cmm/m/it/10 ranscription[]\OT1/cmr/m/n/10 997\OML/cmm/m/it/10 :$ [] ! Undefined control sequence. l.95 \subsection {TF co-binding} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 95--100 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.101 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (20.0pt too wide) in paragraph at lines 102--102 [] [] ! Undefined control sequence. l.103 \includegraphics [scale=0.4]{images/ch_introduction/TF_associations.png} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.103 \includegraphics[scale=0.4]{images/ch_ introduction/TF_associations.png} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.103 ...ages/ch_introduction/TF_associations.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.104 \captionof {figure}{\textbf{Possible interaction scenarios between TFs}... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! LaTeX Error: Command \end{center} invalid in math mode. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! Missing $ inserted. $ l.106 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Missing } inserted. } l.106 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{document} ended by \end{figure}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.107 \end{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (2035.32068pt too wide) in paragraph at lines 103--108 []\OML/cmm/m/it/10 ntroduction=TF[]ssociations:png[][][]$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Undefined control sequence. l.109 ...pes of combinatorial TF co-binding \citep {field_methods_2011}. By T... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! ! Missing $ inserted. $ l.109 ...combinatorial TF co-binding \citep{field_ methods_2011}. By TF co-bi... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.109 ... TF co-binding \citep{field_methods_2011} . By TF co-binding, I mean... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.110 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 109--110 [] [] Overfull \hbox (103.98174pt too wide) in paragraph at lines 109--110 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :ByTFco \OMS/cms y/m/n/10 ^^@ [] Overfull \hbox (625.8786pt too wide) in paragraph at lines 109--110 \OML/cmm/m/it/10 binding; ImeanafunctionalassociationofTFsthatrequiresthemtobin deitherasacomplexorinclosevicinity:Furthermore; fromastrictlyDNA \OMS/cmsy/m/n/ 10 ^^@ [] Overfull \hbox (524.92316pt too wide) in paragraph at lines 109--110 \OML/cmm/m/it/10 centricpointofview; thebindingofeachTFdoesnotneedtobesynchrono us:OneTFmaybindaftertheother; evenafteritleft:$ [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...intro_tf_association' on page \thepage \space undefined\on@line . l.112 ... DBDs (Figure \ref{intro_tf_association} A). This is for instance t... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_tf_association' on page undefined on input lin e 112. Missing character: There is no A in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! ! Undefined control sequence. l.112 ...ligated dimer in order to bind DNA \citep {weirauch_methods_2011}. T... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.112 ...mer in order to bind DNA \citep{weirauch_ methods_2011}. This can be... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.112 ...to bind DNA \citep{weirauch_methods_2011} . This can be referred to ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.113 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 112--113 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 112--113 [] [] Overfull \hbox (210.25188pt too wide) in paragraph at lines 112--113 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Thiscanbereferr edtoas\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 directco \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (41.29774pt too wide) in paragraph at lines 112--113 \OML/cmm/m/it/10 binding\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 :$ [] Missing character: There is no S in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...intro_tf_association' on page \thepage \space undefined\on@line . l.115 ...her TF (Figure \ref{intro_tf_association} B). This can be referred t... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_tf_association' on page undefined on input lin e 115. Missing character: There is no B in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 115--116 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 115--116 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...intro_tf_association' on page \thepage \space undefined\on@line . l.118 ...action (Figure \ref{intro_tf_association} C). This is for instance t... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_tf_association' on page undefined on input lin e 118. Missing character: There is no C in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! ! Undefined control sequence. l.118 ... be opened and distal RE activated \citep {field_methods_2011,heinz_... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! ! Missing $ inserted. $ l.118 ...ned and distal RE activated \citep{field_ methods_2011,heinz_selecti... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.118 ...{field_methods_2011,heinz_selection_2015} . On the other hand, the b... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.118 ... and B cell progenitors commitment \citep {heinz_simple_2010}. This ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.119 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 118--119 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 118--119 [] [] Overfull \hbox (1377.03394pt too wide) in paragraph at lines 118--119 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 ; heinz[]electio n[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 :Ontheotherhand; thebindingofdifferentTF toagivenregioncanbeasynchronous:ThisisthecaseforTFinvolvedatdifferenttimeofthea ctivationcascade; suchashappeningduringmacrophageandBcellprogenitorscommitment[ ]:Thiscanbereferredtoas\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 independentco \OMS/cms y/m/n/10 ^^@ [] Overfull \hbox (41.29774pt too wide) in paragraph at lines 118--119 \OML/cmm/m/it/10 binding\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 :$ [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...intro_tf_association' on page \thepage \space undefined\on@line . l.123 ...verlap (Figure \ref{intro_tf_association} D). The end result is not ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_tf_association' on page undefined on input lin e 123. Missing character: There is no D in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 123--124 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 123--124 [] [] ! Undefined control sequence. l.126 \section {Gene regulation in a nutshell} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no G in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 126--128 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 130--131 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 136--137 [] [] ! Undefined control sequence. l.139 \subsection {The chromatin barrier} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 139--140 [] [] Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ntro_about_chromatin' on page \thepage \space undefined\on@line . l.142 ... (see section \ref{intro_about_chromatin} ), the genome is stored as... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_about_chromatin' on page undefined on input li ne 142. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no O in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! ! Undefined control sequence. l.142 ... spurious activation of the RNAPII \citep {von_bakel_methods_2011}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.142 ...ious activation of the RNAPII \citep{von_ bakel_methods_2011}. On th... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.142 ...the RNAPII \citep{von_bakel_methods_2011} . On the other hand, this ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.142 ...sm that opens the chromatin at REs \citep {von_bakel_methods_2011}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.143 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 142--143 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 142--143 [] [] Overfull \hbox (1212.54391pt too wide) in paragraph at lines 142--143 []\OML/cmm/m/it/10 akel[]ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Ontheothe rhand; thisobviouslyalsosuppressesanygeneexpression:Inhuman; theobservationthat TFsbindingishinderedbynucleosomeandthatREsarenucleosomedepletedsuggesttheexiste nceofamechanismthatopensthechromatinatREs[]:$ [] ! Undefined control sequence. l.144 \subsection {TFs cooperative binding} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 144--145 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! ! Undefined control sequence. l.147 ...nd the chromatin is locally opened \citep {von_bakel_methods_2011}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.147 ...e chromatin is locally opened \citep{von_ bakel_methods_2011}. ATPas... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.147 ...lly opened \citep{von_bakel_methods_2011} . ATPase chromatin remodel... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.147 ... up a proper chromatin environment \citep {von_bakel_methods_2011}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.148 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 147--148 [] [] Overfull \hbox (695.11975pt too wide) in paragraph at lines 147--148 []\OML/cmm/m/it/10 akel[]ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :ATPasechr omatinremodelersand=orofhistonemodifiercanberecruitedbyTFstosetupaproperchromat inenvironment[]:$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no " in font nullfont! ! Undefined control sequence. l.149 ...erred to as "nucleosome breathing" \citep {von_bakel_methods_2011}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.149 ... to as "nucleosome breathing" \citep{von_ bakel_methods_2011}. This ... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.149 ...breathing" \citep{von_bakel_methods_2011} . This has the potential o... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.149 ...ng the linkers somewhat accessible \citep {field_methods_2011}. Toge... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.150 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 149--150 [] [] Overfull \hbox (2623.09003pt too wide) in paragraph at lines 149--150 []\OML/cmm/m/it/10 akel[]ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Thishasth epotentialofcreatingwindowsofopportunityforTFstoengagetheirbindingsites; innucl eosomearrays:Second; ithasbeenhypothesizedthat; inhuman; theregionsthatshowahig hnuclosomedensitymayfacilitatetheexclusionoftheH\OT1/cmr/m/n/10 1\OML/cmm/m/it/ 10 histone:TherationalisthattheDNAlinkersbetweenanytwonucleosomesistooshortforH \OT1/cmr/m/n/10 1\OML/cmm/m/it/10 tobind:Eventually; H\OT1/cmr/m/n/10 1\OML/cmm /m/it/10 exclusionpreventstheinclusionsoftheseregionsinmorecondensedchromatinst ructureswhileleavingthelinkerssomewhataccessible[]:Together; withnucleosomebrea thing; thishasthepotentialofcreatingengageable \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (56.40294pt too wide) in paragraph at lines 149--150 \OML/cmm/m/it/10 butnotopen \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (139.72787pt too wide) in paragraph at lines 149--150 \OML/cmm/m/it/10 windowsthroughoutthegenome:$ [] ! Undefined control sequence. l.151 \subsection {Pioneer TFs} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no P in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 151--152 [] [] Missing character: There is no A in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Undefined control sequence. l.154 ...ce chromatin opening after binding \citep {zaret_pioneer_2011,iwafuc... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! ! Missing $ inserted. $ l.154 ...matin opening after binding \citep{zaret_ pioneer_2011,iwafuchi-doi_... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.154 ...t_pioneer_2011,iwafuchi-doi_pioneer_2014} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.155 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 154--155 [] [] Overfull \hbox (105.83994pt too wide) in paragraph at lines 154--155 []\OML/cmm/m/it/10 ioneer[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 ; iwafuchi \OMS/ cmsy/m/n/10 ^^@ [] Overfull \hbox (68.50235pt too wide) in paragraph at lines 154--155 \OML/cmm/m/it/10 doi[]ioneer[]\OT1/cmr/m/n/10 014\OML/cmm/m/it/10 :$ [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Undefined control sequence. l.157 ...hancer and prime it for activation \citep {cirillo_opening_2002}. Th... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! ! Missing $ inserted. $ l.157 ...d prime it for activation \citep{cirillo_ opening_2002}. The enhance... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.157 ...r activation \citep{cirillo_opening_2002} . The enhancer activation ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.157 ...ich leads to the chromatin opening \citep {cirillo_opening_2002}. Al... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.157 ...N-terminal trans-activation domain \citep {zaret_pioneer_2011}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.158 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 157--158 [] [] Overfull \hbox (11.24437pt too wide) in paragraph at lines 157--158 \OT1/cmr/m/it/10 al- [] Overfull \hbox (13.54434pt too wide) in paragraph at lines 157--158 \OT1/cmr/m/it/10 bu- [] Overfull \hbox (16.86658pt too wide) in paragraph at lines 157--158 \OT1/cmr/m/it/10 min [] Overfull \hbox (1221.33939pt too wide) in paragraph at lines 157--158 []\OML/cmm/m/it/10 pening[]\OT1/cmr/m/n/10 002\OML/cmm/m/it/10 :Theenhanceracti vationispossiblebecauseofthehybridnatureofFoxA\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 :ItbindsDNAthroughitsDBD; whichhasasimilarstructuretotheH\OT1/cmr/m/n/10 1\OML /cmm/m/it/10 linkerhistone:Strikingly; FoxA\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 ca nbinditsrecognizedmotifdirectlyonthenucleosomesurface:Furthermore; FoxA\OT1/cmr /m/n/10 1\OML/cmm/m/it/10 possesaC \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (653.8379pt too wide) in paragraph at lines 157--158 \OML/cmm/m/it/10 terminaldomainthatdirectlybindsthehistonecore; whichleadstothe chromatinopening[]:Alternatively; FoxA\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 isalsoa bletorecruitco \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (89.28389pt too wide) in paragraph at lines 157--158 \OML/cmm/m/it/10 regulatorsviaitsN \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (71.90485pt too wide) in paragraph at lines 157--158 \OML/cmm/m/it/10 terminaltrans \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (157.07108pt too wide) in paragraph at lines 157--158 \OML/cmm/m/it/10 activationdomain[]:$ [] Missing character: There is no C in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no O in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no K in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no 4 in font nullfont! ! Undefined control sequence. l.159 ...vered, such as Oct4, Sox2 and Klf4 \citep {soufi_pioneer_2015} - als... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! ! Missing $ inserted. $ l.159 ...such as Oct4, Sox2 and Klf4 \citep{soufi_ pioneer_2015} - also known... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.159 ... Sox2 and Klf4 \citep{soufi_pioneer_2015} - also known together wit... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.159 ...hage and B-cell specific enhancers \citep {heinz_simple_2010}. Inter... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.159 ...rogram fibroblasts into stem cells \citep {takahashi_induction_2006}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.160 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 159--160 [] [] Overfull \hbox (60.00514pt too wide) in paragraph at lines 159--160 []\OML/cmm/m/it/10 ioneer[]\OT1/cmr/m/n/10 015 \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (248.25476pt too wide) in paragraph at lines 159--160 \OML/cmm/m/it/10 alsoknowntogetherwithmycasthe\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 Yamanakafactors\OT1/cmr/m/n/10 " \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (358.19063pt too wide) in paragraph at lines 159--160 \OML/cmm/m/it/10 orPU:\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 whichhasbeenshowntoindu cenucleosomeremodelingatmacrophageandB \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1105.53796pt too wide) in paragraph at lines 159--160 \OML/cmm/m/it/10 cellspecificenhancers[]:Interestinginthisregard; mostoftheTFsd iscoveredtodrivecellularreprogramming; suchastheYamanakafactorswhichhavebeensho wntobesufficienttoreprogramfibroblastsintostemcells[]:$ [] ! Undefined control sequence. l.162 \subsection {Regulatory elements} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no R in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 162--163 [] [] Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 165--166 [] [] Missing character: There is no P in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.168 ...t to their chromatin architectures \citep {cairns_logic_2009}. The f... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! ! Missing $ inserted. $ l.168 ...ir chromatin architectures \citep{cairns_ logic_2009}. The first gro... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.168 ...n architectures \citep{cairns_logic_2009} . The first group include ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.168 ...ding to the assembly of the RNAPII \citep {lenhard_metazoan_2012}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.169 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 168--169 [] [] Overfull \hbox (3098.28784pt too wide) in paragraph at lines 168--169 []\OML/cmm/m/it/10 ogic[]\OT1/cmr/m/n/10 009\OML/cmm/m/it/10 :Thefirstgroupincl udehousekeepinggenes:Thisgroupchromatinarchitecturetendstobeconstituvelyopenwit hanucleosomedepletedregion\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 NDR\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 ; promotinggeneexpression:Thesecondgroupcontainshighlyregulat edgenes:Unlikethefirstgroup; thesepromoterstendtobeconstituvelycoveredbynucleos omes; hinderingTFandRNAPIIrecruitment:Theiractivationrequireanactivechromatinre modelingthatiscarriedoutbySWI=SNFATPasefamilymembers:However; inbothcasesthechr omatinisremodeledandaNDRisformed:TheNDRusuallycontainsTFbindingsitescoreregulat oryelements\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 CREs\OT1/cmr/m/n/10 )\OML/cmm/m/it /10 involvedintherecruitmentofgeneralTFsleadingtotheassemblyoftheRNAPII[]:$ [] Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ' in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ' in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ' in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ' in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.171 ...gulators such as histone modifiers \citep {heinz_selection_2015}. Th... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! ! Missing $ inserted. $ l.171 ...s such as histone modifiers \citep{heinz_ selection_2015}. Through c... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.171 ...ne modifiers \citep{heinz_selection_2015} . Through chromatin loopin... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.171 ...rectly where the RNAPII is sitting \citep {heinz_selection_2015}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.172 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 171--172 [] [] Overfull \hbox (1506.27238pt too wide) in paragraph at lines 171--172 []\OML/cmm/m/it/10 election[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 :Throughchroma tinloopingphenomenons; therecruitedTF\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 andallot herfactors\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 arebroughtinclosespatialvicinityfro mtargetgenepromoters:ThisincreasesTFconcentrations\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 aswellasotherregulatoryfactorsbound\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 atthe promoterlevelandallowstostrengthenregulatorysignalsdirectlywheretheRNAPIIissitt ing[]:$ [] Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. l.173 ...t determinant of the cell identity \citep {heinz_selection_2015}. Di... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! ! Missing $ inserted. $ l.173 ...minant of the cell identity \citep{heinz_ selection_2015}. Distal RE... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.173 ...ell identity \citep{heinz_selection_2015} . Distal REs activation re... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.173 ...n chromatin opening and remodeling \citep {heinz_selection_2015}. Up... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.173 ...H3 lysine 27 acetylation (H3K27Ac) \citep {zhou_charting_2011}. For ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.173 ...t of differential genomic programs \citep {boller_pioneering_2016, h... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.173 ...eads to lineage commitment defects \citep {hagman_early_2005,kurotak... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.174 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 173--174 [] [] Overfull \hbox (1405.18188pt too wide) in paragraph at lines 173--174 []\OML/cmm/m/it/10 election[]\OT1/cmr/m/n/10 015\OML/cmm/m/it/10 :DistalREsacti vationrequirestoopenthechromatininordertobeaccessibleforTFstobind:Currently; bo thcooperativeTFbindingandpioneerTFsarethoughtobeinvolvedinchromatinopeningandre modeling[]:Uponchromatinopening; specifichistonePTMsaredeposited; suchasH\OT1/c mr/m/n/10 3\OML/cmm/m/it/10 lysine\OT1/cmr/m/n/10 4\OML/cmm/m/it/10 mono \OMS/c msy/m/n/10 ^^@ [] Overfull \hbox (511.15764pt too wide) in paragraph at lines 173--174 \OML/cmm/m/it/10 methylation\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 3\OML/cmm/m/it/10 K\OT1/cmr/m/n/10 4\OML/cmm/m/it/10 me\OT1/cmr/m/n/10 1)\OML/c mm/m/it/10 ; H\OT1/cmr/m/n/10 3\OML/cmm/m/it/10 K\OT1/cmr/m/n/10 4\OML/cmm/m/it /10 me\OT1/cmr/m/n/10 2\OML/cmm/m/it/10 orH\OT1/cmr/m/n/10 3\OML/cmm/m/it/10 ly sine\OT1/cmr/m/n/10 27\OML/cmm/m/it/10 acetylation\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 H\OT1/cmr/m/n/10 3\OML/cmm/m/it/10 K\OT1/cmr/m/n/10 27\OML/cmm/m/it/10 Ac\ OT1/cmr/m/n/10 )[]\OML/cmm/m/it/10 :Forinstance; duringB \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1398.24312pt too wide) in paragraph at lines 173--174 \OML/cmm/m/it/10 cellandmacrophagelineagecommitment; PU:\OT1/cmr/m/n/10 1\OML/c mm/m/it/10 andEBF\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 areessentialTFswhichactionac tivatescelltypespecificenhancers; leadingtotheenforcementofdifferentialgenomicp rograms[]:Failuretodosoleadstolineagecommitmentdefects[]:$ [] ! Undefined control sequence. l.175 \subsection {The genome goes 3D} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no D in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 175--176 [] [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Undefined control sequence. l.178 ...d that it has a functional meaning \citep {bonev_organization_2016}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! ! Missing $ inserted. $ l.178 ...it has a functional meaning \citep{bonev_ organization_2016}. I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.178 ...l meaning \citep{bonev_organization_2016} . I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.179 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 178--179 [] [] Overfull \hbox (79.6444pt too wide) in paragraph at lines 178--179 []\OML/cmm/m/it/10 rganization[]\OT1/cmr/m/n/10 016\OML/cmm/m/it/10 :$ [] Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 180--181 [] [] Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! ! Undefined control sequence. l.182 ...uding CTCF and the cohesin complex \citep {bonev_organization_2016}.... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! ! Missing $ inserted. $ l.182 ...TCF and the cohesin complex \citep{bonev_ organization_2016}. CTCF s... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.182 ...n complex \citep{bonev_organization_2016} . CTCF seem to have two ma... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.182 ...tant for their proper delimitation \citep {ong_ctcf:_2014}, likely t... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.182 ...through a loop extrusion mechanism \citep {ghirlando_ctcf:_2016}. Th... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.182 ... interact with the cohesin complex \citep {stedman_cohesins_2008}. T... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.182 ...3, RAD21 and either STAG1 or STAG2 \citep {losada_cohesin_2014}. Tog... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.182 ... interactions and TADs maintenance \citep {losada_cohesin_2014,bonev... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.183 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 182--183 [] [] Overfull \hbox (2856.14746pt too wide) in paragraph at lines 182--183 []\OML/cmm/m/it/10 rganization[]\OT1/cmr/m/n/10 016\OML/cmm/m/it/10 :CTCFseemto havetwomajorfunctions:Firstitseemstofacilitatepromoter=enhancersinteractions; w ithinTADsandpromotegeneexpression:Second; CTCFisfoundtobeenrichedatTADbordersan dseemstobeimportantfortheirproperdelimitation[]; likelythroughaloopextrusionmec hanism[]:ThissecondfunctioniscompatiblewiththeinsulatorfunctionofCTCF:Becauseit markstheboundarybetweenTADs; enhancer=promoterinteractionoverthislimitcannothap pen:Finally; CTCFisoftenfoundintointeractwiththecohesincomplex[]:Thecohesincomp lexiscomposedoffourmembers \OT1/cmr/m/n/10 : [] Overfull \hbox (426.0185pt too wide) in paragraph at lines 182--183 \OML/cmm/m/it/10 SMC\OT1/cmr/m/n/10 1\OML/cmm/m/it/10 ; SMC\OT1/cmr/m/n/10 3\OM L/cmm/m/it/10 ; RAD\OT1/cmr/m/n/10 21\OML/cmm/m/it/10 andeitherSTAG\OT1/cmr/m/n /10 1\OML/cmm/m/it/10 orSTAG\OT1/cmr/m/n/10 2[]\OML/cmm/m/it/10 :Togethertheyfo rmaring \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1286.03893pt too wide) in paragraph at lines 182--183 \OML/cmm/m/it/10 likestructureinwhichtwoDNAmoleculesaretrappedandmaintainedtoge ther:ThisstructureisoneofthemechanismsallowingtopinchDNAandtoformloops:Thecohes incomplexisimportantforbothpromoter=enhancerinteractionsandTADsmaintenance[]:$ [] ! Undefined control sequence. l.186 \section {Measuring chromatin features} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no M in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 186--188 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 189--190 [] [] ! Undefined control sequence. l.191 \subsection {Measuring nucleosome occupancy} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no M in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 191--192 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no â in font nullfont! Missing character: There is no € in font nullfont! Missing character: There is no ˜ in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no â in font nullfont! Missing character: There is no € in font nullfont! Missing character: There is no ™ in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no " in font nullfont! ! Undefined control sequence. l.194 ...dder’ of discrete DNA fragments" \citep {voong_genome-wide_2017} w... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Missing $ inserted. $ l.194 ... of discrete DNA fragments" \citep{voong_ genome-wide_2017} which si... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.194 ...fragments" \citep{voong_genome-wide_2017} which sizes correspond to... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.194 ... the MNase access to its substrate \citep {voong_genome-wide_2017}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.195 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 194--195 [] [] Overfull \hbox (41.3725pt too wide) in paragraph at lines 194--195 []\OML/cmm/m/it/10 enome \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (610.70547pt too wide) in paragraph at lines 194--195 \OML/cmm/m/it/10 wide[]\OT1/cmr/m/n/10 017\OML/cmm/m/it/10 whichsizescorrespond tomono\OMS/cmsy/m/n/10 ^^@\OML/cmm/m/it/10 ; di\OMS/cmsy/m/n/10 ^^@\OML/cmm/m/i t/10 ; tri\OMS/cmsy/m/n/10 ^^@\OML/cmm/m/it/10 ; andsoonnucleosomefragments:The MNaseisabletodigestaccessiblelinkerDNA\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 endo \O MS/cmsy/m/n/10 ^^@ [] Overfull \hbox (206.72429pt too wide) in paragraph at lines 194--195 \OML/cmm/m/it/10 nucleaseactivity\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 andtotrimthe nickedges\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 exo \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (708.53015pt too wide) in paragraph at lines 194--195 \OML/cmm/m/it/10 nucleaseactivity\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 :Thenucleoso malDNAisprotectedfromdigestionasthehistoneoctamerstericallyhindertheMNaseaccess toitssubstrate[]:$ [] Missing character: There is no O in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Undefined control sequence. l.197 ...ated had relatively low resolution \citep {jiang_nucleosome_2009}. E... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no j in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Missing $ inserted. $ l.197 ...d relatively low resolution \citep{jiang_ nucleosome_2009}. Eventual... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.197 ... resolution \citep{jiang_nucleosome_2009} . Eventually, this limitat... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.197 ... next generation sequencing (-seq) \citep {schones_dynamic_2008}. Th... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.197 ...omes - genome-wide nucleosome maps \citep {schones_dynamic_2008, gaf... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.198 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 197--198 [] [] Overfull \hbox (838.74527pt too wide) in paragraph at lines 197--198 []\OML/cmm/m/it/10 ucleosome[]\OT1/cmr/m/n/10 009\OML/cmm/m/it/10 :Eventually; thislimitationwascircumventbysubjectingtheMNasetreatedchromatinfragmenttonextge nerationsequencing\OT1/cmr/m/n/10 (\OMS/cmsy/m/n/10 ^^@\OML/cmm/m/it/10 seq\OT1 /cmr/m/n/10 )[]\OML/cmm/m/it/10 :TheadventofMNase \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (176.43185pt too wide) in paragraph at lines 197--198 \OML/cmm/m/it/10 seqleadtothecreationofhighresolution \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (142.26054pt too wide) in paragraph at lines 197--198 \OML/cmm/m/it/10 downtoindividualnucleosomes \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (41.84851pt too wide) in paragraph at lines 197--198 \OML/cmm/m/it/10 genome \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (487.46576pt too wide) in paragraph at lines 197--198 \OML/cmm/m/it/10 widenucleosomemaps[]:$ [] Missing character: There is no M in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no 7 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 5 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 200--201 [] [] Missing character: There is no I in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 203--204 [] [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.205 ...some fragments in A/T rich regions \citep {voong_genome-wide_2017}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! ! Missing $ inserted. $ l.205 ...agments in A/T rich regions \citep{voong_ genome-wide_2017}. Second,... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.205 ...ch regions \citep{voong_genome-wide_2017} . Second, some nucleosomes... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.205 ... with reduced MNase concentrations \citep {kubik_nucleosome_2015}. H... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.205 ... used during a ChIP-seq experiment \citep {jin_h3.3/h2a.z_2009}. Thu... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.206 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 205--206 [] [] Overfull \hbox (41.3725pt too wide) in paragraph at lines 205--206 []\OML/cmm/m/it/10 enome \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (2235.38988pt too wide) in paragraph at lines 205--206 \OML/cmm/m/it/10 wide[]\OT1/cmr/m/n/10 017\OML/cmm/m/it/10 :Second; somenucleos omeshavebeendemonstratedtobe\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 fragile\OT1/cmr/m /n/10 "\OML/cmm/m/it/10 totheexperimentalconditions:Inyeast; specificnucleosome swerefoundtobesensitivetotheMNaseconcentrationandcouldonlybedetectedwithreduced MNaseconcentrations[]:Here; theMNasesequencepreferencemaybeatplay:Butanothercas eoffragilenucleosomeswasfoundinhuman; independentlyoftheuseofMNase:Inthiscase; thefragilenucleosomesweresensitivetoregularsaltconcentrationsusedduringaChIP \O MS/cmsy/m/n/10 ^^@ [] Overfull \hbox (277.22572pt too wide) in paragraph at lines 205--206 \OML/cmm/m/it/10 seqexperiment[]:Thus; itislikelythatMNase \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (235.13576pt too wide) in paragraph at lines 205--206 \OML/cmm/m/it/10 seqisnotabletomapallthenucleosomeinagivengenome:$ [] ! Undefined control sequence. l.207 \subsection {Digital footprinting} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 207--210 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.211 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (20.0pt too wide) in paragraph at lines 212--212 [] [] ! Undefined control sequence. l.213 \includegraphics [scale=0.3]{images/ch_introduction/dgf.png} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.213 \includegraphics[scale=0.3]{images/ch_ introduction/dgf.png} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.213 ...cale=0.3]{images/ch_introduction/dgf.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.214 \captionof {figure}{\textbf{Digital footprinting :} \textbf{A} DNase-s... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.214 ... and legend taken and adapted from \citep {vierstra_genomic_2016, kl... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! LaTeX Error: Command \end{center} invalid in math mode. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.216 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.216 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.216 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! Missing $ inserted. $ l.216 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Missing } inserted. } l.216 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{document} ended by \end{figure}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.217 \end{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (3922.24004pt too wide) in paragraph at lines 213--218 []\OML/cmm/m/it/10 ntroduction=dgf:png[][][]$ [] Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.220 ...to a chromatin-stored DNA template \citep {tsompana_chromatin_2014, ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! ! Missing $ inserted. $ l.220 ...atin-stored DNA template \citep{tsompana_ chromatin_2014, vierstra_g... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.220 ...na_chromatin_2014, vierstra_genomic_2016} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.221 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 220--221 [] [] Overfull \hbox (163.19507pt too wide) in paragraph at lines 220--221 []\OML/cmm/m/it/10 hromatin[]\OT1/cmr/m/n/10 014\OML/cmm/m/it/10 ; vierstra[]en omic[]\OT1/cmr/m/n/10 016$ [] Missing character: There is no D in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no [ in font nullfont! \citation{neph_expansive_2012} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.222 ...eI (DNase-seq, \cite{neph_expansive_2012} ) or a modified Tn5 transp... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `neph_expansive_2012' on page undefined on input line 222. Missing character: There is no ] in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no 5 in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no [ in font nullfont! \citation{adey_rapid_2010} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.222 ...rapid_2010,buenrostro_transposition_2013} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `adey_rapid_2010' on page undefined on input line 222. Missing character: There is no , in font nullfont! \citation{buenrostro_transposition_2013} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.222 ...rapid_2010,buenrostro_transposition_2013} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `buenrostro_transposition_2013' on page undefined on i nput line 222. Missing character: There is no ] in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 222--223 [] [] Overfull \hbox (5.43053pt too wide) in paragraph at lines 222--223 [] [] Overfull \hbox (5.43053pt too wide) in paragraph at lines 222--223 [] [] Overfull \hbox (5.43053pt too wide) in paragraph at lines 222--223 [] [] Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no U in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. l.225 ... with a minor sequence specificity \citep {herrera_characterization_... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! ! Missing $ inserted. $ l.225 ...inor sequence specificity \citep{herrera_ characterization_1994}, as... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.225 ...ity \citep{herrera_characterization_1994} , as shown in Figure \ref{... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. ...ce `intro_figure_dgf' on page \thepage \space undefined\on@line . l.225 ...as shown in Figure \ref{intro_figure_dgf} A. On a technical note, DN... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_dgf' on page undefined on input line 22 5. ! Missing $ inserted. $ l.226 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 225--226 [] [] Overfull \hbox (322.53096pt too wide) in paragraph at lines 225--226 []\OML/cmm/m/it/10 haracterization[]\OT1/cmr/m/n/10 994\OML/cmm/m/it/10 ; assho wninFigure[]A:Onatechnicalnote; DNase \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (342.11769pt too wide) in paragraph at lines 225--226 \OML/cmm/m/it/10 seqassaysarequitesensitiveassays:Achievingaproperchromatindegr adation \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (96.68848pt too wide) in paragraph at lines 225--226 \OML/cmm/m/it/10 thatis; avoidingover \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (48.80585pt too wide) in paragraph at lines 225--226 \OML/cmm/m/it/10 digestion \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (253.4532pt too wide) in paragraph at lines 225--226 \OML/cmm/m/it/10 isnotaneasytaskandrequirescarefulenzymatictitrations:$ [] Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no 5 in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.228 ...e accessible regions of the genome \citep {adey_rapid_2010,buenrostr... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! ! Missing $ inserted. $ l.228 ...ssible regions of the genome \citep{adey_ rapid_2010,buenrostro_tran... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.228 ...rapid_2010,buenrostro_transposition_2013} , Figure \ref{intro_figure... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. ...ce `intro_figure_dgf' on page \thepage \space undefined\on@line . l.228 ...tion_2013}, Figure \ref{intro_figure_dgf} B. The enzyme inserts smal... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_dgf' on page undefined on input line 22 8. ! Undefined control sequence. l.228 ...s separated from each other by 9bp \citep {adey_rapid_2010}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.229 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 228--229 [] [] Overfull \hbox (1900.2295pt too wide) in paragraph at lines 228--229 []\OML/cmm/m/it/10 apid[]\OT1/cmr/m/n/10 010\OML/cmm/m/it/10 ; buenrostro[]rans position[]\OT1/cmr/m/n/10 013\OML/cmm/m/it/10 ; Figure[]B:Theenzymeinsertssmall doublestrandedbarcodesinsidetheDNAwhereveritisaccessibleresultingathecreationof doublestrandbreaks:Thisprocess; knownastagmentation; allowstoi\OT1/cmr/m/n/10 ) \OML/cmm/m/it/10 fragmentthegenomeandii\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 insert ssequencingbarcodesatonce:ItshouldbenotedthattheTn\OT1/cmr/m/n/10 5\OML/cmm/m/i t/10 actsasanhomodimerandthusinsertstwocopiesofthesameadaptorsseparatedfromeach otherby\OT1/cmr/m/n/10 9\OML/cmm/m/it/10 bp[]:$ [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ce `intro_figure_dgf' on page \thepage \space undefined\on@line . l.231 ...q) density (Figure \ref{intro_figure_dgf} C). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_dgf' on page undefined on input line 23 1. Missing character: There is no C in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 231--232 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 231--232 [] [] Missing character: There is no W in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ce `intro_figure_dgf' on page \thepage \space undefined\on@line . l.234 ...footprint" (Figure \ref{intro_figure_dgf} C). Formally, a footprint ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_dgf' on page undefined on input line 23 4. Missing character: There is no C in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! ! Undefined control sequence. l.234 ...gradation because of binding event \citep {vierstra_genomic_2016}, b... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! ! Missing $ inserted. $ l.234 ...because of binding event \citep{vierstra_ genomic_2016}, but I will ... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.234 ...nding event \citep{vierstra_genomic_2016} , but I will later use the... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.235 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 234--235 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 234--235 [] [] Overfull \hbox (548.90063pt too wide) in paragraph at lines 234--235 []\OML/cmm/m/it/10 enomic[]\OT1/cmr/m/n/10 016\OML/cmm/m/it/10 ; butIwilllateru setheterm\OT1/cmr/m/n/10 "\OML/cmm/m/it/10 footprint\OT1/cmr/m/n/10 "\OML/cmm/m /it/10 therefertosignaldropinadegradationsignalforaggregationprofilesaswell:$ [] Missing character: There is no D in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no ) in font nullfont! ! Undefined control sequence. l.236 ... followed by sequencing (ChIP-seq) \citep {barski_high-resolution_20... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no i in font nullfont! ! Missing $ inserted. $ l.236 ...d by sequencing (ChIP-seq) \citep{barski_ high-resolution_2007} to k... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.236 ...-seq) \citep{barski_high-resolution_2007} to know where each TF is ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.237 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 236--237 [] [] Overfull \hbox (27.29472pt too wide) in paragraph at lines 236--237 []\OML/cmm/m/it/10 igh \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1682.44576pt too wide) in paragraph at lines 236--237 \OML/cmm/m/it/10 resolution[]\OT1/cmr/m/n/10 007\OML/cmm/m/it/10 toknowwhereeac hTFisbinding; itissufficienttorunasinglechromatinaccessibilityassay:Additionall y; DGFistotallyagnosticinthesensethatitdoesnotrequireapriorknowledgeofthefactor stolookfor:However; ifDGFrevealstheactiveregulatoryregions; itdoesnotprovidethe informationaboutwhichfactorsbound:Methodstocircumventthislimitationwillbediscus sedlater:$ [] ! Undefined control sequence. l.238 \subsection {Measuring TF binding in vivo} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no M in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 238--241 [] [] Missing character: There is no D in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.243 ...umber of pre-selected loci at once \citep {odom_methods_2011}. Final... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! ! Missing $ inserted. $ l.243 ...of pre-selected loci at once \citep{odom_ methods_2011}. Finally, pr... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.243 ...ed loci at once \citep{odom_methods_2011} . Finally, protocols subje... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.243 ...h throughput sequencing (ChIP-seq) \citep {barski_high-resolution_20... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.244 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 243--244 [] [] Overfull \hbox (427.74219pt too wide) in paragraph at lines 243--244 []\OML/cmm/m/it/10 ethods[]\OT1/cmr/m/n/10 011\OML/cmm/m/it/10 :Finally; protoc olssubjectingthepurifiedDNAtohighthroughputsequencing\OT1/cmr/m/n/10 (\OML/cmm/ m/it/10 ChIP \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (641.1548pt too wide) in paragraph at lines 243--244 \OML/cmm/m/it/10 seq\OT1/cmr/m/n/10 )[]\OML/cmm/m/it/10 allowedtoidentifythebou ndlociinanagnosticway; withanunprecedentedthroughput:$ [] Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 246--247 [] [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! ! Undefined control sequence. l.248 ...reflected in the density of signal \citep {jothi_genome-wide_2008}. ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no j in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! ! Missing $ inserted. $ l.248 ...ed in the density of signal \citep{jothi_ genome-wide_2008}. Thus Ch... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.248 ... of signal \citep{jothi_genome-wide_2008} . Thus ChIP-seq allows to ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. ...igning_binding_sites' on page \thepage \space undefined\on@line . l.248 ...ection \ref{intro_aligning_binding_sites} ). Typically, the identifi... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_aligning_binding_sites' on page undefined on i nput line 248. ! Undefined control sequence. ... `intro_tf_cobinding' on page \thepage \space undefined\on@line . l.248 ...ers (see section \ref{intro_tf_cobinding} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_tf_cobinding' on page undefined on input line 248. ! Missing $ inserted. $ l.249 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 248--249 [] [] Overfull \hbox (41.3725pt too wide) in paragraph at lines 248--249 []\OML/cmm/m/it/10 enome \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (100.79623pt too wide) in paragraph at lines 248--249 \OML/cmm/m/it/10 wide[]\OT1/cmr/m/n/10 008\OML/cmm/m/it/10 :ThusChIP \OMS/cmsy/ m/n/10 ^^@ [] Overfull \hbox (130.16785pt too wide) in paragraph at lines 248--249 \OML/cmm/m/it/10 seqallowstoidentifyregions \OT1/cmr/m/n/10 + [] Overfull \hbox (12.77782pt too wide) in paragraph at lines 248--249 \OML/cmm/m/it/10 = \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (290.90755pt too wide) in paragraph at lines 248--249 \OT1/cmr/m/n/10 100\OML/cmm/m/it/10 bpinwhichaTFbinds:Nonetheless; itispossible toidentifyover \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (814.81442pt too wide) in paragraph at lines 248--249 \OML/cmm/m/it/10 representedDNAsequencemotifsfromtheseregionsusingdenovomotifdi scoverymethods\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 seesection[]\OT1/cmr/m/n/10 )\O ML/cmm/m/it/10 :Typically; theidentifiedsequencemotifsbelongtoi\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 theTFofinterestand=orii\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 co \ OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (100.07095pt too wide) in paragraph at lines 248--249 \OML/cmm/m/it/10 binders\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 seesection[]\OT1/cmr/ m/n/10 )\OML/cmm/m/it/10 :$ [] ! Undefined control sequence. l.250 \subsection {Measuring TF binding in vitro} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no M in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 250--251 [] [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. l.252 ...ures of the TF binding specificity \citep {stormo_determining_2010}.... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! ! Missing $ inserted. $ l.252 ...the TF binding specificity \citep{stormo_ determining_2010}. Additio... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.252 ...ecificity \citep{stormo_determining_2010} . Additionally, in vivo, t... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. ...ntro_gene_regulation' on page \thepage \space undefined\on@line . l.252 ... (see section \ref{intro_gene_regulation} ). In regards of these lim... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_gene_regulation' on page undefined on input li ne 252. ! Missing $ inserted. $ l.253 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 252--253 [] [] Overfull \hbox (1733.6688pt too wide) in paragraph at lines 252--253 []\OML/cmm/m/it/10 etermining[]\OT1/cmr/m/n/10 010\OML/cmm/m/it/10 :Additionall y; invivo; thechromatinexertaneffectonTFbinding\OT1/cmr/m/n/10 (\OML/cmm/m/it/1 0 seesection[]\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 :Inregardsoftheselimitations; i nvitrobindingassaysofferexperimentalsolutionstoinvestigatei\OT1/cmr/m/n/10 )\OM L/cmm/m/it/10 TFbindingoverawiderrangeofaffinitiesandii\OT1/cmr/m/n/10 )\OML/cm m/m/it/10 TFintrinsicspecificity; withoutthechromatininfluence:Intherecentyears ; manydifferenttechnologieshavebeendevelopedtoinvestigateTFbindinginvitro:$ [] Missing character: There is no M in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.255 ...ion volumes. Maerkl and colleagues \citep {maerkl_systems_2007,geert... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no l in font nullfont! ! Missing $ inserted. $ l.255 ...mes. Maerkl and colleagues \citep{maerkl_ systems_2007,geertz_massiv... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.255 ...aerkl_systems_2007,geertz_massively_2012} have developed the mechan... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.256 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 255--256 [] [] Overfull \hbox (1228.20584pt too wide) in paragraph at lines 255--256 []\OML/cmm/m/it/10 ystems[]\OT1/cmr/m/n/10 007\OML/cmm/m/it/10 ; geertz[]assive ly[]\OT1/cmr/m/n/10 012\OML/cmm/m/it/10 havedevelopedthemechanicallyinducedtrap pingofmolecularinteractions\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 MITOMI\OT1/cmr/m/n /10 )\OML/cmm/m/it/10 :Thisassayisbasedonamicrofluidicdevicethatallowstorunhund redofaffinityassayswithagivenTF; inparallel:Eachassayisrunusingadifferentdesign edoligo \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (128.58792pt too wide) in paragraph at lines 255--256 \OML/cmm/m/it/10 nucleotideofknownsequence:$ [] ! LaTeX Error: The font size command \normalsize is not defined: there is probably something wrong with the class file. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.256 Your command was ignored. Type I to replace it with another command, or to continue without it. [1 ! Undefined control sequence. \newlabel{intro}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro}{{}{}} ! Undefined control sequence. ...sline {chapter}{Introduction}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \@writefile{toc}{\contentsline {chapter}{Introduction}{}} ! Undefined control sequence. ...bel{intro_about_chromatin}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_about_chromatin}{{}{}} {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} ! Undefined control sequence. \newlabel{intro_chromatin}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_chromatin}{{}{}} ! Undefined control sequence. ...ro_nucleosome_positioning}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_nucleosome_positioning}{{}{}} ! Undefined control sequence. \newlabel{intro_tf_cobinding}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_tf_cobinding}{{}{}} ! Undefined control sequence. ...abel{intro_tf_association}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_tf_association}{{}{}} ! Undefined control sequence. ...bel{intro_gene_regulation}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_gene_regulation}{{}{}} ! Undefined control sequence. ...suring_chromatin_features}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{measuring_chromatin_features}{{}{}} ! Undefined control sequence. \newlabel{intro_dgf}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_dgf}{{}{}} ! Undefined control sequence. \newlabel{intro_figure_dgf}{{}{\thepage }} l.256 The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. \newlabel{intro_figure_dgf}{{}{}} ] Missing character: There is no O in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no X in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! ! Undefined control sequence. l.258 ...ew high affinity binding sequences \citep {tuerk_systematic_1990}. T... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! ! Missing $ inserted. $ l.258 ... affinity binding sequences \citep{tuerk_ systematic_1990}. The SELE... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.258 ...g sequences \citep{tuerk_systematic_1990} . The SELEX assay was adap... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.258 ...e high throughput SELEX (HT-SELEX, \citep {roulet_high-throughput_20... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.258 ...ynamic scale of binding affinities \citep {stormo_determining_2010} ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.259 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 258--259 [] [] Overfull \hbox (379.87451pt too wide) in paragraph at lines 258--259 []\OML/cmm/m/it/10 ystematic[]\OT1/cmr/m/n/10 990\OML/cmm/m/it/10 :TheSELEXassa ywasadaptedtobecomehighthroughputSELEX\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 HT \OMS /cmsy/m/n/10 ^^@ [] Overfull \hbox (392.60468pt too wide) in paragraph at lines 258--259 \OML/cmm/m/it/10 SELEX; []\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 :HT \OMS/cmsy/m/n/1 0 ^^@ [] -Overfull \hbox (610.07622pt too wide) in paragraph at lines 258--259 +Overfull \hbox (600.70352pt too wide) in paragraph at lines 258--259 \OML/cmm/m/it/10 SELEXassaysaTFspecificitybyallowingabindingreactionbetweentheT -FandtenthsofmillionsofdifferentDNAsequencesoftypically\OT1/cmr/m/n/10 20 \OMS/c -msy/m/n/10 ^^@ +FandtensofmillionsofdifferentDNAsequencesoftypically\OT1/cmr/m/n/10 20 \OMS/cms +y/m/n/10 ^^@ [] Overfull \hbox (2387.84547pt too wide) in paragraph at lines 258--259 \OT1/cmr/m/n/10 30\OML/cmm/m/it/10 bp:TheboundDNAmoleculesarepurifiedbypullingd owntheTF:ThepurifiedDNAcaneitherbesequencedusinghighthroughputsequencingorbesub jectedtoanothercycleofselection:Repeatedcyclesallowtoisolatehigheraffinitybinde r; eventuallyonlyreturningafewhundreds:Underalimitednumberofcycles; thismethodh asalargedynamicscaleofbindingaffinities[]andallowtoobtainadigitalreadout:Howeve r; therepeatedcyclescanintroducebiaisesthatarehardtomodelproperlyinordertoprope rlyestimatethebindingaffinities:$ [] Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! ! Undefined control sequence. l.261 ...protein binding microarrays (PBMs, \citep {bulyk_exploring_2001,mukh... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no k in font nullfont! ! Missing $ inserted. $ l.261 ... binding microarrays (PBMs, \citep{bulyk_ exploring_2001,mukherjee_r... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.261 ...mukherjee_rapid_2004,berger_compact_2006} ) also should be mentioned... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. Missing character: There is no 4 in font nullfont! ! Missing $ inserted. $ l.261 ...can be present. Assaying all possible $4^ {L}$ sequences of a given ... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! ! Undefined control sequence. l.261 ...e the information on a single chip \citep {berger_universal_2009}. A... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! ! Missing $ inserted. $ l.261 ...formation on a single chip \citep{berger_ universal_2009}. Additiona... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.261 ...single chip \citep{berger_universal_2009} . Additionally, it has bee... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Missing $ inserted. $ l.262 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 261--262 [] [] -Overfull \hbox (1481.1469pt too wide) in paragraph at lines 261--262 +Overfull \hbox (1461.45981pt too wide) in paragraph at lines 261--262 []\OML/cmm/m/it/10 xploring[]\OT1/cmr/m/n/10 001\OML/cmm/m/it/10 ; mukherjee[]a pid[]\OT1/cmr/m/n/10 004\OML/cmm/m/it/10 ; berger[]ompact[]\OT1/cmr/m/n/10 006) -\OML/cmm/m/it/10 alsoshouldbementioned:Typically; aPBMdeviceisachiponwhichtenth -ofthousandsofDNAprobesareimmobilized:Theprobesarearrangedintospotssuchthatonlyo -neprobespecieispresentineachspot:ApurifiedTFisthenaddedonthechipandtheTFbinding -isrevealedusingafluorescent \OMS/cmsy/m/n/10 ^^@ +\OML/cmm/m/it/10 alsoshouldbementioned:Typically; aPBMdeviceisachiponwhichtenso +fthousandsofDNAprobesareimmobilized:Theprobesarearrangedintospotssuchthatonlyon +eprobespecieispresentperspot:ApurifiedTFisthenaddedonthechipandtheTFbindingisre +vealedusingafluorescent \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1772.76152pt too wide) in paragraph at lines 261--262 \OML/cmm/m/it/10 labeledAb:Becausetheidentityoftheprobespecieineachspotisknown; theaffinitytothisspeciecanbedirectlymeasuredastheintensityofthefluorescentsign al:Thehighertheaffinityforaprobespecie; themoreTFbindstothespot; thestrongerthe fluorescentsignal:ThemostimportantlimitationofPBMisitslimitedspaceonthechipwhic hrestrictthenumberofdifferentspotsthatcanbepresent:Assayingallpossible$$[]$ [] Overfull \hbox (6.80557pt too wide) in paragraph at lines 261--262 \OML/cmm/m/it/10 L$ [] Overfull \hbox (498.36096pt too wide) in paragraph at lines 261--262 []\OML/cmm/m/it/10 niversal[]\OT1/cmr/m/n/10 009\OML/cmm/m/it/10 :Additionally; ithasbeensuggestedthatthepositionofthespotonthechipcouldinfluencetheTFbinding: $ [] ! Undefined control sequence. l.264 \section {Modeling sequence specificity} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no M in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 264--266 [] [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no T in font nullfont! -Missing character: There is no F in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no m in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 267--268 [] [] Missing character: There is no M in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 269--270 [] [] ! Undefined control sequence. l.271 \subsubsection {The physics approach to PWMs} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 271--272 [] [] Missing character: There is no L in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no , in font nullfont! ! Undefined control sequence. l.273 ...NA sequence $S$, at the equilibrium, \ch {TF + S <>[][] TF.S}. The ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no + in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no < in font nullfont! Missing character: There is no > in font nullfont! Missing character: There is no [ in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no [ in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no : in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 273--274 [] [] Overfull \hbox (15.05211pt too wide) in paragraph at lines 273--274 \OML/cmm/m/it/10 TF$ [] Overfull \hbox (6.70831pt too wide) in paragraph at lines 273--274 \OML/cmm/m/it/10 S$ [] Overfull \hbox (10.04369pt too wide) in paragraph at lines 273--274 \OML/cmm/m/it/10 k[]$ [] Overfull \hbox (20.0pt too wide) in paragraph at lines 275--275 [] [] ! LaTeX Error: Environment aligned undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.276 \begin{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: \begin{equation} on input line 275 ended by \end{aligned}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.278 \end{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (70.8706pt too wide) detected at line 280 \OML/cmm/m/it/10 k[] \OT1/cmr/m/n/10 = [][] [] Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! 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Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 293--294 [] [] Overfull \hbox (15.05211pt too wide) in paragraph at lines 293--294 \OML/cmm/m/it/10 TF$ [] Overfull \hbox (20.68198pt too wide) in paragraph at lines 293--294 \OT1/cmr/m/n/10 ^^A\OML/cmm/m/it/10 G[]$ [] Overfull \hbox (15.05211pt too wide) in paragraph at lines 293--294 \OML/cmm/m/it/10 TF$ [] Missing character: There is no T in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no E in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no j in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. l.295 ...ption was a subject of controversy \citep {man_non-independence_2001... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.295 ... was a subject of controversy \citep{man_ non-independence_2001,buly... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.295 ...independence_2001,bulyk_nucleotides_2002} . However, it is nowadays ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.295 ...esent accurately most of the cases \citep {benos_additivity_2002,zha... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.296 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 295--296 [] [] Overfull \hbox (20.68198pt too wide) in paragraph at lines 295--296 \OT1/cmr/m/n/10 ^^A\OML/cmm/m/it/10 G[]$ [] Overfull \hbox (24.07071pt too wide) in paragraph at lines 295--296 []\OML/cmm/m/it/10 on \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (1017.53291pt too wide) in paragraph at lines 295--296 \OML/cmm/m/it/10 independence[]\OT1/cmr/m/n/10 001\OML/cmm/m/it/10 ; bulyk[]ucl eotides[]\OT1/cmr/m/n/10 002\OML/cmm/m/it/10 :However; itisnowadayscommonlyadmi ttedthat; eveniftheassumptionisviolatedinsomecases; itdoesstillallowtorepresent accuratelymostofthecases[]:$ [] Missing character: There is no O in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. l.297 ... each position of the binding site \citep {stormo_specificity_1998}.... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! ! Missing $ inserted. $ l.297 ...sition of the binding site \citep{stormo_ specificity_1998}. This ma... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.297 ...ding site \citep{stormo_specificity_1998} . This matrix is called a ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! ! Missing $ inserted. $ l.297 ... affinity site is usually given a $\Delta - \Delta G^{0}$ equals to 0 ... + G^{0}$ equals to 0 and al... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 297--298 [] [] Overfull \hbox (10.98616pt too wide) in paragraph at lines 297--298 \OT1/cmr/m/n/10 4[]$ [] Overfull \hbox (6.80557pt too wide) in paragraph at lines 297--298 \OML/cmm/m/it/10 L$ [] Overfull \hbox (10.00003pt too wide) in paragraph at lines 297--298 \OT1/cmr/m/n/10 3 \OMS/cmsy/m/n/10 ^^C [] Overfull \hbox (14.58337pt too wide) in paragraph at lines 297--298 \OML/cmm/m/it/10 L \OT1/cmr/m/n/10 + [] Overfull \hbox (5.00002pt too wide) in paragraph at lines 297--298 \OT1/cmr/m/n/10 1$ [] Overfull \hbox (29.01534pt too wide) in paragraph at lines 297--298 \OT1/cmr/m/n/10 ^^A^^A\OML/cmm/m/it/10 G[]$ [] -Overfull \hbox (801.05138pt too wide) in paragraph at lines 297--298 +Overfull \hbox (792.71802pt too wide) in paragraph at lines 297--298 []\OML/cmm/m/it/10 pecificity[]\OT1/cmr/m/n/10 998\OML/cmm/m/it/10 :Thismatrixi scalledapositionweightmatrix\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 PWM\OT1/cmr/m/n/1 0 )\OML/cmm/m/it/10 andallowstopredicttheaffinityof$$foranysequence:InsuchPWMs; - thestrongestaffinitysiteisusuallygivena$$\OT1/cmr/m/n/10 ^^A^^A\OML/cmm/m/it/1 -0 G[]$ + thestrongestaffinitysiteisusuallygivena$$\OT1/cmr/m/n/10 ^^A\OML/cmm/m/it/10 G +[]$ [] Overfull \hbox (29.01534pt too wide) in paragraph at lines 297--298 \OT1/cmr/m/n/10 ^^A^^A\OML/cmm/m/it/10 G[]$ [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no ( in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 299--300 [] [] Overfull \hbox (29.01534pt too wide) in paragraph at lines 299--300 \OT1/cmr/m/n/10 ^^A^^A\OML/cmm/m/it/10 G[]$ [] + +Overfull \hbox (20.68198pt too wide) in paragraph at lines 299--300 +\OT1/cmr/m/n/10 ^^A\OML/cmm/m/it/10 G[]$ + [] + ! Undefined control sequence. l.301 \subsubsection {The statistical mechanic approach to PWMs} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 301--302 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 303--304 [] [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 303--304 \OML/cmm/m/it/10 A$ [] Overfull \hbox (6.80557pt too wide) in paragraph at lines 303--304 \OML/cmm/m/it/10 L$ [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 303--304 \OML/cmm/m/it/10 A$ [] Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 9 in font nullfont! Missing character: There is no 8 in font nullfont! Missing character: There is no 6 in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! ! Undefined control sequence. l.307 ... $A$ using the information content \citep {schneider_information_198... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! ! Missing $ inserted. $ l.307 ...the information content \citep{schneider_ information_1986}. In 1987... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.307 ...ontent \citep{schneider_information_1986} . In 1987, Berg and von Hi... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.307 ...e estimation of binding affinities \citep {berg_selection_1988}. Giv... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no A in font nullfont! ! Missing $ inserted. $ l.308 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 307--308 [] [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 307--308 \OML/cmm/m/it/10 A$ [] Overfull \hbox (887.15662pt too wide) in paragraph at lines 307--308 []\OML/cmm/m/it/10 nformation[]\OT1/cmr/m/n/10 986\OML/cmm/m/it/10 :In\OT1/cmr/ m/n/10 1987\OML/cmm/m/it/10 ; BergandvonHippeldemonstratedthatthisstatisticalap proachwasmathematicallyrelatedtotheestimationofbindingaffinities[]:Given$$; aPW Mcanbebuildusing \OT1/cmr/m/n/10 :$ [] Overfull \hbox (20.0pt too wide) in paragraph at lines 309--309 [] [] ! LaTeX Error: Environment aligned undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.310 \begin{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: \begin{equation} on input line 309 ended by \end{aligned}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.312 \end{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (64.86134pt too wide) detected at line 314 \OML/cmm/m/it/10 ^^U"[] \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 ln[][] [] Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no y in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 316--317 [] [] Overfull \hbox (16.40138pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 "[]$ [] Overfull \hbox (4.29166pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 b$ [] Overfull \hbox (4.69049pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 j$ [] Overfull \hbox (17.71046pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 f[]$ [] Overfull \hbox (4.29166pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 b$ [] Overfull \hbox (4.69049pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 j$ [] Overfull \hbox (17.71046pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 f[]$ [] Overfull \hbox (4.69049pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 j$ [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 A$ [] Overfull \hbox (5.83336pt too wide) in paragraph at lines 316--317 \OML/cmm/m/it/10 ^^U$ [] - -Overfull \hbox (7.50002pt too wide) in paragraph at lines 316--317 -\OML/cmm/m/it/10 A$ - [] - Missing character: There is no S in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Undefined control sequence. l.318 ...used a slightly different approach \citep {stormo_specificity_1998} ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! ! Missing $ inserted. $ l.318 ...lightly different approach \citep{stormo_ specificity_1998} and prop... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.318 ... approach \citep{stormo_specificity_1998} and proposed to link the ... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. Missing character: There is no A in font nullfont! ! Missing $ inserted. $ l.319 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 318--319 [] [] Overfull \hbox (454.32pt too wide) in paragraph at lines 318--319 []\OML/cmm/m/it/10 pecificity[]\OT1/cmr/m/n/10 998\OML/cmm/m/it/10 andproposedt olinktheinformationcontentof$$totheestimationofthebindingenergyusing \OT1/cmr/m /n/10 :$ [] Overfull \hbox (20.0pt too wide) in paragraph at lines 320--320 [] [] ! LaTeX Error: Environment aligned undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.321 \begin{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: \begin{equation} on input line 320 ended by \end{aligned}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.323 \end{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (69.6672pt too wide) detected at line 325 \OML/cmm/m/it/10 W[] \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 log[][][] [] Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no . in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +! Undefined control sequence. + ...e `intro_eq_pwm_berg' on page \thepage + \space undefined\on@line . +l.327 ...te that equations \ref{intro_eq_pwm_berg} + and \ref{intro_eq_pwm_sto... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Reference `intro_eq_pwm_berg' on page undefined on input line 3 +27. + +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +! Undefined control sequence. + ...`intro_eq_pwm_stormo' on page \thepage + \space undefined\on@line . +l.327 ...q_pwm_berg} and \ref{intro_eq_pwm_stormo} + give inversly proportiona... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Reference `intro_eq_pwm_stormo' on page undefined on input line + 327. + +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 327--328 [] [] Overfull \hbox (15.00108pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 f[]$ [] Overfull \hbox (4.29166pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 b$ [] Overfull \hbox (4.69049pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 j$ [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 A$ [] Overfull \hbox (17.10071pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 b\OT1/cmr/m/n/10 )$ [] Overfull \hbox (4.29166pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 b$ [] Overfull \hbox (10.83334pt too wide) in paragraph at lines 327--328 \OML/cmm/m/it/10 W$ [] + +Overfull \hbox (10.86105pt too wide) in paragraph at lines 327--328 +[] + [] + + +Overfull \hbox (10.86105pt too wide) in paragraph at lines 327--328 +[] + [] + ! Undefined control sequence. l.329 \subsection {Aligning binding sites} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no A in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 329--331 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no R in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 333--334 [] [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 333--334 \OML/cmm/m/it/10 A$ [] Missing character: There is no M in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no " in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! ! Undefined control sequence. l.335 ...m developed by Stormo and Hartzell \citep {stormo_identifying_1989} ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! ! Missing $ inserted. $ l.335 ...ped by Stormo and Hartzell \citep{stormo_ identifying_1989} finds an... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.335 ... Hartzell \citep{stormo_identifying_1989} finds an optimal alignmen... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.335 ... the alignment information content \citep {schneider_information_198... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.335 ...thms developed by Hertz and Stormo \citep {hertz_identification_1990... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.335 ...tion_1990} and Lawrence and Reilly \citep {lawrence_expectation_1990... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.335 ...e of binding and non-binding sites \citep {bailey_fitting_1994}. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.336 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 335--336 [] [] Overfull \hbox (2140.74011pt too wide) in paragraph at lines 335--336 []\OML/cmm/m/it/10 dentifying[]\OT1/cmr/m/n/10 989\OML/cmm/m/it/10 findsanoptim alalignmentbymaximizingamodifiedversionofthealignmentinformationcontent[]:Alter natively; thealgorithmsdevelopedbyHertzandStormo[]andLawrenceandReilly[]buildan LPMthatmaximizethelikelihoodofobservingthedataunderthehypothesisthattheyhavebee ngeneratedfromthediscoveredmodel:LawrenceandReillyalgorithmsolvesthealignmentpr oblemusinganExpectation \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (879.43967pt too wide) in paragraph at lines 335--336 \OML/cmm/m/it/10 Maximization\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 EM\OT1/cmr/m/n/1 0 )\OML/cmm/m/it/10 algorithm; whichmakestheiralgorithmaheuristic:Thistypeoffra meworkhasalsobeenusedtodevelopMEME; exceptedthatitexplicitlymodelsthedataasamix tureofbindingandnon \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (132.70235pt too wide) in paragraph at lines 335--336 \OML/cmm/m/it/10 bindingsites[]:$ [] ! Undefined control sequence. l.337 \subsection {Platitudes} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no P in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 337--338 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.339 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (20.0pt too wide) in paragraph at lines 340--340 [] [] ! Undefined control sequence. l.341 \includegraphics [scale=0.2]{images/ch_introduction/figure_pwm.png} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ l.341 \includegraphics[scale=0.2]{images/ch_ introduction/figure_pwm.png} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.341 ...2]{images/ch_introduction/figure_pwm.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.342 \captionof {figure} {\textbf{Position weight matrix : } \textbf{A} Huma... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Command \textunderscore invalid in math mode on input line 342. \citation{kulakovskiy_hocomoco:_2016} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.342 ...lection \cite{kulakovskiy_hocomoco:_2016} . \textbf{B} Corresponding... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `kulakovskiy_hocomoco:_2016' on page undefined on inpu t line 342. ! LaTeX Error: Command \end{center} invalid in math mode. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.344 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.344 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.344 \end{center} Try typing to proceed. If that doesn't work, type X to quit. ! Missing $ inserted. $ l.344 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Missing } inserted. } l.344 \end{center} I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! LaTeX Error: \begin{document} ended by \end{figure}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.345 \end{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (2114.70833pt too wide) in paragraph at lines 341--346 []\OML/cmm/m/it/10 ntroduction=figure[]wm:png[][]:[]$ [] Missing character: There is no L in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 348--349 [] [] Overfull \hbox (7.50002pt too wide) in paragraph at lines 348--349 \OML/cmm/m/it/10 A$ [] Missing character: There is no O in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no [ in font nullfont! \citation{schneider_sequence_1990} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . l.351 ...ence logo (\cite{schneider_sequence_1990} , Figure \ref{intro_pwm_lo... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Citation `schneider_sequence_1990' on page undefined on input l ine 351. Missing character: There is no ] in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ence `intro_pwm_logo' on page \thepage \space undefined\on@line . l.351 ...quence_1990}, Figure \ref{intro_pwm_logo} ). Because of this and of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_pwm_logo' on page undefined on input line 351. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 351--352 [] [] Overfull \hbox (5.43053pt too wide) in paragraph at lines 351--352 [] [] Overfull \hbox (10.86105pt too wide) in paragraph at lines 351--352 [] [] Missing character: There is no N in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no J in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no R in font nullfont! ! Undefined control sequence. l.354 ...available libraries such as JASPAR \citep {khan_jaspar_2018}, HOCOMO... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no k in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ l.354 ...ble libraries such as JASPAR \citep{khan_ jaspar_2018}, HOCOMOCO \ci... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. l.354 ...s such as JASPAR \citep{khan_jaspar_2018} , HOCOMOCO \citep{kulakovs... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. l.354 ...\citep{khan_jaspar_2018}, HOCOMOCO \citep {kulakovskiy_hocomoco:_201... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. l.354 ...akovskiy_hocomoco:_2018} or CIS-BP \citep {weirauch_determination_20... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing $ inserted. $ l.355 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Overfull \hbox (20.0pt too wide) in paragraph at lines 354--355 [] [] Overfull \hbox (281.04335pt too wide) in paragraph at lines 354--355 []\OML/cmm/m/it/10 aspar[]\OT1/cmr/m/n/10 018\OML/cmm/m/it/10 ; HOCOMOCO[]orCIS \OMS/cmsy/m/n/10 ^^@ [] Overfull \hbox (258.41634pt too wide) in paragraph at lines 354--355 \OML/cmm/m/it/10 BP[]tociteonlythemostfamous:$ [] ! Undefined control sequence. l.356 \subsection {Predicting binding sites} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no P in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 356--357 [] [] Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no W in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 358--359 [] [] Overfull \hbox (6.70831pt too wide) in paragraph at lines 358--359 \OML/cmm/m/it/10 S$ [] Overfull \hbox (6.80557pt too wide) in paragraph at lines 358--359 \OML/cmm/m/it/10 L$ [] Overfull \hbox (11.88882pt too wide) in paragraph at lines 358--359 \OT1/cmr/bx/n/10 W [] Overfull \hbox (17.52086pt too wide) in paragraph at lines 358--359 \OML/cmm/m/it/10 Lx\OT1/cmr/m/n/10 4$ [] Overfull \hbox (6.70831pt too wide) in paragraph at lines 358--359 \OML/cmm/m/it/10 S$ [] Overfull \hbox (3.61111pt too wide) in paragraph at lines 358--359 \OML/cmm/m/it/10 t$ [] Overfull \hbox (20.0pt too wide) in paragraph at lines 360--360 [] [] ! LaTeX Error: Environment aligned undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.361 \begin{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: \begin{equation} on input line 360 ended by \end{aligned}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.363 \end{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (85.90375pt too wide) detected at line 365 \OML/cmm/m/it/10 score\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 S\OT1/cmr/m/n/10 ) = [] \OML/cmm/m/it/10 W[][] [] Missing character: There is no I in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no : in font nullfont! Overfull \hbox (20.0pt too wide) in paragraph at lines 367--368 [] [] Overfull \hbox (39.65651pt too wide) in paragraph at lines 367--368 \OML/cmm/m/it/10 score[] \OMS/cmsy/m/n/10 ^^U [] Overfull \hbox (3.61111pt too wide) in paragraph at lines 367--368 \OML/cmm/m/it/10 t$ [] Overfull \hbox (6.70831pt too wide) in paragraph at lines 367--368 \OML/cmm/m/it/10 S$ [] Overfull \hbox (10.91661pt too wide) in paragraph at lines 367--368 \OT1/cmr/bx/n/10 M [] Overfull \hbox (33.0868pt too wide) in paragraph at lines 367--368 \OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 S\OMS/cmsy/m/n/10 j\OML/cmm /m/it/10 M\OT1/cmr/m/n/10 )$ [] Overfull \hbox (20.0pt too wide) in paragraph at lines 369--369 [] [] ! LaTeX Error: Environment aligned undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.370 \begin{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. ! LaTeX Error: \begin{equation} on input line 369 ended by \end{aligned}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.372 \end{aligned} Your command was ignored. Type I to replace it with another command, or to continue without it. Overfull \hbox (79.96333pt too wide) detected at line 374 \OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 S\OMS/cmsy/m/n/10 j\OML/cmm /m/it/10 M\OT1/cmr/m/n/10 ) = [] \OML/cmm/m/it/10 M[][] [] +Missing character: There is no I in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no ' in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no : in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 376--377 +[] + [] + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 378--378 +[] + [] + + +! LaTeX Error: Environment aligned undefined. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.379 \begin{aligned} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +! LaTeX Error: \begin{equation} on input line 378 ended by \end{aligned}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.381 \end{aligned} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (140.53702pt too wide) detected at line 383 +\OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 M\OMS/cmsy/m/n/10 j\OML/cmm +/m/it/10 S\OT1/cmr/m/n/10 ) = [][] + [] + +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 385--386 +[] + [] + + +Overfull \hbox (23.60071pt too wide) in paragraph at lines 385--386 +\OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 M\OT1/cmr/m/n/10 )$ + [] + + +Overfull \hbox (25.83974pt too wide) in paragraph at lines 385--386 +\OML/cmm/m/it/10 p\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 M[]\OT1/cmr/m/n/10 )$ + [] + ! Undefined control sequence. -l.377 \section +l.389 \section {Over-represented patterns discovery} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no O in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 377--379 +Overfull \hbox (20.0pt too wide) in paragraph at lines 389--391 [] [] ! LaTeX Error: Environment figure undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.380 \begin{figure} +l.392 \begin{figure} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 381--381 +Overfull \hbox (20.0pt too wide) in paragraph at lines 393--393 [] [] ! Undefined control sequence. -l.382 \includegraphics +l.394 \includegraphics [scale=0.3]{images/ch_introduction/shift_flip.png} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no [ in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 3 in font nullfont! Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! ! Missing $ inserted. $ -l.382 \includegraphics[scale=0.3]{images/ch_ +l.394 \includegraphics[scale=0.3]{images/ch_ introduction/shift_flip.png} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. -l.382 ...3]{images/ch_introduction/shift_flip.png} +l.394 ...3]{images/ch_introduction/shift_flip.png} I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. -l.383 \captionof +l.395 \captionof {figure}{\textbf{Signal comparison} between two regions $r_... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Missing } inserted. } -l.383 ...{Signal comparison} between two regions $ +l.395 ...{Signal comparison} between two regions $ r_{1}$ and $r_{2}$ bearing... I've inserted something that you may have forgotten. (See the above.) With luck, this will get me unwedged. But if you really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. Missing character: There is no r in font nullfont! ! Missing $ inserted. $ -l.383 ...ignal comparison} between two regions $r_ +l.395 ...ignal comparison} between two regions $r_ {1}$ and $r_{2}$ bearing a... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! 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Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 388--389 +Overfull \hbox (20.0pt too wide) in paragraph at lines 400--401 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 388--389 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 400--401 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Undefined control sequence. ...igning_binding_sites' on page \thepage \space undefined\on@line . -l.392 ...ection \ref{intro_aligning_binding_sites} +l.404 ...ection \ref{intro_aligning_binding_sites} . The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_aligning_binding_sites' on page undefined on i -nput line 392. +nput line 404. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 392--393 +Overfull \hbox (20.0pt too wide) in paragraph at lines 404--405 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 392--393 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 404--405 [] [] Missing character: There is no M in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no K in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! 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Undefined control sequence. ...ro_figure_comparison' on page \thepage \space undefined\on@line . -l.396 ...alf (Figure \ref{intro_figure_comparison} +l.408 ...alf (Figure \ref{intro_figure_comparison} A). In this case, detectin... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_comparison' on page undefined on input -line 396. +line 408. Missing character: There is no A in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! 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Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ro_figure_comparison' on page \thepage \space undefined\on@line . -l.396 ...dge (Figure \ref{intro_figure_comparison} +l.408 ...dge (Figure \ref{intro_figure_comparison} B) or ii) by searching arc... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_comparison' on page undefined on input -line 396. +line 408. Missing character: There is no B in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ( in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ro_figure_comparison' on page \thepage \space undefined\on@line . -l.396 ...ons (Figure \ref{intro_figure_comparison} +l.408 ...ons (Figure \ref{intro_figure_comparison} C). The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. LaTeX Warning: Reference `intro_figure_comparison' on page undefined on input -line 396. +line 408. Missing character: There is no C in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 396--397 +Overfull \hbox (20.0pt too wide) in paragraph at lines 408--409 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 396--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--409 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 396--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--409 [] [] -Overfull \hbox (20.16664pt too wide) in paragraph at lines 396--397 +Overfull \hbox (20.16664pt too wide) in paragraph at lines 408--409 \OML/cmm/m/it/10 L[] \OMS/cmsy/m/n/10 ^^T [] -Overfull \hbox (6.80557pt too wide) in paragraph at lines 396--397 +Overfull \hbox (6.80557pt too wide) in paragraph at lines 408--409 \OML/cmm/m/it/10 L$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 396--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--409 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no P in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no + in font nullfont! Missing character: There is no / in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no 1 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no F in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 400--401 +Overfull \hbox (20.0pt too wide) in paragraph at lines 412--413 [] [] Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no - in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 402--403 +Overfull \hbox (20.0pt too wide) in paragraph at lines 414--415 [] [] Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no D in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no C in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no g in font nullfont! ! Undefined control sequence. -l.404 ...omatin patterns, such as ChromaSig \citep +l.416 ...omatin patterns, such as ChromaSig \citep {hon_chromasig:_2008}, Arc... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! ! Missing $ inserted. $ -l.404 ...n patterns, such as ChromaSig \citep{hon_ +l.416 ...n patterns, such as ChromaSig \citep{hon_ chromasig:_2008}, ArchAlig... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. -l.404 ... as ChromaSig \citep{hon_chromasig:_2008} +l.416 ... as ChromaSig \citep{hon_chromasig:_2008} , ArchAlign \citep{lai_arc... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and you forgot something else, as in `\hbox{$x}'. In such cases the way to recover is to insert both the forgotten and the deleted material, e.g., by typing `I$}'. ! Undefined control sequence. -l.404 ...ep{hon_chromasig:_2008}, ArchAlign \citep +l.416 ...ep{hon_chromasig:_2008}, ArchAlign \citep {lai_archalign:_2010}, CAT... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.404 ...ai_archalign:_2010}, CATCHProfiles \citep +l.416 ...ai_archalign:_2010}, CATCHProfiles \citep {nielsen_catchprofiles}, C... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.404 ...citep{nielsen_catchprofiles}, CAGT \citep +l.416 ...citep{nielsen_catchprofiles}, CAGT \citep {kundaje_ubiquitous_2012} ... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.404 ...iquitous_2012} and ChIPPartitioning\citep +l.416 ...iquitous_2012} and ChIPPartitioning\citep {nair_probabilistic_2014}.... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ) ! Emergency stop. <*> ch_introduction.tex *** (job aborted, no legal \end found) Here is how much of TeX's memory you used: - 37 strings out of 492982 - 752 string characters out of 6134895 + 39 strings out of 492982 + 792 string characters out of 6134895 89429 words of memory out of 5000000 - 3699 multiletter control sequences out of 15000+600000 + 3701 multiletter control sequences out of 15000+600000 4294 words of font info for 16 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 - 18i,5n,21p,1945b,295s stack positions out of 5000i,500n,10000p,200000b,80000s + 18i,5n,21p,1945b,297s stack positions out of 5000i,500n,10000p,200000b,80000s ! ==> Fatal error occurred, no output PDF file produced! diff --git a/main/ch_introduction.tex b/main/ch_introduction.tex index 338f19d..b649a72 100644 --- a/main/ch_introduction.tex +++ b/main/ch_introduction.tex @@ -1,404 +1,416 @@ \cleardoublepage \chapter{Introduction} \label{intro} \markboth{Introduction}{Introduction} \addcontentsline{toc}{chapter}{Introduction} Each living organism contains DNA which is the molecular support on which genes are encoded. Genes are the hereditary unit of life and code for a set of instructions involved in all the aspects of life, from an organism development to the functions of a specific cell type. However, since all these instructions are not needed at the same time, gene expression needs to be regulated. Transcription factors (TFs) are a class of nuclear proteins that can bind to specific DNA sequences and drive target gene expression. Thus TFs are a major regulator of gene expression. The results reported in this work can be sub-divided in two sub-topics. The first topic focuses on data mining projects and reports the results of different computational genomic research projects that were focus on the characterization of the chromatin structure in the vicinity of TF binding sites as well as TF-TF interaction identification and on the modeling of TF DNA sequence specificity. The second topic focuses on the development of algorithms and computational methods to solve bioinformatic problems that are met in genomics. Several algorithms to identify important chromatin signatures or over-represented DNA sequences in the genome using a data partition approach are presented as well as a software that predicts TF binding sites in a genome given a specificity model. The two topics are not entirely separated and can be presented jointly in some chapters. \section{About chromatin} \label{intro_about_chromatin} In eukaryotes, the DNA is stored in the nucleus. Each human cell contains about two meters of DNA. In order to fit the DNA inside the nucleus, the cells have to organize and compact the genome while maintaining it readable. Unbeatable, evolution came out with an elegant solution : the chromatin. The chromatin is the association of the DNA with specialized proteins - the histones - around which it wraps. Other families of proteins are also found in the chromatin, such as RNA polymerases, histone chaperones, helicases or TFs. \subsection{The chromatin structure} % structure, histones, nucleosomes, genome compaction \begin{figure} \begin{center} \includegraphics[scale=0.3]{images/ch_introduction/chromatin.png} \captionof{figure}{\textbf{A} Top view of a nucleosome core particle displayed as a ribbon representation on the left and space filling representation on the right. The NCP is made of a four hetero-dimers histone octamer around which 146-148 DNA bp wraps. The histone tails protrude out of the nucleosome core particle and are accessible to other factors, unlike the inner part of the histone octamer. \textbf{B} The chromatin structure. Inside eukaryotes, DNA is wrapped around histones cores forming nucleosomes. Nucleosomes can then be organized into higher-level helical-like structure, compacting the DNA. The ultimate compaction state is reached at mitosis meta-phase, when the mitotic chromosomes are visible. Figure and legend taken and modified from \cite{mcginty_robert_k._and_tan_song_fundamentals_2014}.} \label{intro_chromatin} \end{center} \end{figure} % histones In human, there are four major (canonical) histones : H2A, H2B, H3 and H4. These four histones are found assembled together into an octamer, composed of two H2A/H2B and two H3/H4 hetero-dimers, around which ~146/8bp of DNA wrap, forming the nucleosome core particule (that I will later simply refer to as "nucleosome", Figure \ref{intro_chromatin}A). The DNA is kept wrapped around the histone octamer because of strong electrostatic interactions. Indeed, the DNA backbone, which is negatively charged in physiological conditions, shows a high affinity for the positively charged histones. As a consequence, the nucleosome is a quite stable structure. The histones proteins are highly conserved among eukaryotes at both the sequence and the structure level. All the histones share the overall same design. They are composed of a N-terminal tail, a central histone-fold domain and of C-terminal tail. Histones associate with each other through their histone-fold domains which compose the center of the nucleosome. In contrast, the histone N-terminal tails are extruding out from the nucleosome and are hotspots for post-translational modifications (PTMs) \citep{kouzarides_chromatin_2007}. For completeness, it should be mentioned that "variant histones" - also called "replacement histone", by opposition to the "canonical replicative histones" - exist and can replace canonical histones in nucleosomes, at specific genome locations, to fulfill dedicated functions \citep{henikoff_histone_2015}. However, this topic is outside the scope of this work. % chromatin fibers The genome is organized into a repetition of nucleosomes, each separated by a linker DNA, forming the 11-nm chromatin fiber. This chromatin conformation is quite relaxed and the DNA accessible. The H1 linker histone can be recruited in the chromatin, in which case it binds the linker DNA and makes it inaccessible. The 11-nm fiber is itself stored into a denser and less accessible structure called the 30-nm fiber (Figure \ref{intro_chromatin}B). Eventually, higher order structure are achieved, further increasing the genome compaction level \citep{ mcginty_robert_k._and_tan_song_fundamentals_2014}. % compaction It is now commonly accepted that the compaction of the genome comes with a trade-off. The DNA sequences found in nucleosomes are though the be unaccessible for DNA reading processes such as TF binding whereas the linker DNA remains accessible \citep{weirauch_methods_2011}. Thus storing the genome impedes its readability. Because transcribing genes is all about reading the DNA template, the state of the chromatin eventually impact gene expression. Consequently, the cell faces a situation where it needs to keep only the immediately useful genomic regions readable while keeping the ability to open/close other regions on demand. \subsection{The chromatin is dynamic} % chromatin modification/remodelling Because the required activated genes may vary over time, for instance because of lineage commitment, the chromatin structure needs to be adapted. Some regions needs to become accessible in order to be read while other are not needed anymore. Consequently, the chromatin is a highly dynamic structure that undergoes constant modifications. Two broad families of chromatin modifiers exist : ATPase chromatin remodelers and histone modifiers. % chromatin remodelers ATPase chromatin remodelers are a group of proteins that are able to affect the chromatin packaging by interfering directly with the nucleosome, at the cost of hydrolyzing ATP molecules. Chromatin remodelers can be subdivided into 4 sub-groups, each fulfilling a different function \citep{langst_chromatin_2015}. SWI/SNF members can slide and/or to evict nucleosomes from DNA and are linked with chromatin opening. ISWI members tend to recognize unmodified H4 histone and catalyze nucleosome spacing and chromatin compaction. CHD members are less well functionally characterized but bear chromo domains that allows them to recognize histone methylation. Finally, INO80 members seem to be able to slide and evict nucleosomes and seems to be involved in DNA repair and replication. % histone modifiers Histone modifiers are enzymes that can deposite PTMs on the histone tails. Different types of PTMs exist such as acetylation or methylation. Each histone has several residues that can be modified, sometimes together. This leads to an astonishingly high number of combinations. So far more than a hundred histone PTMs have been identified, each linked with different biological functions. If the deposition of PTMs is made by dedicated factors (referred to as writers), their recognition is also performed by dedicated proteins (referred to as readers) \citep{kouzarides_chromatin_2007,hyun_writing_2017}. This allows histone PTMs to be used to recruit specific factors at given genomic location. For instance, H3 lysine 4 di-methylation (H3K4me2) has been shown to be enriched at the promoters of actively transcribed genes and at enhancers \citep{zhou_charting_2011,hyun_writing_2017} and to be specifically recognized by CHD1, a member of the CHD chromatin remodelers \citep{hyun_writing_2017}. \subsection{About nucleosome positioning} % statistical positioning, sequence positioning \begin{figure} \begin{center} \includegraphics[scale=0.2]{images/ch_introduction/nucleosome_positioning.png} \captionof{figure}{\textbf{Nucleosome positioning} \textbf{A} Activated gene transcription start site (TSS) region. The nucleosomes located immediately downstream of the TSS show a strong positioning. The positioning of the first nucleosome can be influence by sequence preferences. Eventually the phasing is propagated to neighboring nucleosomes through statistical positioning. The nucleosome array is not anymore visible as the nucleosomes become fuzzily positioned among the cells. \textbf{B} Influence of the rotational positioning on the sequence accessibility. Left, a sequence (indicated by the black ‘rungs’ on the DNA helix) has its major groove facing toward the nucleosome outside and is accessible. Center, a 5bp rotation of the nucleosome hides the sequence as its major groove is now facing the histone octamer. Right, another 5bp rotation makes the sequence accessible again. Both images are taken and adapted from \citep{jiang_nucleosome_2009}.} \label{intro_nucleosome_positioning} \end{center} \end{figure} The advent of MNase-seq allowed to draw high resolution maps of nucleosome occupancy in many species, such as in yeast \citep{kubik_nucleosome_2015}, mouse \citep{west_nucleosomal_2014} or human \citep{schones_dynamic_2008, gaffney_controls_2012}. % strongly positioned nucleosomes The wealth of data collected allowed to determined that nucleosomes do not cover the genome uniformly. Nucleosomes rather seem to show preferred locations were they sit at. Interestingly, single nucleosomes can be visualize from batch sequencing experiments, indicating that an important fraction of the cells bear nucleosomes at the same positions. In these cases, the nucleosomes are said to be "phased" or "strongly positioned" (see Figure \ref{intro_nucleosome_positioning}A). % statistical positioning Nucleosome arrays are a striking case of strongly positioned nucleosome. Their most prominent feature is the regularity of the spacing between the pairs of nucleosomes that are part of the array. Arrays can occur throughout the human genome \citep{gaffney_controls_2012}. However, there are regions where they are enriched, for instance at the CCCTC-binding factor (CTCF) binding sites \citep{fu_insulator_2008}. It has been proposed that the arrays resulted from the nucleosomes organizing with respect to a barrier (or anchor). In this case, the barrier would be CTCF. The regular array organization has been proposed to be propagated far from their anchors because the immediately flanking nucleosome positions are constrained by the barrier. In turn, these nucleosomes become a barrier for the following ones, and so one, eventually forming the array. However, because the degree of constrain diminishes at each new nucleosome, the nucleosomes are not sufficiently phased anymore throughout the cell population. They become fuzzy and the signal blur out at some point. This phenomenon is referred to as "statistical positioning" \citep{jiang_nucleosome_2009}. % effect of sequence Another important driver of nucleosome positioning is the DNA sequence. For instance, strongly positioned nucleosomes are also visible at the transcription start sites (TSSs) of activated genes. However, unlike for CTCF binding sites, the DNA sequence composition seem to be a major factor driving the nucleosome positioning \citep{dreos_influence_2016}. To wrap around the histone octamer the DNA should be curved, which requires some flexibility. WW (W=A/T) and SS (S=C/G) dinucleotides have been shown to curve the DNA by extending the major and the minor groove respectively \citep{jiang_nucleosome_2009}. However, because the major and minor grooves precess around the DNA helix axis, each groove alternatively faces the nucleosome center (the histone octamer) and the nucleosome outside (the opposite direction) every ~5bp (thus the DNA helix periodicity is ~10.4bp, see Figure \ref{intro_nucleosome_positioning}B). Consequently, dinucleotides favoring DNA flexibility are required to occur at different locations around the nucleosome, according to their effect on the DNA helix structure. For instance, stretching the major groove needs to occur when it is facing the nucleosome outside, to force the adjacent DNA segment to be curved toward (around) the nucleosome center. If a nucleosome is bound to a favorable sequence, the next most likely favorable binding sites are located 10bp upstream or downstream. These correspond to the locations at which all the dinucleotides will reacquire the same orientation with respect to the histone octamer. This is referred to as "rotational positioning" \citep{jiang_nucleosome_2009}. In 2011, Trifonov identified the YRRRRRYYYYYR (where R=A/G and Y=C/T) consensus sequence to be a nucleosome positioning sequence matching these criteria \citep{trifonov_cracking_2011}. The first and last positions indicate the cyclic nature of this pattern. Interestingly, the exact positioning of a nucleosome has a deep impact on the accessibility of the DNA. None 10bp displacements have the potential of changing a sequence orientation with respect to the histone core and thus its accessibility.(Figure \ref{intro_nucleosome_positioning}B). In vivo, both statistical and rotational positioning occur. Additionally, chromatin remodelers are also constantly catalyzing thermodynamically unfavorable nucleosome displacements in exchange of ATP hydrolysis. It is likely that each nucleosome is subjected to all of these phenomenons. However, on a single nucleosome basis, one may predominate over the others. \section{About transcription factors} % 1) specificity models, additivity, sequence scoring given model % 2) TF complexes % 3) co-binding scenarios % About TF and their structure Transcription factors (TFs) are a special class of proteins that is crucial for gene expression regulation. TFs have the special ability to recognize specific DNA sequences among others. Once recruited on the DNA template, TFs have the ability to regulate transcription by promoting or repressing the activity of the RNA polymerase II complex (RNAPII). In the first case, one speak of (transcriptional) activators, in the second of (transcriptional) repressors. TFs share a modular architecture. Two types of domains are of particular importance for TF functions: the DNA binding domain (DBD) and the activation domain (AD). % DNA binding domain The DBD allows TFs to bind their DNA target. Many different DBD exist, each one being structurally different than the others. The DBD structure if typically used to classify TFs into families. This is for instance the case in the TFclass database \citep{wingender_tfclass:_2013}. In metazoans, TFs have been grouped into four distinct super-families : i) the basic domain TFs, ii) the zinc coordinated TFs, iii) the helix-turn-helix TFs and iv) the $\beta$ scaffold TFs. Each type of domain has a different structure and thus can interact with different DNA structures and sequences \citep{weirauch_methods_2011}. Of further importance, a single DBD is able to recognize different yet similar sequences. Because the sequence differences have an impact on the TF-protein interaction interface, each sequence is bound with a different affinity. Biologically, having high and low affinity binding sites may be useful to tune the intensity of one TF action on a given gene. % activation domain In addition to their DBD, many TFs also bear an AD that is important for the regulation of transcription. ADs allow TFs to regulate gene expression directly, by interacting with the basal transcriptional machinery, or indirectly by recruiting co-regulators. Coupled with specific DNA recognition, this allows TFs to regulate the transcription of specific regions of the genome. Whether TFs exert an activator or a repressor role, depends on the exact interaction it can exert with the transcriptional machinery and on the co-regulators it can recruit \citep{latchman_transcription_1997}. Ultimately, the activity of a TF is regulated by controlling its access to the DNA. This can be done by sequestrating it in the cytoplasm (by any mean) or even by occupying its binding sites to impede the TF recruitement on the genome \citep{latchman_transcription_1997}. \subsection{TF co-binding} \label{intro_tf_cobinding} % TF complexe, homo-dimer, hetero-dimers, independent co-binding % Jolma and Taipale book 2011 chapter 8 % Jolman and Taipale book 2011 chapter 11.4 (nucleosome breathing / TFs cooperate to evict nucleosome and open chromatin) \begin{figure} \begin{center} \includegraphics[scale=0.4]{images/ch_introduction/TF_associations.png} \captionof{figure}{\textbf{Possible interaction scenarios between TFs} \textbf{A} Direct co-binding. The TFs dimerize and bind together on DNA. \textbf{B} Indirect co-binding. Both TF dimerize but only one binds the DNA, the other (the blue) is the tethering factor. \textbf{C} Independent co-binding. Both TF bind in close vicinity but without forming a complex. Both TFs may not be necessarily bound at the same time. \textbf{D} Interference. Both motifs partially or totally overlap each other.} \label{intro_tf_association} \end{center} \end{figure} The four above-mentioned TF super-families offer a huge variety of different TFs and thus allows a substantial complexity in terms of transcriptional regulation. Nonetheless, life further expended the possible complexity of regulatory wiring by evolving different types of combinatorial TF co-binding \citep{field_methods_2011}. By TF co-binding, I mean a functional association of TFs that requires them to bind either as a complex or in close vicinity. Furthermore, from a strictly DNA-centric point of view, the binding of each TF does not need to be synchronous. One TF may bind after the other, even after it left. % direct co-binding First, two TFs can dimerize, forming either homo- or hetero-dimers, and bind to DNA using both DBDs (Figure \ref{intro_tf_association}A). This is for instance the case of the members of the basic domain super-family, which contains the leucine zipper and helix-loop-helix families, which are obligated dimer in order to bind DNA \citep{weirauch_methods_2011}. This can be referred to as "direct co-binding". % tethering Second, two TFs can dimerize and bind to DNA using only one of the DBDs. This will result in having one of the TF binding to DNA while the other one is tethering DNA through its interaction with the other TF (Figure \ref{intro_tf_association}B). This can be referred to as "indirect co-binding". % independent co-binding Third, two TFs can both bind DNA using their own DBDs, in close vicinity but without any physical interaction (Figure \ref{intro_tf_association}C). This is for instance the case at distal REs, where many TFs can be found to be bound at the same time. Synergistic co-binding of several TFs has been proposed as a mechanism by which close chromatin structures could be opened and distal RE activated \citep{field_methods_2011,heinz_selection_2015}. On the other hand, the binding of different TF to a given region can be asynchronous. This is the case for TF involved at different time of the activation cascade, such as happening during macrophage and B cell progenitors commitment \citep{heinz_simple_2010}. This can be referred to as "independent co-binding". % interference %Finally, two TFs binding motifs can overlap (Figure \ref{intro_tf_association}D). Different mechanisms may explain this phenomenon. A first possible explanation would be that two TFs compete to bind to the same region. This can occur in mechanisms linked to the regulation of a TF activity. In that case, as its binding site is occupied, TF binding is sterically hindered. A second possible explanation would be that, for some reason, only one TF binds, never the other. This can be referred to as "interference". Finally, two TFs binding motifs can overlap (Figure \ref{intro_tf_association}D). The end result is not clear but this can result in different plausible scenarios such as both TFs transiently binding the DNA or one TF winning the competition and stably binding, sterically excluding other TFs. This can be referred to as "interference". \section{Gene regulation in a nutshell} \label{intro_gene_regulation} % regulation gene expression definition The regulation of gene expression is a highly complex biological phenomenon which allows a proper allocation of resources to each individual gene such that overall gene product output fits the cell needs as precisely as possible. % summary and aim of the section %The mechanisms that act to regulate gene expressions are diverse and operate in an intricate manner that is highly dynamic. The status of a gene, at a given time, is the results of the actions of activating and repressing mechanisms that act either on i) the recruitement of the pre-initiation complex (PIC) and the assembly of a functional RNAPII complex at gene regulatory elements (REs) or ii) the activation of the RNAPII complex. This section will briefly introduce each of these aspects and provide the necessary information for the further understanding of this work by the reader. The status of a gene, at a given time, is the results of the actions of activating and repressing mechanisms that, in fine, modulate the activity of the transcriptional machinery. This modulation takes place at different steps of the activation cascade of the transcriptional machinery. The really first step that occurs is the binding of general TFs, such as TFIID, that allows to recruit the catalytic subunits of the RNAPII, forming the pre-initiation complex (PIC). The further downstream steps include the recruitment of transcriptional regulator and chromatin remodelers, the proper positioning of the full RNAPII complex at the TSS and the activation of the RNAPII complex. This section will briefly introduce some of these aspects to provide the necessary information for the further understanding of this work by the reader. \subsection{The chromatin barrier} % chromatin is a barrier As discussed above (see section \ref{intro_about_chromatin}), the genome is stored as chromatin in the nuclei. Because nucleosome are bound to the DNA, they compete with other factors for binding. As such, the chromatin structure is a barrier to the recruitment of the PIC. On the brigh side, this is though to limit spurious activation of the RNAPII \citep{von_bakel_methods_2011}. On the other hand, this obviously also suppresses any gene expression. In human, the observation that TFs binding is hindered by nucleosome and that REs are nucleosome depleted suggest the existence of a mechanism that opens the chromatin at REs \citep{von_bakel_methods_2011}. \subsection{TFs cooperative binding} % cooperative binding to open nucleosomes The cooperative binding of TFs has been demonstrated to be able to open closed chromatin. In essence, this is a step-wise process during which a first TF binds its target on an accessible linker, leading to the destabilization of the neighboring nucleosome. This in turn increase the accessibility of a second TF binding site that can be engaged, further openining the chromatin. Eventually, the nucleosome is displaced of even evicted and the chromatin is locally opened \citep{von_bakel_methods_2011}. ATPase chromatin remodelers and/or of histone modifier can be recruited by TFs to set up a proper chromatin environment \citep{von_bakel_methods_2011}. The conditions for this phenomenon to ignite are not precisely known however several hypotheses and observations are of interest. First, compacted chromatin has been observed, in vitro, to undergo spontaneous transient local openings at the nucleosome entry sites. This phenomenon has been referred to as "nucleosome breathing" \citep{von_bakel_methods_2011}. This has the potential of creating windows of opportunity for TFs to engage their binding sites, in nucleosome arrays. Second, it has been hypothesized that, in human, the regions that show a high nuclosome density may facilitate the exclusion of the H1 histone. The rational is that the DNA linkers between any two nucleosomes is too short for H1 to bind. Eventually, H1 exclusion prevents the inclusions of these regions in more condensed chromatin structures while leaving the linkers somewhat accessible \citep{field_methods_2011}. Together, with nucleosome breathing, this has the potential of creating engageable - but not open - windows throughout the genome. \subsection{Pioneer TFs} % pioneer TFs Alternatively, a special class of TFs named "pioneer factors" have been shown to be able to bind their target in a closed chromatin environment and to induce chromatin opening after binding \citep{zaret_pioneer_2011,iwafuchi-doi_pioneer_2014}. % introduce Fox1 to describe the precise mechanism of action The case of the prototypical pioneer factor FoxA1 (also called HNF3) is enlightening regarding the mechanistics of pioneer TFs. In liver, FoxA1 is able to bind the inactive \textit{albumin} enhancer and prime it for activation \citep{cirillo_opening_2002}. The enhancer activation is possible because of the hybrid nature of FoxA1. It binds DNA through its DBD, which has a similar structure to the H1 linker histone. Strikingly, FoxA1 can bind its recognized motif directly on the nucleosome surface. Furthermore, FoxA1 posses a C-terminal domain that directly binds the histone core, which leads to the chromatin opening \citep{cirillo_opening_2002}. Alternatively, FoxA1 is also able to recruit co-regulators via its N-terminal trans-activation domain \citep{zaret_pioneer_2011}. Currently, many other pioneer TFs have been discovered, such as Oct4, Sox2 and Klf4 \citep{soufi_pioneer_2015} - also known together with myc as the "Yamanaka factors" - or PU.1 which has been shown to induce nucleosome remodeling at macrophage and B-cell specific enhancers \citep{heinz_simple_2010}. Interesting in this regard, most of the TFs discovered to drive cellular reprogramming, such as the Yamanaka factors which have been shown to be sufficient to reprogram fibroblasts into stem cells \citep{takahashi_induction_2006}. \subsection{Regulatory elements} % RE definition Chromatin opening and the recruitment of the transcriptional machinery do not happen at random in the genome but is concentrated at regulatory elements (REs). The specific recruitment of the transcriptional machinery regulators at given genomic locations allows to concentrate the regulatory signals on specific target genes. REs can be divided in two broad classes based on their vicinity to the gene(s) they regulate : proximal REs - or promoters - and distal REs. Both classes interact together by the mean of the genome 3D structural organization. % promoters Promoters are located immediately upstream of the target genes they regulate. Promoters functions are to recruit the RNAPII and position it properly for transcription. Interestingly two constrasting promoter groups have been identified with respect to their chromatin architectures \citep{cairns_logic_2009}. The first group include house keeping genes. This group chromatin architecture tends to be constituvely open with a nucleosome depleted region (NDR), promoting gene expression. The second group contains highly regulated genes. Unlike the first group, these promoters tend to be constituvely covered by nucleosomes, hindering TF and RNAPII recruitment. Their activation require an active chromatin remodeling that is carried out by SWI/SNF ATPase family members. However, in both cases the chromatin is remodeled and a NDR is formed. The NDR usually contains TF binding sites core regulatory elements (CREs) involved in the recruitment of general TFs leading to the assembly of the RNAPII \citep{lenhard_metazoan_2012}. % enhancers Distal REs are located at distances that vary from kilobases to megabases from their target gene and have the ability to influence gene expression positively, in which case they are referred to as 'enhancers', or negatively, in which case they are referred to as 'silencers'. Distal REs are enriched with closely spaced TF recognition sequences that serve for the recruitement of TFs. In turn, TFs allow to recruit other transcriptional co-regulators such as histone modifiers \citep{heinz_selection_2015}. Through chromatin looping phenomenons, the recruited TF (and all other factors) are brought in close spatial vicinity from target gene promoters. This increases TF concentrations (as well as other regulatory factors bound) at the promoter level and allows to strengthen regulatory signals directly where the RNAPII is sitting \citep{heinz_selection_2015}. Distal REs are not always active. Instead they are highly cell line specific and thus are important determinant of the cell identity \citep{heinz_selection_2015}. Distal REs activation requires to open the chromatin in order to be accessible for TFs to bind. Currently, both cooperative TF binding and pioneer TFs are though to be involved in chromatin opening and remodeling \citep{heinz_selection_2015}. Upon chromatin opening, specific histone PTMs are deposited, such as H3 lysine 4 mono-methylation (H3K4me1), H3K4me2 or H3 lysine 27 acetylation (H3K27Ac) \citep{zhou_charting_2011}. For instance, during B-cell and macrophage lineage commitment, PU.1 and EBF1 are essential TFs which action activates cell type specific enhancers, leading to the enforcement of differential genomic programs \citep{boller_pioneering_2016, heinz_simple_2010}. Failure to do so leads to lineage commitment defects \citep{hagman_early_2005,kurotaki_transcriptional_2017}. \subsection{The genome goes 3D} % TADs Finally, another layer of complexity involved in the regulation of gene expression can be added : the 3D organization of the genome. Nowadays it is clear that in the nucleus, the genome spatial organization is tightly regulated and that it has a functional meaning \citep{bonev_organization_2016}. As described above, enhancer and promoters physically interact together through loops. These looping phenomenons do not happen at random. The genome is organized into compartments, also called topological association domains (TADs). A TAD can be seen as high level chromatin loop in which the physical interaction between loci are favored compared to interaction with loci outside of the TAD. As a matter of fact, enhancers action is limited to the TAD it is located in. Thus TADs can be seen as a functional regulatory genomic domains. TADs are thought to be established and maintained by a dedicated set of structural and complexes including CTCF and the cohesin complex \citep{bonev_organization_2016}. CTCF seem to have two major functions. First it seems to facilitate promoter/enhancers interactions, within TADs and promote gene expression. Second, CTCF is found to be enriched at TAD borders and seems to be important for their proper delimitation \citep{ong_ctcf:_2014}, likely through a loop extrusion mechanism \citep{ghirlando_ctcf:_2016}. This second function is compatible with the insulator function of CTCF. Because it marks the boundary between TADs, enhancer/promoter interaction over this limit cannot happen. Finally, CTCF is often found in to interact with the cohesin complex \citep{stedman_cohesins_2008}. The cohesin complex is composed of four members : SMC1, SMC3, RAD21 and either STAG1 or STAG2 \citep{losada_cohesin_2014}. Together they form a ring-like structure in which two DNA molecules are trapped and maintained together. This structure is one of the mechanisms allowing to pinch DNA and to form loops. The cohesin complex is important for both promoter/enhancer interactions and TADs maintenance \citep{losada_cohesin_2014,bonev_organization_2016}. \section{Measuring chromatin features} \label{measuring_chromatin_features} The occupancy of the difference components of the chromatin, the chromatin accessibility or even the sequence preference of TFs can be measured using dedicated assays. This section introduce the necessary information to further understand this work. \subsection{Measuring nucleosome occupancy} % MNase The micrococcal nuclease (MNase) - an endo-exo nuclease - is a key factor in producing nucleosome occupancy maps. Subjecting a chromatin extract to a MNase treatment, upon proper experimental conditions, releases "a ‘ladder’ of discrete DNA fragments" \citep{voong_genome-wide_2017} which sizes correspond to mono-, di-, tri-, and so on nucleosome fragments. The MNase is able to digest accessible linker DNA (endo-nuclease activity) and to trim the nick edges (exo-nuclease activity). The nucleosomal DNA is protected from digestion as the histone octamer sterically hinder the MNase access to its substrate \citep{voong_genome-wide_2017}. % MNase-seq Originally, MNase treated DNA was then selectively amplified using PCR to map precise nucleosomes. The advent of microarray technologies allowed to interrogate the entire genome, even though the map created had relatively low resolution \citep{jiang_nucleosome_2009}. Eventually, this limitation was circumvent by subjecting the MNase treated chromatin fragment to next generation sequencing (-seq) \citep{schones_dynamic_2008}. The advent of MNase-seq lead to the creation of high resolution - down to individual nucleosomes - genome-wide nucleosome maps \citep{schones_dynamic_2008, gaffney_controls_2012, west_nucleosomal_2014, kubik_nucleosome_2015}. % data treatment Mapping the sequenced fragment of MNase-seq assay against a genome of reference produces a digital readout of the nucleosome density per genomic position. If single-end sequencing is used, the nucleosome center (the dyad) can be inferred by shifting the read position by ~70bp. If paired-end sequencing is performed, mono-nucleosome fragments can be selected based on their sizes (~150bp) and the dyads can be inferred as being their central positions. % limitations i) A/T sequence specificity ii) all nucleosomes likely not mapped If MNase-seq allows to unravel nucleosome occupancy with an unprecedented resolution, it suffers some limitations. First, MNase has been demonstrated to exhibit a sequence preference toward A/T rich sequences, which could potentially lead to an overdigestion of nucleosome fragments in A/T rich regions \citep{voong_genome-wide_2017}. Second, some nucleosomes have been demonstrated to be "fragile" to the experimental conditions. In yeast, specific nucleosomes were found to be sensitive to the MNase concentration and could only be detected with reduced MNase concentrations \citep{kubik_nucleosome_2015}. Here, the MNase sequence preference may be at play. But another case of fragile nucleosomes was found in human, independently of the use of MNase. In this case, the fragile nucleosomes were sensitive to regular salt concentrations used during a ChIP-seq experiment \citep{jin_h3.3/h2a.z_2009}. Thus, it is likely that MNase-seq is not able to map all the nucleosome in a given genome. \subsection{Digital footprinting} \label{intro_dgf} % DGF / DNase-seq / ATAC-seq, footprint \begin{figure} \begin{center} \includegraphics[scale=0.3]{images/ch_introduction/dgf.png} \captionof{figure}{\textbf{Digital footprinting :} \textbf{A} DNase-seq uses the endonuclease DNase to cleave DNA within accessible chromatin. Endonuclease cleavage is greatly attenuated at the protein-bound loci (the red crosses denote cleavage blockade). Accessible library fragments are generated by barcoding each cleavage site independently after restriction digestion (single cut) or as proximal cleavage pairs (double cut). \textbf{B} Assay for transposase-accessible chromatin using sequencing (ATAC-seq) uses a hyperactive transposase (Tn5) to simultaneously cleave and ligate adaptors to accessible DNA. \textbf{C} The purified DNA fragments are then subjected to massively parallel sequencing and mapped to the reference genome to generate a digital readout of per-nucleotide insertion (DNaseI nick or Tn5 transposition event) genome-wide. Figure and legend taken and adapted from \citep{vierstra_genomic_2016, klemm_chromatin_2019}.} \label{intro_figure_dgf} \end{center} \end{figure} % DGF Digital genomic footprinting (DGF) methods are a powerful mean to reveal the active REs in a genome. DGF gives a measure of the chromatin accessibility genome-wide. The essence of DGF assay relies on reagents - enzymes or chemicals (this work will only cover enzymes) - that are able to generate single- or double-stranded DNA cleavages into a chromatin-stored DNA template \citep{tsompana_chromatin_2014, vierstra_genomic_2016} DGF assays relies on a selective degradation of the loci stored in accessible chromatin followed by high throughput sequencing (-seq). The degradation of the accessible chromatin regions can be performed using either DNaseI (DNase-seq, \cite{neph_expansive_2012}) or a modified Tn5 transposon system (assay for transposable accessible chromatin, abbreviated ATAC-seq, \cite{adey_rapid_2010,buenrostro_transposition_2013}). % DNase-seq DNaseI is an endonuclease. Under proper ionic conditions, this enzyme introduces double-strand breaks in the genome based on the DNA accessibility, with a minor sequence specificity \citep{herrera_characterization_1994}, as shown in Figure \ref{intro_figure_dgf}A. On a technical note, DNase-seq assays are quite sensitive assays. Achieving a proper chromatin degradation - that is, avoiding over-digestion - is not an easy task and requires careful enzymatic titrations. % ATAC-seq ATAC-seq assays rely on a modified Tn5 transposase enzyme to selectively fragment the accessible regions of the genome \citep{adey_rapid_2010,buenrostro_transposition_2013}, Figure \ref{intro_figure_dgf}B. The enzyme inserts small double stranded barcodes inside the DNA wherever it is accessible resulting a the creation of double strand breaks. This process, known as tagmentation, allows to i) fragment the genome and ii) inserts sequencing barcodes at once. It should be noted that the Tn5 acts as an homodimer and thus inserts two copies of the same adaptors separated from each other by 9bp \citep{adey_rapid_2010}. % output In both cases, the genome is chopped down into fragments starting (and ending) wherever the chromatin is accessible. A sequencing library is then created from the fragments and the fragment ends are sequenced using high throughput sequencing technologies. Finally, the insertion sites are located by mapping the sequenced reads against the reference genome of interest. This eventually leads to the creation of a per position cut (nicks for DNase-seq, insertions for ATAC-seq) density (Figure \ref{intro_figure_dgf}C). % footprinting Whenever a TF, a nucleosome or any other factor is engaged in a binding interaction with the DNA template, steric hindrance phenomenons protect the DNA from being degraded by the enzyme, leading to the creation of a typical signal diminution called "footprint" (Figure \ref{intro_figure_dgf}C). Formally, a footprint is a degradation signal drop over a DNA sequence that is protected from degradation because of binding event \citep{vierstra_genomic_2016}, but I will later use the term "footprint" the refer to signal drop in a degradation signal for aggregation profiles as well. DGF assays encounter a yet ever-growing popularity because of the wealth of data produced in a single experiment. Indeed, instead of running thousands - one per transcription factor (TF) - of chromatin immonuprecitpitation followed by sequencing (ChIP-seq) \citep{barski_high-resolution_2007} to know where each TF is binding, it is sufficient to run a single chromatin accessibility assay. Additionally, DGF is totally agnostic in the sense that it does not require a prior knowledge of the factors to look for. However, if DGF reveals the active regulatory regions, it does not provide the information about which factors bound. Methods to circumvent this limitation will be discussed later. \subsection{Measuring TF binding in vivo} % ChIP The advent of chromatin immuno-precipitation (ChIP) is central for the study of TFs. In essence, it consists in extracting the chromatin from the cell nuclei, shearing it either mechanically or enzymatically and adding an antibody (Ab) against a DNA binding protein of interest. The IP step allows to pull-down the Ab, its target as well as the DNA fragment it is bound to. % history of DNA detection methods Different methods, with varying throughput, have been used to identify of the purified DNA fragments. First, specific loci of interest were assayed by PCR. Then the growing availability of DNA microarrays allowed to drastically increase the throughput by testing a wide number of pre-selected loci at once \citep{odom_methods_2011}. Finally, protocols subjecting the purified DNA to high throughput sequencing (ChIP-seq) \citep{barski_high-resolution_2007,robertson_genome-wide_2007} allowed to identify the bound loci in an agnostic way, with an unprecedented throughput. % ChIP-seq ChIP-seq has truly revolutionized genomics and the study of TFs. In a single assay, it is possible to obtain a digital readout of TF binding sites. Mapping the sequenced reads to the genome of interest allowed to create a per position occupancy score, creating a digital readout of the TF occupancy. However, because the TF binding sites are smaller than the sequenced fragments, the precise location of the TF binding remains unknown. Interestingly, ChIP-seq allows to list the regions of the genome that are occupied and also provide an estimate of the binding affinity for the regions. Indeed, the stronger the propensity to bind to a given sequence (the affinity), the higher the probability of binding. This should be proportionally reflected in the density of signal \citep{jothi_genome-wide_2008}. Thus ChIP-seq allows to identify regions +/- 100bp in which a TF binds. Nonetheless, it is possible to identify over-represented DNA sequence motifs from these regions using de novo motif discovery methods (see section \ref{intro_aligning_binding_sites}). Typically, the identified sequence motifs belong to i) the TF of interest and/or ii) co-binders (see section \ref{intro_tf_cobinding}). \subsection{Measuring TF binding in vitro} In vivo measurement of TF binding as several drawbacks. ChIP-seq allows to estimate the binding specificity of TF however it has been proposed that de novo motif discovery method mostly capture the high affinity features of the TF binding specificity \citep{stormo_determining_2010}. Additionally, in vivo, the chromatin exert an effect on TF binding (see section \ref{intro_gene_regulation}). In regards of these limitations, in vitro binding assays offer experimental solutions to investigate i) TF binding over a wider range of affinities and ii) TF intrinsic specificity, without the chromatin influence. In the recent years, many different technologies have been developed to investigate TF binding in vitro. % MITOMI Microfluidic devices are typically composed of hundreds (if not more) of individual chambers and of the necessary piping to flow all the necessary reagents within each cell to run as many reactions in parallel. The reaction chambers are small and allow to use microliter reaction volumes. Maerkl and colleagues \citep{maerkl_systems_2007,geertz_massively_2012} have developed the mechanically induced trapping of molecular interactions (MITOMI). This assay is based on a microfluidic device that allows to run hundred of affinity assays with a given TF, in parallel. Each assay is run using a different designed oligo-nucleotide of known sequence. % HT-SELEX -Originally, systematic evolution of ligands by exponential enrichment (SELEX) has been designed to discover few high affinity binding sequences \citep{tuerk_systematic_1990}. The SELEX assay was adapted to become high throughput SELEX (HT-SELEX, \citep{roulet_high-throughput_2002,zhao_inferring_2009,jolma_multiplexed_2010}). HT-SELEX assays a TF specificity by allowing a binding reaction between the TF and tenths of millions of different DNA sequences of typically 20-30bp. The bound DNA molecules are purified by pulling down the TF. The purified DNA can either be sequenced using high throughput sequencing or be subjected to another cycle of selection. Repeated cycles allow to isolate higher affinity binder, eventually only returning a few hundreds. Under a limited number of cycles, this method has a large dynamic scale of binding affinities \citep{stormo_determining_2010} and allow to obtain a digital readout. However, the repeated cycles can introduce biaises that are hard to model properly in order to properly estimate the binding affinities. +Originally, systematic evolution of ligands by exponential enrichment (SELEX) has been designed to discover few high affinity binding sequences \citep{tuerk_systematic_1990}. The SELEX assay was adapted to become high throughput SELEX (HT-SELEX, \citep{roulet_high-throughput_2002,zhao_inferring_2009,jolma_multiplexed_2010}). HT-SELEX assays a TF specificity by allowing a binding reaction between the TF and tens of millions of different DNA sequences of typically 20-30bp. The bound DNA molecules are purified by pulling down the TF. The purified DNA can either be sequenced using high throughput sequencing or be subjected to another cycle of selection. Repeated cycles allow to isolate higher affinity binder, eventually only returning a few hundreds. Under a limited number of cycles, this method has a large dynamic scale of binding affinities \citep{stormo_determining_2010} and allow to obtain a digital readout. However, the repeated cycles can introduce biaises that are hard to model properly in order to properly estimate the binding affinities. % PBM -For completeness, protein binding microarrays (PBMs, \citep{bulyk_exploring_2001,mukherjee_rapid_2004,berger_compact_2006}) also should be mentioned. Typically, a PBM device is a chip on which tenth of thousands of DNA probes are immobilized. The probes are arranged into spots such that only one probe specie is present in each spot. A purified TF is then added on the chip and the TF binding is revealed using a fluorescent-labeled Ab. Because the identity of the probe specie in each spot is known, the affinity to this specie can be directly measured as the intensity of the fluorescent signal. The higher the affinity for a probe specie, the more TF binds to the spot, the stronger the fluorescent signal. The most important limitation of PBM is its limited space on the chip which restrict the number of different spots that can be present. Assaying all possible $4^{L}$ sequences of a given length $L$ is not possible passed a given length. To circumvent this, the sampling of the deposited sequences should be performed with caution to maximize the information on a single chip \citep{berger_universal_2009}. Additionally, it has been suggested that the position of the spot on the chip could influence the TF binding. +For completeness, protein binding microarrays (PBMs, \citep{bulyk_exploring_2001,mukherjee_rapid_2004,berger_compact_2006}) also should be mentioned. Typically, a PBM device is a chip on which tens of thousands of DNA probes are immobilized. The probes are arranged into spots such that only one probe specie is present per spot. A purified TF is then added on the chip and the TF binding is revealed using a fluorescent-labeled Ab. Because the identity of the probe specie in each spot is known, the affinity to this specie can be directly measured as the intensity of the fluorescent signal. The higher the affinity for a probe specie, the more TF binds to the spot, the stronger the fluorescent signal. The most important limitation of PBM is its limited space on the chip which restrict the number of different spots that can be present. Assaying all possible $4^{L}$ sequences of a given length $L$ is not possible passed a given length. To circumvent this, the sampling of the deposited sequences should be performed with caution to maximize the information on a single chip \citep{berger_universal_2009}. Additionally, it has been suggested that the position of the spot on the chip could influence the TF binding. \section{Modeling sequence specificity} \label{intro_specificity_modeling} -In the nuclei, TFs are in presence of an incredibly high number of potential binding sites. Most of them are non-sites and a minority are bona fide binding sites. The ability of a TF to distinguish between both is called "specificity". Additionally, all binding site are not equal. Some are bound tighter than others. The forces and the propensity with which a sequence is bound by a given TF is called the affinity. +In the nucleus, the number of potential binding sites for TFs is incredibly high. Most of these sites are non-sites and a minority are bona fide binding sites. The ability of a TF to distinguish between both is called "specificity". Additionally, all binding site are not equal. Some are bound tighter than others. The forces and the propensity with which a sequence is bound by a given TF is called the affinity. Modeling TF specificity has been an crucial issue in biology as it allows to predict where a given TF binds in the genome and to infer its regulatory targets. However because TFs recognize degenerated sequences, solving this problem turned out to be complicated. \subsubsection{The physics approach to PWMs} Let us assume a simple binding reaction between a TF $TF$ and a DNA sequence $S$, at the equilibrium, \ch{TF + S <>[][] TF.S}. The chemical definition of the affinity is the association constant $k_{a}$ : \begin{equation} \begin{aligned} -k_{a} = \frac {[TF-S]} {[TF] \times [S]} +k_{a} = \frac {[TF \cdot S]} {[TF] \times [S]} \end{aligned} \label{intro_ka} \end{equation} where the square brackets indicate the concentrations. Once at the equilibrium, this reaction releases a standard free energy equals to : \begin{equation} \begin{aligned} -\Delta G^{0} = -R \times T \times ln(K) +\Delta G^{0} = -R \times T \times ln(k_{a}) \end{aligned} \label{intro_delta_free_energy} \end{equation} -where $R$ is the perfect gaz constant, $T$ the absolute temperature and $K$ the reaction equilibrium constant, which here is equal to $k_{a}$. When $\Delta G^{0} < 0$, $K>1$ indicating that, at the equilibrium, the product TF-S of the reaction is favored. The more product at equilibrium, the stronger the affinity of $TF$ for $S$ (see equation \ref{intro_ka}). The more energy is released by the reaction, the stronger $S$ is bound by $TF$. +where $R$ is the perfect gaz constant and $T$ the absolute temperature. When $\Delta G^{0} < 0$, $K>1$ indicating that, at the equilibrium, the product TF-S of the reaction is favored. The more product at equilibrium, the stronger the affinity of $TF$ for $S$ (see equation \ref{intro_ka}). The more energy is released by the reaction, the stronger $S$ is bound by $TF$. From this, for a given $TF$, it is possible to create a $\Delta G^{0}$ tables for all possible sequences which would allow to predict the $TF$ specificity. In competition, the probability of binding to a sequence is directly proportional to the affinity. However, this is at least labor intensive and at most experimentally intractable. To circumvent this obstacle, the hypothesis of positional independence was formulated. The hypothesis states that the reaction $\Delta G^{0}$ is an additive function of the individually recognized bases. Thus, each base recognized does not influence the recognition of any base at any other position. From the beginning, this hypothesis was recognized to be an approximation that would apply to most of the cases but no all. Even though, this assumption was a subject of controversy \citep{man_non-independence_2001,bulyk_nucleotides_2002}. However, it is nowadays commonly admitted that, even if the assumption is violated in some cases, it does still allow to represent accurately most of the cases \citep{benos_additivity_2002,zhao_quantitative_2011}. -Originally, the measurement of affinity was a labor intensive - and still is today - and was assayed using gel shift assays. Thus performing one affinity measurement for each of the $4^{L}$ sequences of length $L$ did not belong to the realm of the possible. Instead, working under the hypothesis of positional independence allowed to drastically lower the experimental workload and only requires to run an assay for each of the $3*L+1$ single position mutants. In turn, this allows to construct a matrix containing the $\Delta\Delta G^{0}$ induced by each base being recognized at each position of the binding site \citep{stormo_specificity_1998}. This matrix is called a position weight matrix (PWM) and allows to predict the affinity of $TF$ for any sequence. In such PWMs, the strongest affinity site is usually given a $\Delta\Delta G^{0}$ equals to 0 and all other $\Delta\Delta G^{0}$ values are expressed with respect to this strongest affinity site. +Originally, the measurement of affinity was a labor intensive - and still is today - and was assayed using gel shift assays. Thus performing one affinity measurement for each of the $4^{L}$ sequences of length $L$ did not belong to the realm of the possible. Instead, working under the hypothesis of positional independence allowed to drastically lower the experimental workload and only requires to run an assay for each of the $3*L+1$ single position mutants. In turn, this allows to construct a matrix containing the $\Delta\Delta G^{0}$ induced by each base being recognized at each position of the binding site \citep{stormo_specificity_1998}. This matrix is called a position weight matrix (PWM) and allows to predict the affinity of $TF$ for any sequence. In such PWMs, the strongest affinity site is usually given a $\Delta G^{0}$ equals to 0 and all other $\Delta\Delta G^{0}$ values are expressed with respect to this strongest affinity site. -Finally, it should be noted that inside PWM, negative $\Delta\Delta G^{0}$ are often turned to positive values such that the highest affinity binding site achieves the maximal score. +Finally, it should be noted that inside PWM, positive $\Delta\Delta G^{0}$ are often turned to negative values such that the highest affinity binding site achieves the maximal score (corresponding to the lowest $\Delta G^{0}$). \subsubsection{The statistical mechanic approach to PWMs} -The TF sequence specificity has also be tackled from a statistical point of view. Given an alignment $A$ of binding sites of length $L$, it is possible to construct a letter probability matrix (LPM) or a letter frequency matrix (LFM) that contrain either the number of time each base appears at each position of $A$ or the corresponding probabilities, respectively. +The TF sequence specificity has also be tackled from a statistical point of view. Given an alignment $A$ of binding sites of length $L$, it is possible to construct a letter probability matrix (LPM) or a letter frequency matrix (LFM) that contains either the number of time each base appears at each position of $A$ or the corresponding probabilities, respectively. % Obviously, the importance of a particular base at a given position within the binding site is directly proportional to its probability of appearing. In 1986, Schneider and colleagues quantified the importance of each positions in a binding site using the information content \citep{schneider_information_1986}. Nonetheless, this approach is not yet quantitative, only qualitative. It does not allow to predict whether a site will be bound with a stronger affinity than an other one. Indeed, the most frequent binding site is not necessarily the highest affinity binding site. In 1986, Schneider and colleagues quantified the sequence conservation at each position of $A$ using the information content \citep{schneider_information_1986}. In 1987, Berg and von Hippel demonstrated that this statistical approach was mathematically related to the estimation of binding affinities \citep{berg_selection_1988}. Given $A$, a PWM can be build using : \begin{equation} \begin{aligned} \lambda \varepsilon_{jb}^{obs} = ln \frac{f_{j0}^{obs}} {f_{jb}^{obs}} \end{aligned} \label{intro_eq_pwm_berg} \end{equation} -where $\varepsilon_{lb}^{obs}$ is the free energy released by the binding of base $b$ at position $j$, $f_{jb}^{obs}$ is the probability of observing a base $b$ at position $j$ in the binding site, $f_{j0}^{obs}$ is the probability of the base present at position $j$ in the strongest binder present in $A$ and $\lambda$ is a dimensionless scaling factor determined by the whole set of sites $A$. +where $\varepsilon_{lb}^{obs}$ is a dimension less positive number that expresses the decrease of binding energy by the binding of base $b$ at position $j$, $f_{jb}^{obs}$ is the probability of observing a base $b$ at position $j$ in the binding site, $f_{j0}^{obs}$ is the probability of the base present at position $j$ in the strongest binder present in $A$ and $\lambda$ is a dimensionless scaling factor. Stormo and Fields used a slightly different approach \citep{stormo_specificity_1998} and proposed to link the information content of $A$ to the estimation of the binding energy using : \begin{equation} \begin{aligned} W_{b,j} = log_{2} \frac {F_{b,j}} {p(b)} \end{aligned} \label{intro_eq_pwm_stormo} \end{equation} -where $f_{b,j}$ is the number of occurrences of base $b$ at position $j$ in the alignment $A$, $p(b)$ the probability of a given base $b$ and $W$ is the PWM. +where $f_{b,j}$ is the number of occurrences of base $b$ at position $j$ in the alignment $A$, $p(b)$ the probability of a given base $b$ and $W$ is the PWM. Note that equations \ref{intro_eq_pwm_berg} and \ref{intro_eq_pwm_stormo} give inversly proportional results because of the inverted fractions. \subsection{Aligning binding sites} \label{intro_aligning_binding_sites} % obtaining the alignment The above solution request to have a set of aligned binding sites $A$ to compute the PWM. However, most of the times, we do not have access to this information. Rather, we have a set of longer sequences in which we know that the TF of interest binds, but not exactly where. Many algorithms - typically called "de novo motif discovery" algorithms - have been developed to construct a matrix from a set of unaligned sequences. The algorithm developed by Stormo and Hartzell \citep{stormo_identifying_1989} finds an optimal alignment by maximizing a modified version of the alignment information content \citep{schneider_information_1986}. Alternatively, the algorithms developed by Hertz and Stormo \citep{hertz_identification_1990} and Lawrence and Reilly \citep{lawrence_expectation_1990} build an LPM that maximize the likelihood of observing the data under the hypothesis that they have been generated from the discovered model. Lawrence and Reilly algorithm solves the alignment problem using an Expectation-Maximization (EM) algorithm, which makes their algorithm a heuristic. This type of framework has also been used to develop MEME, excepted that it explicitly models the data as a mixture of binding and non-binding sites \citep{bailey_fitting_1994}. \subsection{Platitudes} \begin{figure} \begin{center} \includegraphics[scale=0.2]{images/ch_introduction/figure_pwm.png} \captionof{figure} {\textbf{Position weight matrix : } \textbf{A} Human JunD (JUND\textunderscore HUMAN.H10MO) PWM from the HOCOMOCO version 10 collection \cite{kulakovskiy_hocomoco:_2016}. \textbf{B} Corresponding PWM logo. The palindromic nature of the recognized motif is explained by the fact that JunD belongs to the basic helix-loop-helix family. As such, it is obligated to hetero- or homo-dimerize with another member of its family to bind DNA. Both \textbf{A} and \textbf{B} were taken from http://ccg.vital-it.ch/ssa/oprof.php}. \label{intro_pwm_logo} \end{center} \end{figure} % types of matrices, conversion possible LFMs and LPMs are often use to summarize an alignment $A$ and are often falsely referred to as PWMs. In all cases, LFMs and LPMs can always be converted to a PWM. % popularity Overall, PWMs (and related matrices) are conceptually straightforward to apprehend and easy to work with. For instance, they can be visualized as a sequence logo (\cite{schneider_sequence_1990}, Figure \ref{intro_pwm_logo}). Because of this and of the possibility to estimate affinity values from a sequence alignment, PWMs are popular and remain the most widely used type of model to represent TF specificity. % databases Nowadays, large collections of TF specificity matrices are available from publicly available libraries such as JASPAR \citep{khan_jaspar_2018}, HOCOMOCO \citep{kulakovskiy_hocomoco:_2018} or CIS-BP \citep{weirauch_determination_2014} to cite only the most famous. \subsection{Predicting binding sites} TF specificity models are typically used for classifications problems. The problem can be stated as follows : given a sequences $S$ of length $L$ and a PWM \textbf{W} of dimensions $Lx4$, predict whether $S$ will be bound. A common way is to define a threshold score $t$ and compute \begin{equation} \begin{aligned} score(S) = \sum_{i=1}^{L} W_{i,b} \end{aligned} \label{intro_eq_score_pwm} \end{equation} If $score_{S} \geq t$ then $S$ is accepted as a binding site. The non-trivial part is to define a meaningful threshold score. A conceptually similar thing can be done with a LPM \textbf{M}. It is possible to compute probability of observing the data given the model, the likelihood $p(S|M)$ : \begin{equation} \begin{aligned} p(S|M) = \prod_{i=1}^{L} M_{i,b} \end{aligned} \label{intro_eq_score_prob} \end{equation} +In turn, using Bayes'theorem, the posterior probability can be computed : + +\begin{equation} +\begin{aligned} +p(M|S) = \frac{P(S|M) \times p(M)} {\sum_{i} P(S|M_{i}) \times p(M_{i})} +\end{aligned} +\label{intro_eq_post_prob} +\end{equation} + +where $p(M)$ and $p(M_{i})$ are model probabilities, which can be interpreted as the prevalence of a given family of sites in the case of a mixtures of binding site families. + + \section{Over-represented patterns discovery} \label{intro_pattern_discovery} \begin{figure} \begin{center} \includegraphics[scale=0.3]{images/ch_introduction/shift_flip.png} \captionof{figure}{\textbf{Signal comparison} between two regions $r_{1}$ and $r_{2}$ bearing a nucleosome array, measured by MNase-seq, at their beginning and ending edges. The bars indicate the density of sequencing reads stacked at each position. \textbf{A} The regions are compared position-wise, as they are, which results in a strong dissimilarity as the arrays are not aligned. \textbf{B} Performing the comparison after flipping $r_{2}$ result in both regions being highly similar. \textbf{C} A shorter stretch of signal of length $L' < L$ from $r_{1}$, highlighted in red and corresponding to the array, is searched in $r_{2}$. In this case, because a highly ressembling strech of signal, in red, can be found in $r_{2}$, both regions are considered highly similar.} \label{intro_figure_comparison} \end{center} \end{figure} -Next generation sequencing (NGS) technologies allowed to easily characterize many of the chromatin features genome wide (see section \ref{measuring_chromatin_features}). The amount and wealth such datasets rapidly required automated discovery procedures in order to extract leading trends. For instance, MNase-seq reveals the nucleosomes over a genome but do not label individual genomic regions. Asking whether the nucleosome architecture is overall the same or how many different types of nucleosome architectures are present over a set of selected regions are quite reasonable questions. To answer them, automated discovery procedures of over-represented patterns are needed. +Next generation sequencing (NGS) technologies allowed to easily characterize many of the chromatin features genome wide (see section \ref{measuring_chromatin_features}). The wealth of such datasets rapidly required automated discovery procedures in order to extract leading trends. For instance, MNase-seq reveals the nucleosomes over a genome and asking whether the nucleosome architecture is overall the same between two regions or how many different types of nucleosome architectures are present over a set of selected regions are quite reasonable questions. To answer them, automated discovery procedures of over-represented patterns are needed. % The need for procedures discovery of over-represented patterns in the genome - either DNA sequences or sequencing signal - is a crucial technical part of genomic bioinformatics as they allow to extract prominent signals. The de-novo discovery of archetypical chromatin architectures, from sequencing read densities, over a set of regions of interest is a long standing problem in bioinformatics which is related to the problem of binding site alignment discussed in section \ref{intro_aligning_binding_sites}. More formerly, given a matrix $R$ of dimensions $NxL$ containing $N$ vectors of read counts $r_{1}, r_{2}, ..., r_{N}$ of length $L$, each containing the number of reads mapping at a given position in a given region, find $K \leq N$ vectors of length $L' = L$ that contain archetypical signals found in the $N$ regions of $R$. This can actually be solved using clustering methods which groups regions that look alike into $K$ groups. Partitioning methods compare pairs of regions in order to state whether they resemble each other or not and breaks down $R$ in $K$ groups. The summary of the signal inside each group - for instance the mean signal for the K-means algorithm - can then be interpreted as the archetypical chromatin architectures. Biologically, these different organization may reflect different functions associated with the regions of interest. However, this can only be done properly if the positions in two regions are functionally similar. Indeed, a second issue is entangled with this heterogeneity problem : an alignment problem. Two stretches of signal, in two different regions, may be similar but located at different positions in the region. For instance two regions can be covered at 50\% by a nucleosome array, in one case over the first half, in the second case, over the second half (Figure \ref{intro_figure_comparison}A). In this case, detecting that both regions bear an array can be done in two ways : i) flipping one region such that both arrays are localized at the same edge (Figure \ref{intro_figure_comparison}B) or ii) by searching archetypical signals of length $L' \leq L$ by scanning the entire regions (Figure \ref{intro_figure_comparison}C). % Positional correlations are a usual way or representing data in bioinformatics. They consists of measuring a signal of interest (the target signal) around a set of positions of interest (the references) in order to shed light on their functional relationship. The data are usually represented as a $N$ rows and $L$ columns matrix in which each row represent the signal over a region which contains a reference at a constant position. This alignment problem has several roots. Let us assume that we measured nucleosome occupancy around TF binding sites. The nucleosome occupancy signal may not be aligned from one region to the next for at least three non-exclusive reasons. First, there may be an error in the estimation of the position of the TF binding site. For instance, ChIP-seq estimates binding +/-100bp. Assuming that a TF binding in the center of this region or where the signal is the highest do not guarantee to properly estimate the binding site. Second, the chromatin features appearing at a varying distance from the reference. For instance, two binding sites may be located at different distance from the closest nucleosome. Finally, the regions can show a functional orientation. For instance, TF binding sites have an upstream and a downstream, the same is true for TSSs. Finally, if both regions are aligned, it is worth mentioning that the signal over one region may be sparser because of a sub-optimal sequencing depth that has nothing to do with biology. -The study of signal distribution over genomic regions has been a quite active field for sequencing experiments during the last decade. Dedicated algorithms and software have been developed to discover chromatin patterns, such as ChromaSig \citep{hon_chromasig:_2008}, ArchAlign \citep{lai_archalign:_2010}, CATCHProfiles \citep{nielsen_catchprofiles}, CAGT \citep{kundaje_ubiquitous_2012} and ChIPPartitioning\citep{nair_probabilistic_2014}. However, the heterogeneity problem and the realignment problem are not always properly handled. For instance, ArchaAlign only realign the data while CAGT can only handle orientations issues but does not realign the patterns. +The study of signal distribution over genomic regions has been a quite active field for sequencing experiments during the last decade. Dedicated algorithms and software have been developed to discover chromatin patterns, such as ChromaSig \citep{hon_chromasig:_2008}, ArchAlign \citep{lai_archalign:_2010}, CATCHProfiles \citep{nielsen_catchprofiles}, CAGT \citep{kundaje_ubiquitous_2012} and ChIPPartitioning\citep{nair_probabilistic_2014}. However, individual programs do not always handle all aspects of heterogeneity. 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Figure and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }{figure.caption.32}{}} \citation{ambrosini_chip-seq_2016} \citation{ambrosini_signal_2003} \citation{ambrosini_pwmscan:_2018} \citation{ambrosini_pwmscan:_2018} \citation{ambrosini_pwmscan:_2018} \citation{ambrosini_pwmscan:_2018} \citation{hertz_identification_1990} \citation{beckstette_fast_2006} \citation{turatsinze_using_2008} \citation{heinz_simple_2010} \citation{grant_fimo:_2011} \citation{schones_statistical_2007} -\@writefile{lof}{\contentsline {figure}{\numberline {6.2}{\ignorespaces \textbf {Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }}{79}{figure.caption.33}} -\newlabel{lab_resources_pwmscan_benchmark}{{6.2}{79}{\textbf {Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }{figure.caption.33}{}} -\@writefile{toc}{\contentsline {section}{\numberline {6.3}Benchmark}{79}{section.6.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {6.2}{\ignorespaces \textbf {Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }}{81}{figure.caption.33}} +\newlabel{lab_resources_pwmscan_benchmark}{{6.2}{81}{\textbf {Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }{figure.caption.33}{}} +\@writefile{toc}{\contentsline {section}{\numberline {6.3}Benchmark}{81}{section.6.3}} \citation{aerts_toucan:_2003} \citation{fu_motifviz:_2004} \citation{zhao_tred:_2005} -\@writefile{lot}{\contentsline {table}{\numberline {6.1}{\ignorespaces \textbf {Motif scanning software comparison}. 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For the score correlations with matrix\_scan scores, the Spearman correlation was used. Table and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }{table.caption.34}{}} +\@writefile{lot}{\contentsline {table}{\numberline {6.1}{\ignorespaces \textbf {Motif scanning software comparison}. The performances of matrix\_scan were assessed by comparing how many of the regions listed by matrix\_scan were also returned by other programs and if the region scores were comparable. For the percentage of overlap with the match list returned by matrix\_scan, the shorter of the two lists always serves as the reference (100\%). For the score correlations with matrix\_scan scores, the Spearman correlation was used. Table and legend taken and adapted from \citep {ambrosini_pwmscan:_2018}.\relax }}{82}{table.caption.34}} +\newlabel{lab_resources_pwmscan_benchmark_table}{{6.1}{82}{\textbf {Motif scanning software comparison}. 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A snapshot of three units of the microfluidic device is shown. In vitro transcribed and translated bait TF, target dsDNA, and a nonspecific competitor poly-dIdC are mixed and pipetted in one of the wells of the microfluidic device. The mixtures are then passively pumped in the device (bottom panel). Newly formed TF\IeC {\textendash }DNA complexes are trapped under a flexible polydimethylsiloxane membrane, and unbound molecules as well as molecular complexes are washed away (upper panel). Left, schematic representation of three individual chambers. Right, corresponding snapshots of an individual chamber taken before and after mechanical trapping. \textbf {b} Data processing pipeline. The bound DNA is eluted from all the units of the device simultaneously and collected in one tube. Recovered DNA is amplified and sequenced. The sequencing reads are then demultiplexed, and a seed sequence is identified for each sample. This seed is then used to initialize a probability matrix representing the sequence specificity model for the given TF. The model parameters are then optimized using a Hidden Markov Model-based motif discovery pipeline. Figure and legend taken and adapted from \citep {isakova_smile-seq_2017}.\relax }}{68}{figure.caption.29}} -\newlabel{smile_seq_pipeline}{{5.1}{68}{\textbf {SMiLE-seq pipeline :} \textbf {a} Schematic representation of the experimental setup. A snapshot of three units of the microfluidic device is shown. In vitro transcribed and translated bait TF, target dsDNA, and a nonspecific competitor poly-dIdC are mixed and pipetted in one of the wells of the microfluidic device. The mixtures are then passively pumped in the device (bottom panel). Newly formed TF–DNA complexes are trapped under a flexible polydimethylsiloxane membrane, and unbound molecules as well as molecular complexes are washed away (upper panel). Left, schematic representation of three individual chambers. Right, corresponding snapshots of an individual chamber taken before and after mechanical trapping. \textbf {b} Data processing pipeline. The bound DNA is eluted from all the units of the device simultaneously and collected in one tube. Recovered DNA is amplified and sequenced. The sequencing reads are then demultiplexed, and a seed sequence is identified for each sample. This seed is then used to initialize a probability matrix representing the sequence specificity model for the given TF. The model parameters are then optimized using a Hidden Markov Model-based motif discovery pipeline. Figure and legend taken and adapted from \citep {isakova_smile-seq_2017}.\relax }{figure.caption.29}{}} +\newlabel{smile_seq}{{5}{69}{SMiLE-seq data analysis}{chapter.5}{}} +\@writefile{toc}{\contentsline {chapter}{SMiLE-seq data analysis}{69}{chapter.5}} +\@writefile{toc}{\contentsline {section}{\numberline {5.1}Introduction}{69}{section.5.1}} +\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces \textbf {SMiLE-seq pipeline :} \textbf {a} Schematic representation of the experimental setup. A snapshot of three units of the microfluidic device is shown. In vitro transcribed and translated bait TF, target dsDNA, and a nonspecific competitor poly-dIdC are mixed and pipetted in one of the wells of the microfluidic device. The mixtures are then passively pumped in the device (bottom panel). Newly formed TF\IeC {\textendash }DNA complexes are trapped under a flexible polydimethylsiloxane membrane, and unbound molecules as well as molecular complexes are washed away (upper panel). Left, schematic representation of three individual chambers. Right, corresponding snapshots of an individual chamber taken before and after mechanical trapping. \textbf {b} Data processing pipeline. The bound DNA is eluted from all the units of the device simultaneously and collected in one tube. Recovered DNA is amplified and sequenced. The sequencing reads are then demultiplexed, and a seed sequence is identified for each sample. This seed is then used to initialize a probability matrix representing the sequence specificity model for the given TF. The model parameters are then optimized using a Hidden Markov Model-based motif discovery pipeline. Figure and legend taken and adapted from \citep {isakova_smile-seq_2017}.\relax }}{70}{figure.caption.29}} +\newlabel{smile_seq_pipeline}{{5.1}{70}{\textbf {SMiLE-seq pipeline :} \textbf {a} Schematic representation of the experimental setup. A snapshot of three units of the microfluidic device is shown. In vitro transcribed and translated bait TF, target dsDNA, and a nonspecific competitor poly-dIdC are mixed and pipetted in one of the wells of the microfluidic device. The mixtures are then passively pumped in the device (bottom panel). Newly formed TF–DNA complexes are trapped under a flexible polydimethylsiloxane membrane, and unbound molecules as well as molecular complexes are washed away (upper panel). Left, schematic representation of three individual chambers. Right, corresponding snapshots of an individual chamber taken before and after mechanical trapping. \textbf {b} Data processing pipeline. The bound DNA is eluted from all the units of the device simultaneously and collected in one tube. Recovered DNA is amplified and sequenced. The sequencing reads are then demultiplexed, and a seed sequence is identified for each sample. This seed is then used to initialize a probability matrix representing the sequence specificity model for the given TF. The model parameters are then optimized using a Hidden Markov Model-based motif discovery pipeline. Figure and legend taken and adapted from \citep {isakova_smile-seq_2017}.\relax }{figure.caption.29}{}} \citation{isakova_smile-seq_2017} \citation{isakova_smile-seq_2017} \citation{weirauch_evaluation_2013} -\@writefile{lof}{\contentsline {figure}{\numberline {5.2}{\ignorespaces \textbf {Example of a Hidden Markov model :} initial HMM representation with a seed sequence 'ATGCC'. The upper Markov chain models + strand motif containing sequences, the middle one - strand motif containing sequences and the lower zero motif occurrence sequences. The FB, FE, RB and RE positions represents positions in the sequence that occur before and after the binding site on the forward and reverse strand. For these nodes, a self transition exist to allow the binding site to occur at a variable distance from the beginning and the end of the sequence. Once transiting toward the 1st position of the binding site, the next transition is forced toward the 2nd position in the binding site, and so on until the end of the binding site. The + strand and - strand Markov chains emission parameters are paired together (they have the same values), as represented by the grey dashed lines. The transition probabilities in red are not subjected to the Baum-Welch training. 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Figure and legend taken and adapted from \citep {isakova_smile-seq_2017}\relax }{figure.caption.30}{}} +\@writefile{toc}{\contentsline {section}{\numberline {5.2}Hidden Markov Model Motif discovery}{71}{section.5.2}} +\newlabel{section_smileseq_hmm}{{5.2}{71}{Hidden Markov Model Motif discovery}{section.5.2}{}} \citation{schutz_mamot:_2008} \citation{orenstein_comparative_2014} -\@writefile{toc}{\contentsline {section}{\numberline {5.3}Binding motif evaluation}{70}{section.5.3}} -\newlabel{section_smileseq_pwmeval}{{5.3}{70}{Binding motif evaluation}{section.5.3}{}} +\@writefile{toc}{\contentsline {section}{\numberline {5.3}Binding motif evaluation}{72}{section.5.3}} +\newlabel{section_smileseq_pwmeval}{{5.3}{72}{Binding motif evaluation}{section.5.3}{}} \citation{jolma_dna-binding_2013} \citation{mathelier_jaspar_2014} \citation{kulakovskiy_hocomoco:_2016} -\newlabel{smile_seq_pwmeval_score}{{5.1}{71}{Binding motif evaluation}{equation.5.3.1}{}} -\@writefile{toc}{\contentsline {section}{\numberline {5.4}Results}{71}{section.5.4}} -\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces \textbf {Predictive power of SMiLE-seq :} \textbf {A} the motifs compared to that of previously reported motifs that are retrievable from the indicated databases. 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The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.\relax }{figure.caption.31}{}} -\@writefile{toc}{\contentsline {section}{\numberline {5.5}Conclusions}{73}{section.5.5}} +\newlabel{smile_seq_pwmeval_score}{{5.1}{73}{Binding motif evaluation}{equation.5.3.1}{}} +\@writefile{toc}{\contentsline {section}{\numberline {5.4}Results}{73}{section.5.4}} +\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces \textbf {Predictive power of SMiLE-seq :} \textbf {A} the motifs compared to that of previously reported motifs that are retrievable from the indicated databases. For each motif, the AUC-ROC values on the 500 top peaks of the ENCODE ChIP-seq data sets for the corresponding TF was computed. 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The heatmap represents the AUC values computed for each method on the respective ChIP-seq data sets that were selected based on the highest mean AUC values among all five models. \textbf {B} the predictive performances of MAX and YY1 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. 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The color ribbons on the side indicate the cluster assignments. \textbf {D} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 90\% noise ($p_{s}$=0.1, $p_{b}$=0.9) and \textbf {E} one of the corresponding SPar-K partition, with shifting and flipping.\relax }}{59}{figure.caption.23}} -\newlabel{spark_simulated_data}{{4.1}{59}{Synthethic datasets : \textbf {A} The class signal densities. \textbf {B} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 0\% noise ($p_{s}$=1, $p_{b}$=0) and \textbf {C} one of the corresponding SPar-K partition, with shifting and flipping. The color ribbons on the side indicate the cluster assignments. \textbf {D} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 90\% noise ($p_{s}$=0.1, $p_{b}$=0.9) and \textbf {E} one of the corresponding SPar-K partition, with shifting and flipping.\relax }{figure.caption.23}{}} -\@writefile{toc}{\contentsline {section}{\numberline {4.3}Benchmarking}{59}{section.4.3}} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.1}K-means}{59}{subsection.4.3.1}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces \textbf {Clustering accuracy using random seeding :} to compare the clustering accuracies of the different methods, several simulated dataset containing 3 classes, different coverages (10, 50 and 100 reads per region indicated as "cov10", "cov50" and "cov100") and noise proportions (no noise, 10\% noise, 50\% noise and 90\% noise indicated as "0.0", "0.1", "0.5" and "0.9") were generated. Each dataset was clustered 50 times with each method. The Adjusted Rand Index (ARI) was computed for each partition. The ARI values are displayed as boxplots. SPar-K and ChIPPartitioning were run allowing flipping and shifting. The ARI was measured on each of the resulting data partitions. For SPar-K, "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. "R" stands for "random" and indicates the ARI values obtained when comparing the true cluster labels with a randomly shuffled version of it, 100 times. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{60}{figure.caption.24}} -\newlabel{spark_ari}{{4.2}{60}{\textbf {Clustering accuracy using random seeding :} to compare the clustering accuracies of the different methods, several simulated dataset containing 3 classes, different coverages (10, 50 and 100 reads per region indicated as "cov10", "cov50" and "cov100") and noise proportions (no noise, 10\% noise, 50\% noise and 90\% noise indicated as "0.0", "0.1", "0.5" and "0.9") were generated. Each dataset was clustered 50 times with each method. The Adjusted Rand Index (ARI) was computed for each partition. The ARI values are displayed as boxplots. SPar-K and ChIPPartitioning were run allowing flipping and shifting. The ARI was measured on each of the resulting data partitions. For SPar-K, "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. "R" stands for "random" and indicates the ARI values obtained when comparing the true cluster labels with a randomly shuffled version of it, 100 times. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }{figure.caption.24}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces \textbf {Median SSE :} for the simulated ChIP-seq dataset containing 3 classes, with coverage 100 and no noise, partitioned into 2 to 5 clusters. To judge whether the elbow method could be used to estimate the optimal number of clusters, this dataset was partitioned with SPar-K, allowing flip and shifting, into 2 to 5 clusters, 50 times for each set of parameters. For each number of clusters, the median SSE is shown, +/- 1 standard deviation (bars). \textbf {A} Seeding done at random, \textbf {B} seeding done at random and outlier smoothing \textbf {C} seeding done with the K-means++ method \textbf {D} seeding done with the K-means++ method and outlier smoothing. In all cases, the optimal number of clusters seemed to be 3 (which was the expected value). Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{61}{figure.caption.25}} -\newlabel{spark_sse}{{4.3}{61}{\textbf {Median SSE :} for the simulated ChIP-seq dataset containing 3 classes, with coverage 100 and no noise, partitioned into 2 to 5 clusters. To judge whether the elbow method could be used to estimate the optimal number of clusters, this dataset was partitioned with SPar-K, allowing flip and shifting, into 2 to 5 clusters, 50 times for each set of parameters. For each number of clusters, the median SSE is shown, +/- 1 standard deviation (bars). \textbf {A} Seeding done at random, \textbf {B} seeding done at random and outlier smoothing \textbf {C} seeding done with the K-means++ method \textbf {D} seeding done with the K-means++ method and outlier smoothing. In all cases, the optimal number of clusters seemed to be 3 (which was the expected value). Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }{figure.caption.25}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces \textbf {Running times :} to compare the run times of each program, the synthetic dataset with coverage 100 and no noise was partitioned 20 times with each program. The run times (wall clock) in second were measured. For all SPar-K and the regular K-means, the partitions were initialized using a random and K-means++ (indicated as "k++"). For ChIPPartitioning, only a random seeding was used. The partitions were then optimized for 30 iterations at most. For SPar-K and ChIPPartitioning, a shifting of 71 bins and flipping were allowed. For SPar-K, only one thread was used and "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{61}{figure.caption.26}} -\newlabel{spark_time}{{4.4}{61}{\textbf {Running times :} to compare the run times of each program, the synthetic dataset with coverage 100 and no noise was partitioned 20 times with each program. The run times (wall clock) in second were measured. For all SPar-K and the regular K-means, the partitions were initialized using a random and K-means++ (indicated as "k++"). For ChIPPartitioning, only a random seeding was used. The partitions were then optimized for 30 iterations at most. For SPar-K and ChIPPartitioning, a shifting of 71 bins and flipping were allowed. For SPar-K, only one thread was used and "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. 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The color ribbons on the side indicate the cluster assignments. \textbf {D} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 90\% noise ($p_{s}$=0.1, $p_{b}$=0.9) and \textbf {E} one of the corresponding SPar-K partition, with shifting and flipping.\relax }}{61}{figure.caption.23}} +\newlabel{spark_simulated_data}{{4.1}{61}{Synthethic datasets : \textbf {A} The class signal densities. \textbf {B} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 0\% noise ($p_{s}$=1, $p_{b}$=0) and \textbf {C} one of the corresponding SPar-K partition, with shifting and flipping. The color ribbons on the side indicate the cluster assignments. \textbf {D} A synthetic dataset with a mean coverage of a 100 reads per region in average ($c$=100) and 90\% noise ($p_{s}$=0.1, $p_{b}$=0.9) and \textbf {E} one of the corresponding SPar-K partition, with shifting and flipping.\relax }{figure.caption.23}{}} +\@writefile{toc}{\contentsline {section}{\numberline {4.3}Benchmarking}{61}{section.4.3}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.1}K-means}{61}{subsection.4.3.1}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces \textbf {Clustering accuracy using random seeding :} to compare the clustering accuracies of the different methods, several simulated dataset containing 3 classes, different coverages (10, 50 and 100 reads per region indicated as "cov10", "cov50" and "cov100") and noise proportions (no noise, 10\% noise, 50\% noise and 90\% noise indicated as "0.0", "0.1", "0.5" and "0.9") were generated. 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Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{62}{figure.caption.24}} +\newlabel{spark_ari}{{4.2}{62}{\textbf {Clustering accuracy using random seeding :} to compare the clustering accuracies of the different methods, several simulated dataset containing 3 classes, different coverages (10, 50 and 100 reads per region indicated as "cov10", "cov50" and "cov100") and noise proportions (no noise, 10\% noise, 50\% noise and 90\% noise indicated as "0.0", "0.1", "0.5" and "0.9") were generated. Each dataset was clustered 50 times with each method. The Adjusted Rand Index (ARI) was computed for each partition. The ARI values are displayed as boxplots. SPar-K and ChIPPartitioning were run allowing flipping and shifting. The ARI was measured on each of the resulting data partitions. For SPar-K, "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. 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In all cases, the optimal number of clusters seemed to be 3 (which was the expected value). Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{63}{figure.caption.25}} +\newlabel{spark_sse}{{4.3}{63}{\textbf {Median SSE :} for the simulated ChIP-seq dataset containing 3 classes, with coverage 100 and no noise, partitioned into 2 to 5 clusters. To judge whether the elbow method could be used to estimate the optimal number of clusters, this dataset was partitioned with SPar-K, allowing flip and shifting, into 2 to 5 clusters, 50 times for each set of parameters. For each number of clusters, the median SSE is shown, +/- 1 standard deviation (bars). \textbf {A} Seeding done at random, \textbf {B} seeding done at random and outlier smoothing \textbf {C} seeding done with the K-means++ method \textbf {D} seeding done with the K-means++ method and outlier smoothing. In all cases, the optimal number of clusters seemed to be 3 (which was the expected value). 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Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{63}{figure.caption.26}} +\newlabel{spark_time}{{4.4}{63}{\textbf {Running times :} to compare the run times of each program, the synthetic dataset with coverage 100 and no noise was partitioned 20 times with each program. The run times (wall clock) in second were measured. For all SPar-K and the regular K-means, the partitions were initialized using a random and K-means++ (indicated as "k++"). For ChIPPartitioning, only a random seeding was used. The partitions were then optimized for 30 iterations at most. For SPar-K and ChIPPartitioning, a shifting of 71 bins and flipping were allowed. For SPar-K, only one thread was used and "smooth" indicates outlier smoothing. For the regular K-means, "eucl." and "corr." refer to the euclidean and correlation distances. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }{figure.caption.26}{}} \citation{groux_spar-k:_2019} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.2}ChIPPartitioning}{62}{subsection.4.3.2}} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.3}Data}{62}{subsection.4.3.3}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.2}ChIPPartitioning}{64}{subsection.4.3.2}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.3}Data}{64}{subsection.4.3.3}} \citation{ambrosini_chip-seq_2016} \citation{ambrosini_chip-seq_2016} \citation{groux_spar-k:_2019} \citation{groux_spar-k:_2019} \citation{bailey_meme_2009} \citation{kundaje_ubiquitous_2012} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.4}Performances}{63}{subsection.4.3.4}} -\@writefile{toc}{\contentsline {section}{\numberline {4.4}Partition of DNase and MNase data}{63}{section.4.4}} -\@writefile{toc}{\contentsline {section}{\numberline {4.5}Conclusions}{63}{section.4.5}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces Nucleosome occupancy, determined by MNase-seq, in bins of 10bp, +/- 1000bp around 79'957 CTCF binding sites in GM12878 cells. \textbf {A} MNaseI-seq read density around the CTCF binding sites. ChIP-seq peak summits are aligned at position 0. The regions (rows) are ordered according the their resemblance (correlation) to the overall aggregation pattern. \textbf {B} SPar-K data partition. The number of clusters (4) was determined using the elbow method. The cluster labels are indicated by the color ribbons on the left. Within each cluster, the data have been realigned according to the shift and flip informations returned by SPar-K and the regions have been ordered according the their resemblance (correlation) to the cluster aggregation pattern. Because of the realignment, ChIP-seq peak summits are not anymore aligned at position 0. \textbf {C} Corresponding DNaseI hypersensitivity measured by DNaseI-seq at the same loci and realigned as in B. \textbf {D} CTCF motif occurrences predicted using a motif scan, at the same loci and realigned as in B. Each predicted binding site, +/- 1kb around a peak, is represented as a point. \textbf {E} Transcription start site (TSS) density at the same loci and realigned as in B. \textbf {F} Cluster 1 (red) aggregation profiles. The original peak coordinates were modified accordingly to the shift and flip values returned by SPar-K and the read densities the different data types were measured using ChIP-Cor \citep {ambrosini_chip-seq_2016}. For the TSSs and the transcription initiation (CAGE), only the data mapping on the negative strand were used to monitor transcription firing towards the nucleosome array (towards the left). \textbf {G} Proportions of regions having at least one CTCF motif +/- 1kb (same motifs as in D), for each cluster. \textbf {H} Proportions of regions having at least one TSS +/- 1kb (same TSSs as in E), for each cluster.\relax }}{64}{figure.caption.27}} -\newlabel{spark_ctcf}{{4.5}{64}{Nucleosome occupancy, determined by MNase-seq, in bins of 10bp, +/- 1000bp around 79'957 CTCF binding sites in GM12878 cells. \textbf {A} MNaseI-seq read density around the CTCF binding sites. ChIP-seq peak summits are aligned at position 0. The regions (rows) are ordered according the their resemblance (correlation) to the overall aggregation pattern. \textbf {B} SPar-K data partition. The number of clusters (4) was determined using the elbow method. The cluster labels are indicated by the color ribbons on the left. Within each cluster, the data have been realigned according to the shift and flip informations returned by SPar-K and the regions have been ordered according the their resemblance (correlation) to the cluster aggregation pattern. Because of the realignment, ChIP-seq peak summits are not anymore aligned at position 0. \textbf {C} Corresponding DNaseI hypersensitivity measured by DNaseI-seq at the same loci and realigned as in B. \textbf {D} CTCF motif occurrences predicted using a motif scan, at the same loci and realigned as in B. Each predicted binding site, +/- 1kb around a peak, is represented as a point. \textbf {E} Transcription start site (TSS) density at the same loci and realigned as in B. \textbf {F} Cluster 1 (red) aggregation profiles. The original peak coordinates were modified accordingly to the shift and flip values returned by SPar-K and the read densities the different data types were measured using ChIP-Cor \citep {ambrosini_chip-seq_2016}. For the TSSs and the transcription initiation (CAGE), only the data mapping on the negative strand were used to monitor transcription firing towards the nucleosome array (towards the left). \textbf {G} Proportions of regions having at least one CTCF motif +/- 1kb (same motifs as in D), for each cluster. \textbf {H} Proportions of regions having at least one TSS +/- 1kb (same TSSs as in E), for each cluster.\relax }{figure.caption.27}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Partitioning of DNaseI hypersensitivity profiles around SP1 binding sites in K562 cells. The optimal number of clusters was determined using the elbow method. \textbf {A.} Input data based on peak summits provided by ENCODE. \textbf {B.} Same regions clustered, re-aligned and oriented by SPar-K. Clusters 1, 2 and 3 are indicated by colored bars in red, blue, and green, respectively. \textbf {C.} MNase-seq read densities for the same regions, ordered, aligned and oriented as in B. \textbf {D.} Predicted SP1 binding motifs for the same regions, ordered, aligned and oriented as in B. \textbf {E.} Proportion of binding sites within each cluster having a confirmed promoter-associated TSS within +/- 300bp. \textbf {F.} Aggregations profiles for DNase-seq (red), MNase-seq (blue), promoter TSS (green) and CAGE-seq data (violet) for cluster 2 (aligned and oriented as in B). \textbf {G.} Motifs found by MEME-ChIP and Tomtom in the narrow footprints of each cluster. (*) known SP1 interactor, (c) central enrichment. Cluster 2 left and right refer to the left and right footprints seen in \textbf {B}. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{65}{figure.caption.28}} -\newlabel{spark_dnase}{{4.6}{65}{Partitioning of DNaseI hypersensitivity profiles around SP1 binding sites in K562 cells. The optimal number of clusters was determined using the elbow method. \textbf {A.} Input data based on peak summits provided by ENCODE. \textbf {B.} Same regions clustered, re-aligned and oriented by SPar-K. Clusters 1, 2 and 3 are indicated by colored bars in red, blue, and green, respectively. \textbf {C.} MNase-seq read densities for the same regions, ordered, aligned and oriented as in B. \textbf {D.} Predicted SP1 binding motifs for the same regions, ordered, aligned and oriented as in B. \textbf {E.} Proportion of binding sites within each cluster having a confirmed promoter-associated TSS within +/- 300bp. \textbf {F.} Aggregations profiles for DNase-seq (red), MNase-seq (blue), promoter TSS (green) and CAGE-seq data (violet) for cluster 2 (aligned and oriented as in B). \textbf {G.} Motifs found by MEME-ChIP and Tomtom in the narrow footprints of each cluster. (*) known SP1 interactor, (c) central enrichment. Cluster 2 left and right refer to the left and right footprints seen in \textbf {B}. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }{figure.caption.28}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.4}Performances}{65}{subsection.4.3.4}} +\@writefile{toc}{\contentsline {section}{\numberline {4.4}Partition of DNase and MNase data}{65}{section.4.4}} +\@writefile{toc}{\contentsline {section}{\numberline {4.5}Conclusions}{65}{section.4.5}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces Nucleosome occupancy, determined by MNase-seq, in bins of 10bp, +/- 1000bp around 79'957 CTCF binding sites in GM12878 cells. \textbf {A} MNaseI-seq read density around the CTCF binding sites. ChIP-seq peak summits are aligned at position 0. The regions (rows) are ordered according the their resemblance (correlation) to the overall aggregation pattern. \textbf {B} SPar-K data partition. The number of clusters (4) was determined using the elbow method. The cluster labels are indicated by the color ribbons on the left. Within each cluster, the data have been realigned according to the shift and flip informations returned by SPar-K and the regions have been ordered according the their resemblance (correlation) to the cluster aggregation pattern. Because of the realignment, ChIP-seq peak summits are not anymore aligned at position 0. \textbf {C} Corresponding DNaseI hypersensitivity measured by DNaseI-seq at the same loci and realigned as in B. \textbf {D} CTCF motif occurrences predicted using a motif scan, at the same loci and realigned as in B. Each predicted binding site, +/- 1kb around a peak, is represented as a point. \textbf {E} Transcription start site (TSS) density at the same loci and realigned as in B. \textbf {F} Cluster 1 (red) aggregation profiles. The original peak coordinates were modified accordingly to the shift and flip values returned by SPar-K and the read densities the different data types were measured using ChIP-Cor \citep {ambrosini_chip-seq_2016}. For the TSSs and the transcription initiation (CAGE), only the data mapping on the negative strand were used to monitor transcription firing towards the nucleosome array (towards the left). \textbf {G} Proportions of regions having at least one CTCF motif +/- 1kb (same motifs as in D), for each cluster. \textbf {H} Proportions of regions having at least one TSS +/- 1kb (same TSSs as in E), for each cluster.\relax }}{66}{figure.caption.27}} +\newlabel{spark_ctcf}{{4.5}{66}{Nucleosome occupancy, determined by MNase-seq, in bins of 10bp, +/- 1000bp around 79'957 CTCF binding sites in GM12878 cells. \textbf {A} MNaseI-seq read density around the CTCF binding sites. ChIP-seq peak summits are aligned at position 0. The regions (rows) are ordered according the their resemblance (correlation) to the overall aggregation pattern. \textbf {B} SPar-K data partition. The number of clusters (4) was determined using the elbow method. The cluster labels are indicated by the color ribbons on the left. Within each cluster, the data have been realigned according to the shift and flip informations returned by SPar-K and the regions have been ordered according the their resemblance (correlation) to the cluster aggregation pattern. Because of the realignment, ChIP-seq peak summits are not anymore aligned at position 0. \textbf {C} Corresponding DNaseI hypersensitivity measured by DNaseI-seq at the same loci and realigned as in B. \textbf {D} CTCF motif occurrences predicted using a motif scan, at the same loci and realigned as in B. Each predicted binding site, +/- 1kb around a peak, is represented as a point. \textbf {E} Transcription start site (TSS) density at the same loci and realigned as in B. \textbf {F} Cluster 1 (red) aggregation profiles. The original peak coordinates were modified accordingly to the shift and flip values returned by SPar-K and the read densities the different data types were measured using ChIP-Cor \citep {ambrosini_chip-seq_2016}. For the TSSs and the transcription initiation (CAGE), only the data mapping on the negative strand were used to monitor transcription firing towards the nucleosome array (towards the left). \textbf {G} Proportions of regions having at least one CTCF motif +/- 1kb (same motifs as in D), for each cluster. \textbf {H} Proportions of regions having at least one TSS +/- 1kb (same TSSs as in E), for each cluster.\relax }{figure.caption.27}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Partitioning of DNaseI hypersensitivity profiles around SP1 binding sites in K562 cells. The optimal number of clusters was determined using the elbow method. \textbf {A.} Input data based on peak summits provided by ENCODE. \textbf {B.} Same regions clustered, re-aligned and oriented by SPar-K. Clusters 1, 2 and 3 are indicated by colored bars in red, blue, and green, respectively. \textbf {C.} MNase-seq read densities for the same regions, ordered, aligned and oriented as in B. \textbf {D.} Predicted SP1 binding motifs for the same regions, ordered, aligned and oriented as in B. \textbf {E.} Proportion of binding sites within each cluster having a confirmed promoter-associated TSS within +/- 300bp. \textbf {F.} Aggregations profiles for DNase-seq (red), MNase-seq (blue), promoter TSS (green) and CAGE-seq data (violet) for cluster 2 (aligned and oriented as in B). \textbf {G.} Motifs found by MEME-ChIP and Tomtom in the narrow footprints of each cluster. (*) known SP1 interactor, (c) central enrichment. Cluster 2 left and right refer to the left and right footprints seen in \textbf {B}. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }}{67}{figure.caption.28}} +\newlabel{spark_dnase}{{4.6}{67}{Partitioning of DNaseI hypersensitivity profiles around SP1 binding sites in K562 cells. The optimal number of clusters was determined using the elbow method. \textbf {A.} Input data based on peak summits provided by ENCODE. \textbf {B.} Same regions clustered, re-aligned and oriented by SPar-K. Clusters 1, 2 and 3 are indicated by colored bars in red, blue, and green, respectively. \textbf {C.} MNase-seq read densities for the same regions, ordered, aligned and oriented as in B. \textbf {D.} Predicted SP1 binding motifs for the same regions, ordered, aligned and oriented as in B. \textbf {E.} Proportion of binding sites within each cluster having a confirmed promoter-associated TSS within +/- 300bp. \textbf {F.} Aggregations profiles for DNase-seq (red), MNase-seq (blue), promoter TSS (green) and CAGE-seq data (violet) for cluster 2 (aligned and oriented as in B). \textbf {G.} Motifs found by MEME-ChIP and Tomtom in the narrow footprints of each cluster. (*) known SP1 interactor, (c) central enrichment. Cluster 2 left and right refer to the left and right footprints seen in \textbf {B}. Figure and legend taken and adapted from \citep {groux_spar-k:_2019}.\relax }{figure.caption.28}{}} \@setckpt{main/ch_spark}{ -\setcounter{page}{66} +\setcounter{page}{68} \setcounter{equation}{1} \setcounter{enumi}{8} \setcounter{enumii}{0} \setcounter{enumiii}{0} \setcounter{enumiv}{0} \setcounter{footnote}{0} \setcounter{mpfootnote}{0} \setcounter{part}{0} \setcounter{chapter}{4} \setcounter{section}{5} \setcounter{subsection}{0} \setcounter{subsubsection}{0} \setcounter{paragraph}{0} \setcounter{subparagraph}{0} \setcounter{figure}{6} \setcounter{table}{0} \setcounter{NAT@ctr}{0} \setcounter{FBcaption@count}{0} \setcounter{ContinuedFloat}{0} \setcounter{KVtest}{0} \setcounter{subfigure}{0} \setcounter{subfigure@save}{0} \setcounter{lofdepth}{1} \setcounter{subtable}{0} \setcounter{subtable@save}{0} \setcounter{lotdepth}{1} \setcounter{lips@count}{0} \setcounter{lstnumber}{1} \setcounter{Item}{8} \setcounter{Hfootnote}{0} \setcounter{bookmark@seq@number}{0} \setcounter{AM@survey}{0} 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b/my_thesis.log index b1311b2..ec036fc 100644 --- a/my_thesis.log +++ b/my_thesis.log @@ -1,4044 +1,4064 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2018.12.12) 10 JAN 2020 13:23 +This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2018.12.12) 14 JAN 2020 17:05 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **my_thesis.tex (./my_thesis.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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defining Unicode char U+00DF (decimal 223) defining Unicode char U+00E0 (decimal 224) defining Unicode char U+00E1 (decimal 225) defining Unicode char U+00E2 (decimal 226) defining Unicode char U+00E3 (decimal 227) defining Unicode char U+00E4 (decimal 228) defining Unicode char U+00E5 (decimal 229) defining Unicode char U+00E6 (decimal 230) defining Unicode char U+00E7 (decimal 231) defining Unicode char U+00E8 (decimal 232) defining Unicode char U+00E9 (decimal 233) defining Unicode char U+00EA (decimal 234) defining Unicode char U+00EB (decimal 235) defining Unicode char U+00EC (decimal 236) defining Unicode char U+00ED (decimal 237) defining Unicode char U+00EE (decimal 238) defining Unicode char U+00EF (decimal 239) defining Unicode char U+00F0 (decimal 240) defining Unicode char U+00F1 (decimal 241) defining Unicode char U+00F2 (decimal 242) defining Unicode char U+00F3 (decimal 243) defining Unicode char U+00F4 (decimal 244) defining Unicode char U+00F5 (decimal 245) defining Unicode char U+00F6 (decimal 246) defining Unicode char U+00F8 (decimal 248) defining Unicode char U+00F9 (decimal 249) defining Unicode char U+00FA (decimal 250) defining Unicode char U+00FB (decimal 251) defining Unicode char U+00FC (decimal 252) defining Unicode char U+00FD (decimal 253) defining Unicode char U+00FE (decimal 254) defining Unicode char U+00FF (decimal 255) defining Unicode char U+0100 (decimal 256) defining Unicode char U+0101 (decimal 257) defining Unicode char U+0102 (decimal 258) defining Unicode char U+0103 (decimal 259) defining Unicode char U+0104 (decimal 260) defining Unicode char U+0105 (decimal 261) defining Unicode char U+0106 (decimal 262) defining Unicode char U+0107 (decimal 263) defining Unicode char U+0108 (decimal 264) defining Unicode char U+0109 (decimal 265) defining Unicode char U+010A (decimal 266) defining Unicode char U+010B (decimal 267) defining Unicode char U+010C (decimal 268) defining Unicode char U+010D (decimal 269) defining Unicode char U+010E (decimal 270) defining Unicode char U+010F (decimal 271) defining Unicode char U+0110 (decimal 272) defining Unicode char U+0111 (decimal 273) defining Unicode char U+0112 (decimal 274) defining Unicode char U+0113 (decimal 275) defining Unicode char U+0114 (decimal 276) defining Unicode char U+0115 (decimal 277) defining Unicode char U+0116 (decimal 278) defining Unicode char U+0117 (decimal 279) defining Unicode char U+0118 (decimal 280) defining Unicode char U+0119 (decimal 281) defining Unicode char U+011A (decimal 282) defining Unicode char U+011B (decimal 283) defining Unicode char U+011C (decimal 284) defining Unicode char U+011D (decimal 285) defining Unicode char U+011E (decimal 286) defining Unicode char U+011F (decimal 287) defining Unicode char U+0120 (decimal 288) defining Unicode char U+0121 (decimal 289) defining Unicode char U+0122 (decimal 290) defining Unicode char U+0123 (decimal 291) defining Unicode char U+0124 (decimal 292) defining Unicode char U+0125 (decimal 293) defining Unicode char U+0128 (decimal 296) defining Unicode char U+0129 (decimal 297) defining Unicode char U+012A (decimal 298) defining Unicode char U+012B (decimal 299) defining Unicode char U+012C (decimal 300) defining Unicode char U+012D (decimal 301) defining Unicode char U+012E (decimal 302) defining Unicode char U+012F (decimal 303) defining Unicode char U+0130 (decimal 304) defining Unicode char U+0131 (decimal 305) defining Unicode char U+0132 (decimal 306) defining Unicode char U+0133 (decimal 307) defining Unicode char U+0134 (decimal 308) defining Unicode char U+0135 (decimal 309) defining Unicode char U+0136 (decimal 310) defining Unicode char U+0137 (decimal 311) defining Unicode char U+0139 (decimal 313) defining Unicode char U+013A (decimal 314) defining Unicode char U+013B (decimal 315) defining Unicode char U+013C (decimal 316) defining Unicode char U+013D (decimal 317) defining Unicode char U+013E (decimal 318) defining Unicode char U+0141 (decimal 321) defining Unicode char U+0142 (decimal 322) defining Unicode char U+0143 (decimal 323) defining Unicode char U+0144 (decimal 324) defining Unicode char U+0145 (decimal 325) defining Unicode char U+0146 (decimal 326) defining Unicode char U+0147 (decimal 327) defining Unicode char U+0148 (decimal 328) defining Unicode char U+014A (decimal 330) defining Unicode char U+014B (decimal 331) defining Unicode char U+014C (decimal 332) defining Unicode char U+014D (decimal 333) defining Unicode char U+014E (decimal 334) defining Unicode char U+014F (decimal 335) defining Unicode char U+0150 (decimal 336) defining Unicode char U+0151 (decimal 337) defining Unicode char U+0152 (decimal 338) defining Unicode char U+0153 (decimal 339) defining Unicode char U+0154 (decimal 340) defining Unicode char U+0155 (decimal 341) defining Unicode char U+0156 (decimal 342) defining Unicode char U+0157 (decimal 343) defining Unicode char U+0158 (decimal 344) defining Unicode char U+0159 (decimal 345) defining Unicode char U+015A (decimal 346) defining Unicode char U+015B (decimal 347) defining Unicode char U+015C (decimal 348) defining Unicode char U+015D (decimal 349) defining Unicode char U+015E (decimal 350) defining Unicode char U+015F (decimal 351) defining Unicode char U+0160 (decimal 352) defining Unicode char U+0161 (decimal 353) defining Unicode char U+0162 (decimal 354) defining Unicode char U+0163 (decimal 355) defining Unicode char U+0164 (decimal 356) defining Unicode char U+0165 (decimal 357) defining Unicode char U+0168 (decimal 360) defining Unicode char U+0169 (decimal 361) defining Unicode char U+016A (decimal 362) defining Unicode char U+016B (decimal 363) defining Unicode char U+016C (decimal 364) defining Unicode char U+016D (decimal 365) defining Unicode char U+016E (decimal 366) defining Unicode char U+016F (decimal 367) defining Unicode char U+0170 (decimal 368) defining Unicode char U+0171 (decimal 369) defining Unicode char U+0172 (decimal 370) defining 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(/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.greek.cod e.tex File: chemmacros.module.greek.code.tex 2017/08/28 v5.8b chemmacros module `gree k' 2015/06/09 upright greek symbols (/usr/share/texlive/texmf-dist/tex/latex/chemgreek/chemgreek.sty Package: chemgreek 2016/12/20 v1.1 interfaceforuprightgreeklettersforuseinchemi stry (CN) \l__chemgreek_tmpa_int=\count338 \g__chemgreek_tmpa_int=\count339 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \newchemgreekmapping with sig. 'O{}mm' on line 336. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \renewchemgreekmapping with sig. 'O{}mm' on line 339. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \declarechemgreekmapping with sig. 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LaTeX info: "xparse/define-command" . . Defining command \chemgreekmappingsymbol with sig. 'mm' on line 477. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \activatechemgreekmapping with sig. 'sm' on line 486. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \selectchemgreekmapping with sig. 'm' on line 491. ................................................. )) (chemmacros) Loading module `chemformula'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.chemformu la.code.tex File: chemmacros.module.chemformula.code.tex 2017/08/28 v5.8b chemmacros module `chemformula' 2016/05/03 integration of chemical formulas (chemmacros) Loading module `charges'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.charges.c ode.tex File: chemmacros.module.charges.code.tex 2017/08/28 v5.8b chemmacros module `ch arges' 2015/07/30 charges ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemCharge with sig. 'mm' on line 122. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemCharge with sig. 'mm' on line 122. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemCharge with sig. 'mm' on line 122. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemCharge with sig. 'mm' on line 122. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemPartialCharge with sig. 'mm' on line 125. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemPartialCharge with sig. 'mm' on line 125. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemPartialCharge with sig. 'mm' on line 125. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemPartialCharge with sig. 'mm' on line 125. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \mch with sig. 'o' on line 146. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \pch with sig. 'o' on line 147. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \fmch with sig. 'o' on line 148. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \fpch with sig. 'o' on line 149. ................................................. )) (chemmacros) Loading module `acid-base'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.acid-base .code.tex File: chemmacros.module.acid-base.code.tex 2017/08/28 v5.8b chemmacros module ` acid-base' 2016/05/31 acid/base ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemEqConstant with sig. 'mmm' on line 87. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemEqConstant with sig. 'mmm' on line 87. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemEqConstant with sig. 'mmm' on line 87. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemEqConstant with sig. 'mmm' on line 87. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \p with sig. 'm' on line 119. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \pH with sig. '' on line 120. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \pOH with sig. '' on line 121. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \pKa with sig. 'o' on line 130. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \pKb with sig. 'o' on line 139. ................................................. ) (chemmacros) Loading module `symbols'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.symbols.c ode.tex File: chemmacros.module.symbols.code.tex 2017/08/28 v5.8b chemmacros module `sy mbols' 2015/06/09 symbols ................................................. . LaTeX info: "xparse/define-command" . . Defining command \standardstate with sig. '' on line 67. ................................................. ) (chemmacros) Loading module `particles'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.particles .code.tex File: chemmacros.module.particles.code.tex 2017/08/28 v5.8b chemmacros module ` particles' 2016/04/02 particles ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemParticle with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemParticle with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemParticle with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemParticle with sig. 'mm' on line 45. ................................................. \l__chemmacros_nucleophile_dim=\dimen308 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemNucleophile with sig. 'mm' on line 111. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemNucleophile with sig. 'mm' on line 111. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemNucleophile with sig. 'mm' on line 111. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemNucleophile with sig. 'mm' on line 111. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \Nuc with sig. 'o' on line 130. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ba with sig. 'o' on line 131. ................................................. ) (chemmacros) Loading module `phases'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.phases.co de.tex File: chemmacros.module.phases.code.tex 2017/08/28 v5.8b chemmacros module `pha ses' 2016/05/31 phase descriptors \l__chemmacros_phases_space_dim=\dimen309 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemPhase with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemPhase with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemPhase with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemPhase with sig. 'mm' on line 45. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \phase with sig. 'm' on line 93. ................................................. ................................................. . LaTeX info: "xparse/redefine-command" . . Redefining command \sld with sig. 'o' on line 95. ................................................. ................................................. . LaTeX info: "xparse/redefine-command" . . Redefining command \lqd with sig. 'o' on line 96. ................................................. ................................................. . LaTeX info: "xparse/redefine-command" . . Redefining command \gas with sig. 'o' on line 97. ................................................. ................................................. . LaTeX info: "xparse/redefine-command" . . Redefining command \aq with sig. 'o' on line 98. ................................................. ) (chemmacros) Loading module `nomenclature'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.nomenclat ure.code.tex File: chemmacros.module.nomenclature.code.tex 2017/08/28 v5.8b chemmacros modul e `nomenclature' 2017/06/11 chemical names (chemmacros) Loading module `tikz'... (/usr/share/texlive/texmf-dist/tex/latex/chemmacros/chemmacros.module.tikz.code .tex File: chemmacros.module.tikz.code.tex 2017/08/28 v5.8b chemmacros module `tikz' 2015/10/26 upright greek symbols (/usr/share/texlive/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tik zlibrarycalc.code.tex File: tikzlibrarycalc.code.tex 2013/07/15 v3.0.1a (rcs-revision 1.9) ) (/usr/share/texlive/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tik zlibrarydecorations.pathmorphing.code.tex (/usr/share/texlive/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tik zlibrarydecorations.code.tex (/usr/share/texlive/texmf-dist/tex/generic/pgf/modules/pgfmoduledecorations.cod e.tex \pgfdecoratedcompleteddistance=\dimen310 \pgfdecoratedremainingdistance=\dimen311 \pgfdecoratedinputsegmentcompleteddistance=\dimen312 \pgfdecoratedinputsegmentremainingdistance=\dimen313 \pgf@decorate@distancetomove=\dimen314 \pgf@decorate@repeatstate=\count340 \pgfdecorationsegmentamplitude=\dimen315 \pgfdecorationsegmentlength=\dimen316 ) \tikz@lib@dec@box=\box73 ) (/usr/share/texlive/texmf-dist/tex/generic/pgf/libraries/decorations/pgflibrary decorations.pathmorphing.code.tex)) \l__chemmacros_el_length_dim=\dimen317 ) ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemIUPAC with sig. 'mm' on line 209. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemIUPAC with sig. 'mm' on line 212. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemIUPAC with sig. 'mm' on line 215. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemIUPAC with sig. 'mm' on line 218. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \LetChemIUPAC with sig. 'mm' on line 221. ................................................. \l__chemmacros_cip_kern_dim=\dimen318 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \Sconf with sig. 'O{S}' on line 349. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \Rconf with sig. 'O{R}' on line 350. ................................................. \l__chemmacros_iupac_hyphen_pre_dim=\dimen319 \l__chemmacros_iupac_hyphen_post_dim=\dimen320 \l__chemmacros_iupac_break_dim=\dimen321 \l__chemmacros_iupac_break_skip=\skip102 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemIUPACShorthand with sig. 'mm' on line 604. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemIUPACShorthand with sig. 'mm' on line 611. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemIUPACShorthand with sig. 'mm' on line 617. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemIUPACShorthand with sig. 'mm' on line 624. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RemoveChemIUPACShorthand with sig. 'm' on line 627. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \iupac with sig. 'O{}m' on line 673. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemLatin with sig. 'mm' on line 755. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemLatin with sig. 'mm' on line 755. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemLatin with sig. 'mm' on line 755. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemLatin with sig. 'mm' on line 755. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \latin with sig. 'O{}m' on line 826. ................................................. )))) ................................................. . chemmacros info: "default-formula-method" . . You haven't chosen a formula method so I'm assuming the default method . `chemformula'. ................................................. (/usr/share/texlive/texmf-dist/tex/latex/chemformula/chemformula.sty (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xfrac/xfrac.sty (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xtemplate/xtemplate.sty Package: xtemplate 2018/02/21 L3 Experimental prototype document functions \l__xtemplate_tmp_dim=\dimen322 \l__xtemplate_tmp_int=\count341 \l__xtemplate_tmp_muskip=\muskip18 \l__xtemplate_tmp_skip=\skip103 ) Package: xfrac 2018/02/21 L3 Experimental split-level fractions \l__xfrac_slash_box=\box74 \l__xfrac_tmp_box=\box75 \l__xfrac_denominator_bot_sep_dim=\dimen323 \l__xfrac_numerator_bot_sep_dim=\dimen324 \l__xfrac_numerator_top_sep_dim=\dimen325 \l__xfrac_slash_left_sep_dim=\dimen326 \l__xfrac_slash_right_sep_dim=\dimen327 \l__xfrac_slash_left_muskip=\muskip19 \l__xfrac_slash_right_muskip=\muskip20 ................................................. . xtemplate info: "declare-object-type" . . Declaring object type 'xfrac' taking 3 argument(s) on line 80. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \sfrac with sig. 'omom' on line 420. ................................................. ) (/usr/share/texlive/texmf-dist/tex/latex/units/nicefrac.sty Package: nicefrac 1998/08/04 v0.9b Nice fractions \L@UnitsRaiseDisplaystyle=\skip104 \L@UnitsRaiseTextstyle=\skip105 \L@UnitsRaiseScriptstyle=\skip106 ) (/usr/share/texlive/texmf-dist/tex/generic/pgf/libraries/pgflibraryarrows.meta. code.tex File: pgflibraryarrows.meta.code.tex 2015/05/13 v3.0.1a (rcs-revision 1.13) \pgfarrowinset=\dimen328 \pgfarrowlength=\dimen329 \pgfarrowwidth=\dimen330 \pgfarrowlinewidth=\dimen331 ) Package: chemformula 2017/03/23 v4.15e typeset chemical compounds and reactions (CN) \l__chemformula_tmpa_dim=\dimen332 \l__chemformula_tmpb_dim=\dimen333 \l__chemformula_tmpc_dim=\dimen334 \l__chemformula_tmpa_int=\count342 \l__chemformula_tmpb_int=\count343 \l__chemformula_tmpc_int=\count344 \l__chemformula_tmpa_box=\box76 \l__chemformula_tmpb_box=\box77 \l__chemformula_arrow_length_dim=\dimen335 \l__chemformula_arrow_label_height_dim=\dimen336 \l__chemformula_arrow_label_offset_dim=\dimen337 \l__chemformula_arrow_minimum_length_dim=\dimen338 \l__chemformula_arrow_shortage_dim=\dimen339 \l__chemformula_arrow_offset_dim=\dimen340 \l__chemformula_arrow_yshift_dim=\dimen341 \l__chemformula_radical_radius_dim=\dimen342 \l__chemformula_radical_hshift_dim=\dimen343 \l__chemformula_radical_vshift_dim=\dimen344 \l__chemformula_radical_space_dim=\dimen345 \l__chemformula_arrow_head_dim=\dimen346 \l__chemformula_name_dim=\dimen347 \l__chemformula_adduct_space_dim=\dimen348 \l__chemformula_charge_shift_dim=\dimen349 \l__chemformula_subscript_shift_dim=\dimen350 \l__chemformula_superscript_shift_dim=\dimen351 \l__chemformula_subscript_dim=\dimen352 \l__chemformula_superscript_dim=\dimen353 \l__chemformula_bond_dim=\dimen354 \l__chemformula_bond_space_dim=\dimen355 \l__chemformula_elspec_pair_distance_dim=\dimen356 \l__chemformula_elspec_pair_line_length_dim=\dimen357 \l__chemformula_elspec_pair_width_dim=\dimen358 \l__chemformula_kroegervink_positive_radius_dim=\dimen359 \l__chemformula_kroegervink_positive_hshift_dim=\dimen360 \l__chemformula_kroegervink_positive_vshift_dim=\dimen361 \l__chemformula_kroegervink_positive_space_dim=\dimen362 \l__chemformula_stoich_space_skip=\skip107 \l__chemformula_math_space_skip=\skip108 \l__chemformula_count_tokens_int=\count345 \g__chemformula_lewis_int=\count346 \l__chemformula_arrow_arg_i_box=\box78 \l__chemformula_arrow_arg_ii_box=\box79 \l__chemformula_superscript_box=\box80 \l__chemformula_subscript_box=\box81 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \charrow with sig. 'mO{}O{}' on line 823. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemArrow with sig. 'mm' on line 896. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemArrow with sig. 'mm' on line 904. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemArrow with sig. 'mm' on line 911. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemArrow with sig. 'mm' on line 921. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ShowChemArrow with sig. 'm' on line 931. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ch with sig. 'O{}m' on line 1176. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \chcpd with sig. 'O{}m' on line 1198. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \chname with sig. 'R(){}R(){}' on line 1276. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemCompoundProperty with sig. 'mm' on line 1361. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemCompoundProperty with sig. 'mm' on line 1364. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemCompoundProperty with sig. 'mm' on line 1367. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemCompoundProperty with sig. 'mm' on line 1370. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RemoveChemCompoundProperty with sig. 'm' on line 1373. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemBond with sig. 'mm' on line 1571. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemBond with sig. 'mm' on line 1574. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemBond with sig. 'mm' on line 1577. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemBond with sig. 'mm' on line 1580. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemBondAlias with sig. 'mm' on line 1583. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemBondAlias with sig. 'mm' on line 1586. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ShowChemBond with sig. 'm' on line 1589. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \bond with sig. 'm' on line 1592. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \chstoich with sig. 'm' on line 2191. ................................................. \l__chemformula_additions_symbol_space_skip=\skip109 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemAdditionSymbol with sig. 'mmm' on line 2697. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemAdditionSymbol with sig. 'mmm' on line 2706. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemAdditionSymbol with sig. 'mmm' on line 2715. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemAdditionSymbol with sig. 'mmm' on line 2718. ................................................. \l__chemformula_plus_space_skip=\skip110 \l__chemformula_minus_space_skip=\skip111 ................................................. . LaTeX info: "xparse/define-command" . . Defining command \NewChemSymbol with sig. 'mm' on line 2763. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \ProvideChemSymbol with sig. 'mm' on line 2769. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \RenewChemSymbol with sig. 'mm' on line 2776. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \DeclareChemSymbol with sig. 'mm' on line 2779. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \chlewis with sig. 'O{}mm' on line 3334. ................................................. ................................................. . LaTeX info: "xparse/define-command" . . Defining command \setchemformula with sig. 'm' on line 3339. ................................................. ) (./my_thesis.aux (./head/dedication.aux) (./head/acknowledgements.aux) (./head/abstracts.aux) (./main/ch_introduction.aux) (./main/ch_lab_resources.aux) (./main/ch_encode_peaks.aux) (./main/ch_spark.aux) (./main/ch_smile-seq.aux) (./main/ch_pwmscan.aux) (./main/ch_atac-seq.aux LaTeX Warning: Label `encode_peaks_algo_ndr_extend' multiply defined. ) (./main/ch_discussion.aux) (./tail/appendix.aux) (./tail/biblio.aux) (./tail/cv.aux)) \openout1 = `my_thesis.aux'. 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{chapter}{Acknowledgements}{i}{chapter*.1} \contentsline {chapter}{Abstract (English/Fran\IeC {\c c}ais/Deutsch)}{iii}{chapter*.2} \babel@toc {french}{} \babel@toc {english}{} \contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1} \contentsline {chapter}{Introduction}{1}{chapter.1} \contentsline {section}{\numberline {1.1}About chromatin}{1}{section.1.1} \contentsline {subsection}{\numberline {1.1.1}The chromatin structure}{2}{subsection.1.1.1} \contentsline {subsection}{\numberline {1.1.2}The chromatin is dynamic}{2}{subsection.1.1.2} \contentsline {subsection}{\numberline {1.1.3}About nucleosome positioning}{4}{subsection.1.1.3} \contentsline {section}{\numberline {1.2}About transcription factors}{7}{section.1.2} \contentsline {subsection}{\numberline {1.2.1}TF co-binding}{7}{subsection.1.2.1} \contentsline {section}{\numberline {1.3}Gene regulation in a nutshell}{9}{section.1.3} \contentsline {subsection}{\numberline {1.3.1}The chromatin barrier}{9}{subsection.1.3.1} \contentsline {subsection}{\numberline {1.3.2}TFs cooperative binding}{9}{subsection.1.3.2} \contentsline {subsection}{\numberline {1.3.3}Pioneer TFs}{10}{subsection.1.3.3} \contentsline {subsection}{\numberline {1.3.4}Regulatory elements}{10}{subsection.1.3.4} \contentsline {subsection}{\numberline {1.3.5}The genome goes 3D}{11}{subsection.1.3.5} \contentsline {section}{\numberline {1.4}Measuring chromatin features}{12}{section.1.4} \contentsline {subsection}{\numberline {1.4.1}Measuring nucleosome occupancy}{12}{subsection.1.4.1} \contentsline {subsection}{\numberline {1.4.2}Digital footprinting}{13}{subsection.1.4.2} \contentsline {subsection}{\numberline {1.4.3}Measuring TF binding in vivo}{15}{subsection.1.4.3} \contentsline {subsection}{\numberline {1.4.4}Measuring TF binding in vitro}{16}{subsection.1.4.4} \contentsline {section}{\numberline {1.5}Modeling sequence specificity}{17}{section.1.5} \contentsline {subsubsection}{The physics approach to PWMs}{17}{section.1.5} \contentsline {subsubsection}{The statistical mechanic approach to PWMs}{18}{equation.1.5.2} \contentsline {subsection}{\numberline {1.5.1}Aligning binding sites}{19}{subsection.1.5.1} -\contentsline {subsection}{\numberline {1.5.2}Platitudes}{19}{subsection.1.5.2} +\contentsline {subsection}{\numberline {1.5.2}Platitudes}{20}{subsection.1.5.2} \contentsline {subsection}{\numberline {1.5.3}Predicting binding sites}{20}{subsection.1.5.3} \contentsline {section}{\numberline {1.6}Over-represented patterns discovery}{21}{section.1.6} -\contentsline {chapter}{\numberline {2}Laboratory resources}{23}{chapter.2} -\contentsline {chapter}{Laboratory resources}{23}{chapter.2} -\contentsline {section}{\numberline {2.1}Mass Genome Annotation repository}{23}{section.2.1} -\contentsline {subsection}{\numberline {2.1.1}MGA content and organization}{24}{subsection.2.1.1} -\contentsline {subsection}{\numberline {2.1.2}Conclusions}{25}{subsection.2.1.2} -\contentsline {section}{\numberline {2.2}Eukaryotic Promoter Database}{26}{section.2.2} -\contentsline {subsection}{\numberline {2.2.1}EPDnew now annotates (some of) your mushrooms and vegetables}{27}{subsection.2.2.1} -\contentsline {subsection}{\numberline {2.2.2}Increased mapping precision in human}{28}{subsection.2.2.2} -\contentsline {subsection}{\numberline {2.2.3}Integration of EPDnew with other resources}{28}{subsection.2.2.3} -\contentsline {subsection}{\numberline {2.2.4}Conclusions}{29}{subsection.2.2.4} -\contentsline {subsection}{\numberline {2.2.5}Methods}{29}{subsection.2.2.5} -\contentsline {subsubsection}{Motif occurrence profiles}{29}{subsection.2.2.5} -\contentsline {chapter}{\numberline {3}ENCODE peaks analysis}{31}{chapter.3} -\contentsline {chapter}{ENCODE peaks analysis}{31}{chapter.3} -\contentsline {section}{\numberline {3.1}Data}{31}{section.3.1} -\contentsline {section}{\numberline {3.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{33}{section.3.2} -\contentsline {subsection}{\numberline {3.2.1}Data realignment}{34}{subsection.3.2.1} -\contentsline {section}{\numberline {3.3}Nucleosome organization around transcription factor binding sites}{35}{section.3.3} -\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{37}{section.3.4} -\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{41}{section.3.5} -\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{45}{section.3.6} -\contentsline {section}{\numberline {3.7}Discussion}{48}{section.3.7} -\contentsline {section}{\numberline {3.8}Methods}{48}{section.3.8} -\contentsline {subsection}{\numberline {3.8.1}Data and data processing}{48}{subsection.3.8.1} -\contentsline {subsection}{\numberline {3.8.2}Classification of MNase patterns}{49}{subsection.3.8.2} -\contentsline {subsection}{\numberline {3.8.3}Quantifying nucleosome array intensity from classification results}{50}{subsection.3.8.3} -\contentsline {subsection}{\numberline {3.8.4}Peak colocalization}{51}{subsection.3.8.4} -\contentsline {subsection}{\numberline {3.8.5}NDR detection}{52}{subsection.3.8.5} -\contentsline {subsection}{\numberline {3.8.6}CTCF and JunD interactors}{54}{subsection.3.8.6} -\contentsline {subsection}{\numberline {3.8.7}EBF1 and nucleosome}{55}{subsection.3.8.7} -\contentsline {chapter}{\numberline {4}SPar-K}{57}{chapter.4} -\contentsline {section}{\numberline {4.1}Algorithm}{57}{section.4.1} -\contentsline {section}{\numberline {4.2}Implementation}{58}{section.4.2} -\contentsline {section}{\numberline {4.3}Benchmarking}{59}{section.4.3} -\contentsline {subsection}{\numberline {4.3.1}K-means}{59}{subsection.4.3.1} -\contentsline {subsection}{\numberline {4.3.2}ChIPPartitioning}{62}{subsection.4.3.2} -\contentsline {subsection}{\numberline {4.3.3}Data}{62}{subsection.4.3.3} -\contentsline {subsection}{\numberline {4.3.4}Performances}{63}{subsection.4.3.4} -\contentsline {section}{\numberline {4.4}Partition of DNase and MNase data}{63}{section.4.4} -\contentsline {section}{\numberline {4.5}Conclusions}{63}{section.4.5} -\contentsline {chapter}{\numberline {5}SMiLE-seq data analysis}{67}{chapter.5} -\contentsline {chapter}{SMiLE-seq data analysis}{67}{chapter.5} -\contentsline {section}{\numberline {5.1}Introduction}{67}{section.5.1} -\contentsline {section}{\numberline {5.2}Hidden Markov Model Motif discovery}{69}{section.5.2} -\contentsline {section}{\numberline {5.3}Binding motif evaluation}{70}{section.5.3} -\contentsline {section}{\numberline {5.4}Results}{71}{section.5.4} -\contentsline {section}{\numberline {5.5}Conclusions}{73}{section.5.5} -\contentsline {chapter}{\numberline {6}PWMScan}{75}{chapter.6} -\contentsline {section}{\numberline {6.1}Algorithms}{75}{section.6.1} -\contentsline {subsection}{\numberline {6.1.1}Scanner algorithm}{76}{subsection.6.1.1} -\contentsline {subsection}{\numberline {6.1.2}Matches enumeration and mapping}{76}{subsection.6.1.2} -\contentsline {section}{\numberline {6.2}PMWScan architecture}{77}{section.6.2} -\contentsline {section}{\numberline {6.3}Benchmark}{79}{section.6.3} -\contentsline {section}{\numberline {6.4}Conclusions}{81}{section.6.4} -\contentsline {chapter}{\numberline {7}Chromatin accessibility of monocytes}{83}{chapter.7} -\contentsline {section}{\numberline {7.1}Monitoring TF binding}{83}{section.7.1} -\contentsline {section}{\numberline {7.2}The advent of single cell DGF}{84}{section.7.2} -\contentsline {section}{\numberline {7.3}Open issues}{84}{section.7.3} -\contentsline {section}{\numberline {7.4}Data}{84}{section.7.4} -\contentsline {section}{\numberline {7.5}Identifying over-represented signals}{85}{section.7.5} -\contentsline {subsection}{\numberline {7.5.1}ChIPPartitioning algorithm}{85}{subsection.7.5.1} -\contentsline {subsection}{\numberline {7.5.2}EMSequence algorithm}{85}{subsection.7.5.2} -\contentsline {subsubsection}{without shift and flip}{87}{figure.caption.35} -\contentsline {subsubsection}{with shift and flip}{87}{equation.7.5.2} -\contentsline {subsection}{\numberline {7.5.3}EMJoint algorithm}{89}{subsection.7.5.3} -\contentsline {subsection}{\numberline {7.5.4}Data realignment}{90}{subsection.7.5.4} -\contentsline {section}{\numberline {7.6}Results}{90}{section.7.6} -\contentsline {subsection}{\numberline {7.6.1}Data processing}{90}{subsection.7.6.1} -\contentsline {subsection}{\numberline {7.6.2}Aligning the binding sites}{91}{subsection.7.6.2} -\contentsline {subsection}{\numberline {7.6.3}Exploring individual TF classes}{93}{subsection.7.6.3} -\contentsline {section}{\numberline {7.7}Discussions}{94}{section.7.7} -\contentsline {section}{\numberline {7.8}Perspectives}{94}{section.7.8} -\contentsline {section}{\numberline {7.9}Methods}{95}{section.7.9} -\contentsline {subsection}{\numberline {7.9.1}Data sources}{95}{subsection.7.9.1} -\contentsline {subsection}{\numberline {7.9.2}Data post-processing}{96}{subsection.7.9.2} -\contentsline {subsection}{\numberline {7.9.3}Model extension}{96}{subsection.7.9.3} -\contentsline {subsection}{\numberline {7.9.4}Extracting data assigned to a class}{97}{subsection.7.9.4} -\contentsline {subsection}{\numberline {7.9.5}Programs}{99}{subsection.7.9.5} -\contentsline {subsection}{\numberline {7.9.6}Fragment classes}{100}{subsection.7.9.6} -\contentsline {subsection}{\numberline {7.9.7}Simulated sequences}{101}{subsection.7.9.7} -\contentsline {subsection}{\numberline {7.9.8}Binding site prediction}{101}{subsection.7.9.8} -\contentsline {subsection}{\numberline {7.9.9}Realignment using JASPAR motifs}{101}{subsection.7.9.9} -\contentsline {subsection}{\numberline {7.9.10}Per TF sub-classes}{104}{subsection.7.9.10} -\contentsline {chapter}{\numberline {8}Discussion}{107}{chapter.8} -\contentsline {chapter}{Discussions}{107}{chapter.8} +\contentsline {chapter}{\numberline {2}Laboratory resources}{25}{chapter.2} +\contentsline {chapter}{Laboratory resources}{25}{chapter.2} +\contentsline {section}{\numberline {2.1}Mass Genome Annotation repository}{25}{section.2.1} +\contentsline {subsection}{\numberline {2.1.1}MGA content and organization}{26}{subsection.2.1.1} +\contentsline {subsection}{\numberline {2.1.2}Conclusions}{27}{subsection.2.1.2} +\contentsline {section}{\numberline {2.2}Eukaryotic Promoter Database}{28}{section.2.2} +\contentsline {subsection}{\numberline {2.2.1}EPDnew now annotates (some of) your mushrooms and vegetables}{29}{subsection.2.2.1} +\contentsline {subsection}{\numberline {2.2.2}Increased mapping precision in human}{30}{subsection.2.2.2} +\contentsline {subsection}{\numberline {2.2.3}Integration of EPDnew with other resources}{30}{subsection.2.2.3} +\contentsline {subsection}{\numberline {2.2.4}Conclusions}{31}{subsection.2.2.4} +\contentsline {subsection}{\numberline {2.2.5}Methods}{31}{subsection.2.2.5} +\contentsline {subsubsection}{Motif occurrence profiles}{31}{subsection.2.2.5} +\contentsline {chapter}{\numberline {3}ENCODE peaks analysis}{33}{chapter.3} +\contentsline {chapter}{ENCODE peaks analysis}{33}{chapter.3} +\contentsline {section}{\numberline {3.1}Data}{33}{section.3.1} +\contentsline {section}{\numberline {3.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{35}{section.3.2} +\contentsline {subsection}{\numberline {3.2.1}Data realignment}{36}{subsection.3.2.1} +\contentsline {section}{\numberline {3.3}Nucleosome organization around transcription factor binding sites}{37}{section.3.3} +\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{39}{section.3.4} +\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{43}{section.3.5} +\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{47}{section.3.6} +\contentsline {section}{\numberline {3.7}Discussion}{50}{section.3.7} +\contentsline {section}{\numberline {3.8}Methods}{50}{section.3.8} +\contentsline {subsection}{\numberline {3.8.1}Data and data processing}{50}{subsection.3.8.1} +\contentsline {subsection}{\numberline {3.8.2}Classification of MNase patterns}{51}{subsection.3.8.2} +\contentsline {subsection}{\numberline {3.8.3}Quantifying nucleosome array intensity from classification results}{52}{subsection.3.8.3} +\contentsline {subsection}{\numberline {3.8.4}Peak colocalization}{53}{subsection.3.8.4} +\contentsline {subsection}{\numberline {3.8.5}NDR detection}{54}{subsection.3.8.5} +\contentsline {subsection}{\numberline {3.8.6}CTCF and JunD interactors}{56}{subsection.3.8.6} +\contentsline {subsection}{\numberline {3.8.7}EBF1 and nucleosome}{57}{subsection.3.8.7} +\contentsline {chapter}{\numberline {4}SPar-K}{59}{chapter.4} +\contentsline {section}{\numberline {4.1}Algorithm}{59}{section.4.1} +\contentsline {section}{\numberline {4.2}Implementation}{60}{section.4.2} +\contentsline {section}{\numberline {4.3}Benchmarking}{61}{section.4.3} +\contentsline {subsection}{\numberline {4.3.1}K-means}{61}{subsection.4.3.1} +\contentsline {subsection}{\numberline {4.3.2}ChIPPartitioning}{64}{subsection.4.3.2} +\contentsline {subsection}{\numberline {4.3.3}Data}{64}{subsection.4.3.3} +\contentsline {subsection}{\numberline {4.3.4}Performances}{65}{subsection.4.3.4} +\contentsline {section}{\numberline {4.4}Partition of DNase and MNase data}{65}{section.4.4} +\contentsline {section}{\numberline {4.5}Conclusions}{65}{section.4.5} +\contentsline {chapter}{\numberline {5}SMiLE-seq data analysis}{69}{chapter.5} +\contentsline {chapter}{SMiLE-seq data analysis}{69}{chapter.5} +\contentsline {section}{\numberline {5.1}Introduction}{69}{section.5.1} +\contentsline {section}{\numberline {5.2}Hidden Markov Model Motif discovery}{71}{section.5.2} +\contentsline {section}{\numberline {5.3}Binding motif evaluation}{72}{section.5.3} +\contentsline {section}{\numberline {5.4}Results}{73}{section.5.4} +\contentsline {section}{\numberline {5.5}Conclusions}{75}{section.5.5} +\contentsline {chapter}{\numberline {6}PWMScan}{77}{chapter.6} +\contentsline {section}{\numberline {6.1}Algorithms}{77}{section.6.1} +\contentsline {subsection}{\numberline {6.1.1}Scanner algorithm}{78}{subsection.6.1.1} +\contentsline {subsection}{\numberline {6.1.2}Matches enumeration and mapping}{78}{subsection.6.1.2} +\contentsline {section}{\numberline {6.2}PMWScan architecture}{79}{section.6.2} +\contentsline {section}{\numberline {6.3}Benchmark}{81}{section.6.3} +\contentsline {section}{\numberline {6.4}Conclusions}{83}{section.6.4} +\contentsline {chapter}{\numberline {7}Chromatin accessibility of monocytes}{85}{chapter.7} +\contentsline {section}{\numberline {7.1}Monitoring TF binding}{85}{section.7.1} +\contentsline {section}{\numberline {7.2}The advent of single cell DGF}{86}{section.7.2} +\contentsline {section}{\numberline {7.3}Open issues}{86}{section.7.3} +\contentsline {section}{\numberline {7.4}Data}{86}{section.7.4} +\contentsline {section}{\numberline {7.5}Identifying over-represented signals}{87}{section.7.5} +\contentsline {subsection}{\numberline {7.5.1}ChIPPartitioning algorithm}{87}{subsection.7.5.1} +\contentsline {subsection}{\numberline {7.5.2}EMSequence algorithm}{87}{subsection.7.5.2} +\contentsline {subsubsection}{without shift and flip}{89}{figure.caption.35} +\contentsline {subsubsection}{with shift and flip}{89}{equation.7.5.2} +\contentsline {subsection}{\numberline {7.5.3}EMJoint algorithm}{91}{subsection.7.5.3} +\contentsline {subsection}{\numberline {7.5.4}Data realignment}{92}{subsection.7.5.4} +\contentsline {subsection}{\numberline {7.5.5}Soft aggregation plots}{92}{subsection.7.5.5} +\contentsline {section}{\numberline {7.6}Data processing}{93}{section.7.6} +\contentsline {section}{\numberline {7.7}Results}{93}{section.7.7} +\contentsline {subsection}{\numberline {7.7.1}Aligning the binding sites}{93}{subsection.7.7.1} +\contentsline {subsection}{\numberline {7.7.2}Exploring individual TF classes}{95}{subsection.7.7.2} +\contentsline {section}{\numberline {7.8}Discussions}{97}{section.7.8} +\contentsline {section}{\numberline {7.9}Perspectives}{97}{section.7.9} +\contentsline {section}{\numberline {7.10}Methods}{98}{section.7.10} +\contentsline {subsection}{\numberline {7.10.1}Code availability}{98}{subsection.7.10.1} +\contentsline {subsection}{\numberline {7.10.2}Data sources}{99}{subsection.7.10.2} +\contentsline {subsection}{\numberline {7.10.3}Data post-processing}{99}{subsection.7.10.3} +\contentsline {subsection}{\numberline {7.10.4}Model extension}{99}{subsection.7.10.4} +\contentsline {subsection}{\numberline {7.10.5}Extracting data assigned to a class}{100}{subsection.7.10.5} +\contentsline {subsection}{\numberline {7.10.6}Programs}{103}{subsection.7.10.6} +\contentsline {subsection}{\numberline {7.10.7}Fragment classes}{104}{subsection.7.10.7} +\contentsline {subsection}{\numberline {7.10.8}Simulated sequences}{105}{subsection.7.10.8} +\contentsline {subsection}{\numberline {7.10.9}Binding site prediction}{105}{subsection.7.10.9} +\contentsline {subsection}{\numberline {7.10.10}Realignment using JASPAR motifs}{105}{subsection.7.10.10} +\contentsline {subsection}{\numberline {7.10.11}Per TF sub-classes}{108}{subsection.7.10.11} +\contentsline {chapter}{\numberline {8}Discussion}{111}{chapter.8} +\contentsline {chapter}{Discussions}{111}{chapter.8} \vspace {\normalbaselineskip } -\contentsline {chapter}{\numberline {A}Supplementary material}{111}{appendix.A} -\contentsline {section}{\numberline {A.1}ENCODE peaks analysis supplementary material}{112}{section.A.1} -\contentsline {section}{\numberline {A.2}SPar-K supplementary material}{122}{section.A.2} -\contentsline {section}{\numberline {A.3}SMiLE-seq supplementary material}{135}{section.A.3} -\contentsline {section}{\numberline {A.4}Chromatin accessibility of monocytes supplementary material}{135}{section.A.4} -\contentsline {subsection}{\numberline {A.4.1}Fragment size analysis}{135}{subsection.A.4.1} -\contentsline {subsection}{\numberline {A.4.2}Measuring open chromatin and nucleosome occupancy}{136}{subsection.A.4.2} -\contentsline {subsection}{\numberline {A.4.3}Evaluation of EMSequence and ChIPPartitioning}{139}{subsection.A.4.3} -\contentsline {subsubsection}{EMSequence}{139}{subsection.A.4.3} -\contentsline {subsubsection}{ChIPPartitioning}{142}{figure.caption.56} -\contentsline {subsection}{\numberline {A.4.4}Other supplementary figures}{145}{subsection.A.4.4} -\contentsline {chapter}{Bibliography}{149}{section*.64} -\contentsline {chapter}{Bibliography}{161}{appendix*.65} -\contentsline {chapter}{Curriculum Vitae}{163}{section*.66} +\contentsline {chapter}{\numberline {A}Supplementary material}{115}{appendix.A} +\contentsline {section}{\numberline {A.1}ENCODE peaks analysis supplementary material}{116}{section.A.1} +\contentsline {section}{\numberline {A.2}SPar-K supplementary material}{126}{section.A.2} +\contentsline {section}{\numberline {A.3}SMiLE-seq supplementary material}{139}{section.A.3} +\contentsline {section}{\numberline {A.4}Chromatin accessibility of monocytes supplementary material}{139}{section.A.4} +\contentsline {subsection}{\numberline {A.4.1}Fragment size analysis}{139}{subsection.A.4.1} +\contentsline {subsection}{\numberline {A.4.2}Measuring open chromatin and nucleosome occupancy}{140}{subsection.A.4.2} +\contentsline {subsection}{\numberline {A.4.3}Evaluation of EMSequence and ChIPPartitioning}{143}{subsection.A.4.3} +\contentsline {subsubsection}{EMSequence}{143}{subsection.A.4.3} +\contentsline {subsubsection}{ChIPPartitioning}{146}{figure.caption.56} +\contentsline {subsection}{\numberline {A.4.4}Other supplementary figures}{149}{subsection.A.4.4} +\contentsline {chapter}{Bibliography}{153}{section*.64} +\contentsline {chapter}{Bibliography}{165}{appendix*.65} +\contentsline {chapter}{Curriculum Vitae}{167}{section*.66} diff --git a/tail/appendix.aux b/tail/appendix.aux index 9920461..f423142 100644 --- a/tail/appendix.aux +++ b/tail/appendix.aux @@ -1,148 +1,148 @@ \relax \providecommand\hyper@newdestlabel[2]{} -\@writefile{toc}{\contentsline {chapter}{\numberline {A}Supplementary material}{111}{appendix.A}} +\@writefile{toc}{\contentsline {chapter}{\numberline {A}Supplementary material}{115}{appendix.A}} \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} \@writefile{loa}{\addvspace {10\p@ }} -\@writefile{toc}{\contentsline {section}{\numberline {A.1}ENCODE peaks analysis supplementary material}{112}{section.A.1}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.1}{\ignorespaces \textbf {Chromatine architectures around CTCF binding sites} discovered using ChIPPartitioning. 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The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.40}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.3}{\ignorespaces \textbf {Chromatine architectures around cFOS binding sites} discovered using ChIPPartitioning. 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The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.42}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.5}{\ignorespaces \textbf {Chromatine architectures around BRCA1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{116}{figure.caption.43}} -\newlabel{suppl_encode_peaks_em_brca1}{{A.5}{116}{\textbf {Chromatine architectures around BRCA1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.43}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.6}{\ignorespaces \textbf {Nucleosome occupancy around CTCF peaks } measured by MNase-seq, in bins of 10bp. The nucleosome depleted region is displayed in blue.\relax }}{117}{figure.caption.44}} -\newlabel{suppl_encode_peaks_ctcf_ndr}{{A.6}{117}{\textbf {Nucleosome occupancy around CTCF peaks } measured by MNase-seq, in bins of 10bp. The nucleosome depleted region is displayed in blue.\relax }{figure.caption.44}{}} +\@writefile{toc}{\contentsline {section}{\numberline {A.1}ENCODE peaks analysis supplementary material}{116}{section.A.1}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.1}{\ignorespaces \textbf {Chromatine architectures around CTCF binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{116}{figure.caption.39}} +\newlabel{suppl_encode_peaks_em_ctcf}{{A.1}{116}{\textbf {Chromatine architectures around CTCF binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.39}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.2}{\ignorespaces \textbf {Chromatine architectures around NRF1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{117}{figure.caption.40}} +\newlabel{suppl_encode_peaks_em_nrf1}{{A.2}{117}{\textbf {Chromatine architectures around NRF1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.40}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.3}{\ignorespaces \textbf {Chromatine architectures around cFOS binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{118}{figure.caption.41}} +\newlabel{suppl_encode_peaks_em_cfos}{{A.3}{118}{\textbf {Chromatine architectures around cFOS binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.41}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.4}{\ignorespaces \textbf {Chromatine architectures around max binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{119}{figure.caption.42}} +\newlabel{suppl_encode_peaks_em_max}{{A.4}{119}{\textbf {Chromatine architectures around max binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.42}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.5}{\ignorespaces \textbf {Chromatine architectures around BRCA1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }}{120}{figure.caption.43}} +\newlabel{suppl_encode_peaks_em_brca1}{{A.5}{120}{\textbf {Chromatine architectures around BRCA1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.\relax }{figure.caption.43}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.6}{\ignorespaces \textbf {Nucleosome occupancy around CTCF peaks } measured by MNase-seq, in bins of 10bp. The nucleosome depleted region is displayed in blue.\relax }}{121}{figure.caption.44}} +\newlabel{suppl_encode_peaks_ctcf_ndr}{{A.6}{121}{\textbf {Nucleosome occupancy around CTCF peaks } measured by MNase-seq, in bins of 10bp. The nucleosome depleted region is displayed in blue.\relax }{figure.caption.44}{}} \citation{khan_jaspar_2018} \citation{khan_jaspar_2018} -\@writefile{lof}{\contentsline {figure}{\numberline {A.7}{\ignorespaces \textbf {JunD motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The JunD and cFos dataset ORs are too high to be represented in this plot. \textbf {B} Density of JunD motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif.\relax }}{118}{figure.caption.45}} -\newlabel{suppl_encode_peaks_jund_association}{{A.7}{118}{\textbf {JunD motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The JunD and cFos dataset ORs are too high to be represented in this plot. \textbf {B} Density of JunD motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif.\relax }{figure.caption.45}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.8}{\ignorespaces \textbf {EBF1 binding sites} around the dyad of nucleosomes having an occupied EBF1 motif within 100bp (in red) and of all nucleosomes (in blue). The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.\relax }}{119}{figure.caption.46}} -\newlabel{suppl_encode_peaks_ebf1_nucl}{{A.8}{119}{\textbf {EBF1 binding sites} around the dyad of nucleosomes having an occupied EBF1 motif within 100bp (in red) and of all nucleosomes (in blue). 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This function can access and modify all variables declared in distanceFast().\relax }}{132}{algocf.9}} -\newlabel{algo_seed_random}{{10}{133}{SPar-K supplementary material}{algocfline.10}{}} -\@writefile{loa}{\contentsline {algocf}{\numberline {10}{\ignorespaces Random seeding algorithm\relax }}{133}{algocf.10}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.7}{\ignorespaces \textbf {JunD motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The JunD and cFos dataset ORs are too high to be represented in this plot. \textbf {B} Density of JunD motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif.\relax }}{122}{figure.caption.45}} +\newlabel{suppl_encode_peaks_jund_association}{{A.7}{122}{\textbf {JunD motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf {A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The JunD and cFos dataset ORs are too high to be represented in this plot. \textbf {B} Density of JunD motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf {C} Same as in (B) but for TF binding sites that does not have their own motif.\relax }{figure.caption.45}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.8}{\ignorespaces \textbf {EBF1 binding sites} around the dyad of nucleosomes having an occupied EBF1 motif within 100bp (in red) and of all nucleosomes (in blue). The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.\relax }}{123}{figure.caption.46}} +\newlabel{suppl_encode_peaks_ebf1_nucl}{{A.8}{123}{\textbf {EBF1 binding sites} around the dyad of nucleosomes having an occupied EBF1 motif within 100bp (in red) and of all nucleosomes (in blue). 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This function can access and modify variables in distanceFast().\relax }}{130}{algocf.6}} +\@writefile{loa}{\contentsline {algocf}{\numberline {7}{\ignorespaces A routine of distanceFast() computing all distances with $X$ having a shift of 0. This function can access and modify all variables declared in distanceFast().\relax }}{132}{algocf.7}} +\@writefile{loa}{\contentsline {algocf}{\numberline {8}{\ignorespaces A routine of distanceFast() computing all distances with $Y$ having a shift of 0. This function is can access and modify all variables declared in distanceFast().\relax }}{134}{algocf.8}} +\@writefile{loa}{\contentsline {algocf}{\numberline {9}{\ignorespaces A routine of distanceFast() computing all remaining distances between $X$ and $Y$. This function can access and modify all variables declared in distanceFast().\relax }}{136}{algocf.9}} +\newlabel{algo_seed_random}{{10}{137}{SPar-K supplementary material}{algocfline.10}{}} +\@writefile{loa}{\contentsline {algocf}{\numberline {10}{\ignorespaces Random seeding algorithm\relax }}{137}{algocf.10}} \citation{jolma_dna-binding_2013} \citation{jolma_dna-binding_2013} -\newlabel{algo_seed_kmeans++}{{11}{134}{SPar-K supplementary material}{algocfline.11}{}} -\@writefile{loa}{\contentsline {algocf}{\numberline {11}{\ignorespaces Kmeans++ seeding algorithm.\relax }}{134}{algocf.11}} +\newlabel{algo_seed_kmeans++}{{11}{138}{SPar-K supplementary material}{algocfline.11}{}} +\@writefile{loa}{\contentsline {algocf}{\numberline {11}{\ignorespaces Kmeans++ seeding algorithm.\relax }}{138}{algocf.11}} \citation{buenrostro_transposition_2013} \citation{buenrostro_transposition_2013} -\@writefile{toc}{\contentsline {section}{\numberline {A.3}SMiLE-seq supplementary material}{135}{section.A.3}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.11}{\ignorespaces \textbf {Predictive power of SMiLE-seq :} \textbf {A} binding models were derived de novo from HT-SELEX 1st cycle data using the HMM discovery method (labelled HT-SELEX cycle 1 HMM) and their performances were assessed using the AUC-ROC. AUC-ROC values for the corresponding TF models derived from SMiLe-seq data (labelled SMiLE-seq) and reported by Jolma and colleagues (labelled HT-SELEX reported matrices, \cite {jolma_dna-binding_2013}) are also displayed. \textbf {B} the predictive performances of CEBPb, CTCF and TCF7 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.\relax }}{135}{figure.caption.49}} -\newlabel{suppl_smileseq_auc_2}{{A.11}{135}{\textbf {Predictive power of SMiLE-seq :} \textbf {A} binding models were derived de novo from HT-SELEX 1st cycle data using the HMM discovery method (labelled HT-SELEX cycle 1 HMM) and their performances were assessed using the AUC-ROC. AUC-ROC values for the corresponding TF models derived from SMiLe-seq data (labelled SMiLE-seq) and reported by Jolma and colleagues (labelled HT-SELEX reported matrices, \cite {jolma_dna-binding_2013}) are also displayed. \textbf {B} the predictive performances of CEBPb, CTCF and TCF7 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.\relax }{figure.caption.49}{}} -\@writefile{toc}{\contentsline {section}{\numberline {A.4}Chromatin accessibility of monocytes supplementary material}{135}{section.A.4}} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.1}Fragment size analysis}{135}{subsection.A.4.1}} -\newlabel{suppl_atac_seq_fragment_size}{{A.4.1}{135}{Fragment size analysis}{subsection.A.4.1}{}} +\@writefile{toc}{\contentsline {section}{\numberline {A.3}SMiLE-seq supplementary material}{139}{section.A.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.11}{\ignorespaces \textbf {Predictive power of SMiLE-seq :} \textbf {A} binding models were derived de novo from HT-SELEX 1st cycle data using the HMM discovery method (labelled HT-SELEX cycle 1 HMM) and their performances were assessed using the AUC-ROC. AUC-ROC values for the corresponding TF models derived from SMiLe-seq data (labelled SMiLE-seq) and reported by Jolma and colleagues (labelled HT-SELEX reported matrices, \cite {jolma_dna-binding_2013}) are also displayed. \textbf {B} the predictive performances of CEBPb, CTCF and TCF7 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.\relax }}{139}{figure.caption.49}} +\newlabel{suppl_smileseq_auc_2}{{A.11}{139}{\textbf {Predictive power of SMiLE-seq :} \textbf {A} binding models were derived de novo from HT-SELEX 1st cycle data using the HMM discovery method (labelled HT-SELEX cycle 1 HMM) and their performances were assessed using the AUC-ROC. AUC-ROC values for the corresponding TF models derived from SMiLe-seq data (labelled SMiLE-seq) and reported by Jolma and colleagues (labelled HT-SELEX reported matrices, \cite {jolma_dna-binding_2013}) are also displayed. \textbf {B} the predictive performances of CEBPb, CTCF and TCF7 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.\relax }{figure.caption.49}{}} +\@writefile{toc}{\contentsline {section}{\numberline {A.4}Chromatin accessibility of monocytes supplementary material}{139}{section.A.4}} +\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.1}Fragment size analysis}{139}{subsection.A.4.1}} +\newlabel{suppl_atac_seq_fragment_size}{{A.4.1}{139}{Fragment size analysis}{subsection.A.4.1}{}} \citation{adey_rapid_2010} \citation{buenrostro_transposition_2013,li_identification_2019} -\@writefile{lof}{\contentsline {figure}{\numberline {A.12}{\ignorespaces \textbf {Fragment size analysis} \textbf {A} sequenced fragment size density. The three peaks, from left to right, indicate i) the open chromatin fragments, ii) the mono-nucleosome fragments and iii) the di-nucleosome fragments. A mixture model composed of three Gaussian distributions was fitted to the data in order to model the fragment sizes. The class fit is shown as dashed lines : open chromatin (red), mono-nucleosomes (blue) and di-nucleosomes (green). The violet dashed line show the sum of the three classes. \textbf {B :} probability that a fragment belongs to any of the three fragment classes, given its size i) open chromatin (red), ii) mono-nucleosomes (blue) and iii) di-nucleosomes (green). The vertical dashed lines indicates, for each class, the size limit at which the class probability drops below 0.9. With these limites, the class spans are i) 30-84bp for open chromatin (red), ii) 133-266bp for mono-nucleosomes (blue) and iii) 341-500bp for di-nucleosomes (green). The upper limit of the di-nucleosome class was arbitrarily set to 500bp. \textbf {C :} final fragment classes. Each fragments which size overlapped the size range spanned by a class, was assigned to that class. This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.\relax }}{136}{figure.caption.50}} -\newlabel{atac_seq_fragment_size}{{A.12}{136}{\textbf {Fragment size analysis} \textbf {A} sequenced fragment size density. The three peaks, from left to right, indicate i) the open chromatin fragments, ii) the mono-nucleosome fragments and iii) the di-nucleosome fragments. A mixture model composed of three Gaussian distributions was fitted to the data in order to model the fragment sizes. The class fit is shown as dashed lines : open chromatin (red), mono-nucleosomes (blue) and di-nucleosomes (green). The violet dashed line show the sum of the three classes. \textbf {B :} probability that a fragment belongs to any of the three fragment classes, given its size i) open chromatin (red), ii) mono-nucleosomes (blue) and iii) di-nucleosomes (green). The vertical dashed lines indicates, for each class, the size limit at which the class probability drops below 0.9. With these limites, the class spans are i) 30-84bp for open chromatin (red), ii) 133-266bp for mono-nucleosomes (blue) and iii) 341-500bp for di-nucleosomes (green). The upper limit of the di-nucleosome class was arbitrarily set to 500bp. \textbf {C :} final fragment classes. Each fragments which size overlapped the size range spanned by a class, was assigned to that class. This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.\relax }{figure.caption.50}{}} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.2}Measuring open chromatin and nucleosome occupancy}{136}{subsection.A.4.2}} -\newlabel{suppl_atac_seq_measuring_signal}{{A.4.2}{136}{Measuring open chromatin and nucleosome occupancy}{subsection.A.4.2}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.12}{\ignorespaces \textbf {Fragment size analysis} \textbf {A} sequenced fragment size density. The three peaks, from left to right, indicate i) the open chromatin fragments, ii) the mono-nucleosome fragments and iii) the di-nucleosome fragments. A mixture model composed of three Gaussian distributions was fitted to the data in order to model the fragment sizes. The class fit is shown as dashed lines : open chromatin (red), mono-nucleosomes (blue) and di-nucleosomes (green). The violet dashed line show the sum of the three classes. \textbf {B :} probability that a fragment belongs to any of the three fragment classes, given its size i) open chromatin (red), ii) mono-nucleosomes (blue) and iii) di-nucleosomes (green). The vertical dashed lines indicates, for each class, the size limit at which the class probability drops below 0.9. With these limites, the class spans are i) 30-84bp for open chromatin (red), ii) 133-266bp for mono-nucleosomes (blue) and iii) 341-500bp for di-nucleosomes (green). The upper limit of the di-nucleosome class was arbitrarily set to 500bp. \textbf {C :} final fragment classes. Each fragments which size overlapped the size range spanned by a class, was assigned to that class. This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.\relax }}{140}{figure.caption.50}} +\newlabel{atac_seq_fragment_size}{{A.12}{140}{\textbf {Fragment size analysis} \textbf {A} sequenced fragment size density. The three peaks, from left to right, indicate i) the open chromatin fragments, ii) the mono-nucleosome fragments and iii) the di-nucleosome fragments. A mixture model composed of three Gaussian distributions was fitted to the data in order to model the fragment sizes. The class fit is shown as dashed lines : open chromatin (red), mono-nucleosomes (blue) and di-nucleosomes (green). The violet dashed line show the sum of the three classes. \textbf {B :} probability that a fragment belongs to any of the three fragment classes, given its size i) open chromatin (red), ii) mono-nucleosomes (blue) and iii) di-nucleosomes (green). The vertical dashed lines indicates, for each class, the size limit at which the class probability drops below 0.9. With these limites, the class spans are i) 30-84bp for open chromatin (red), ii) 133-266bp for mono-nucleosomes (blue) and iii) 341-500bp for di-nucleosomes (green). The upper limit of the di-nucleosome class was arbitrarily set to 500bp. \textbf {C :} final fragment classes. Each fragments which size overlapped the size range spanned by a class, was assigned to that class. This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.\relax }{figure.caption.50}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.2}Measuring open chromatin and nucleosome occupancy}{140}{subsection.A.4.2}} +\newlabel{suppl_atac_seq_measuring_signal}{{A.4.2}{140}{Measuring open chromatin and nucleosome occupancy}{subsection.A.4.2}{}} \citation{neph_expansive_2012} \citation{fu_insulator_2008} \citation{neph_expansive_2012} -\@writefile{lof}{\contentsline {figure}{\numberline {A.13}{\ignorespaces \textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively. The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }}{137}{figure.caption.51}} -\newlabel{atac_seq_ctcf_all_data}{{A.13}{137}{\textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively.\\ The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }{figure.caption.51}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.14}{\ignorespaces \textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with one PWM per TF to predict their binding sites (see section \ref {atac_seq_method_pwmscan}). For each TF, the open chromatin accessibility was measured (red) as well as and the nucleosome occupancy (blue) around their predicted binding sites. For the chromatin accessibility, the corrected read edges were considered and for nucleosomes, the center of the fragments. The motif location is indicated by the dashed lines.\relax }}{138}{figure.caption.52}} -\newlabel{atac_seq_ctcf_sp1_myc_ebf1_footprint}{{A.14}{138}{\textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with one PWM per TF to predict their binding sites (see section \ref {atac_seq_method_pwmscan}). For each TF, the open chromatin accessibility was measured (red) as well as and the nucleosome occupancy (blue) around their predicted binding sites. For the chromatin accessibility, the corrected read edges were considered and for nucleosomes, the center of the fragments. The motif location is indicated by the dashed lines.\relax }{figure.caption.52}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.13}{\ignorespaces \textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively. The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }}{141}{figure.caption.51}} +\newlabel{atac_seq_ctcf_all_data}{{A.13}{141}{\textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively.\\ The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }{figure.caption.51}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.14}{\ignorespaces \textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with one PWM per TF to predict their binding sites (see section \ref {atac_seq_method_pwmscan}). For each TF, the open chromatin accessibility was measured (red) as well as and the nucleosome occupancy (blue) around their predicted binding sites. For the chromatin accessibility, the corrected read edges were considered and for nucleosomes, the center of the fragments. The motif location is indicated by the dashed lines.\relax }}{142}{figure.caption.52}} +\newlabel{atac_seq_ctcf_sp1_myc_ebf1_footprint}{{A.14}{142}{\textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with one PWM per TF to predict their binding sites (see section \ref {atac_seq_method_pwmscan}). For each TF, the open chromatin accessibility was measured (red) as well as and the nucleosome occupancy (blue) around their predicted binding sites. For the chromatin accessibility, the corrected read edges were considered and for nucleosomes, the center of the fragments. The motif location is indicated by the dashed lines.\relax }{figure.caption.52}{}} \citation{kundaje_ubiquitous_2012} \citation{ou_motifstack_2018} \citation{ou_motifstack_2018} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.3}Evaluation of EMSequence and ChIPPartitioning}{139}{subsection.A.4.3}} -\newlabel{suppl_eval_emseq_chippartitioning}{{A.4.3}{139}{Evaluation of EMSequence and ChIPPartitioning}{subsection.A.4.3}{}} -\@writefile{toc}{\contentsline {subsubsection}{EMSequence}{139}{subsection.A.4.3}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.15}{\ignorespaces \textbf {Simulated data motifs :} motifs used for the data generation (labeled "True motif") and the best scoring - based on the AUC - partition motifs (labeled "Found motif"). The partition with EMSequence was run such that it was searching for motifs of 11bp, slightly longer than those used for the data generation. "RC" stands for reverse complement. The motifs tree and alignment was build using the motifStack R package \citep {ou_motifstack_2018}.\relax }}{140}{figure.caption.53}} -\newlabel{suppl_atac_seq_emseq_best_motifs}{{A.15}{140}{\textbf {Simulated data motifs :} motifs used for the data generation (labeled "True motif") and the best scoring - based on the AUC - partition motifs (labeled "Found motif"). The partition with EMSequence was run such that it was searching for motifs of 11bp, slightly longer than those used for the data generation. "RC" stands for reverse complement. The motifs tree and alignment was build using the motifStack R package \citep {ou_motifstack_2018}.\relax }{figure.caption.53}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.3}Evaluation of EMSequence and ChIPPartitioning}{143}{subsection.A.4.3}} +\newlabel{suppl_eval_emseq_chippartitioning}{{A.4.3}{143}{Evaluation of EMSequence and ChIPPartitioning}{subsection.A.4.3}{}} +\@writefile{toc}{\contentsline {subsubsection}{EMSequence}{143}{subsection.A.4.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.15}{\ignorespaces \textbf {Simulated data motifs :} motifs used for the data generation (labeled "True motif") and the best scoring - based on the AUC - partition motifs (labeled "Found motif"). The partition with EMSequence was run such that it was searching for motifs of 11bp, slightly longer than those used for the data generation. "RC" stands for reverse complement. The motifs tree and alignment was build using the motifStack R package \citep {ou_motifstack_2018}.\relax }}{144}{figure.caption.53}} +\newlabel{suppl_atac_seq_emseq_best_motifs}{{A.15}{144}{\textbf {Simulated data motifs :} motifs used for the data generation (labeled "True motif") and the best scoring - based on the AUC - partition motifs (labeled "Found motif"). The partition with EMSequence was run such that it was searching for motifs of 11bp, slightly longer than those used for the data generation. "RC" stands for reverse complement. The motifs tree and alignment was build using the motifStack R package \citep {ou_motifstack_2018}.\relax }{figure.caption.53}{}} \citation{kent_blatblast-like_2002} \citation{chatr-aryamontri_biogrid_2017} \citation{castro-mondragon_rsat_2017} -\@writefile{lof}{\contentsline {figure}{\numberline {A.16}{\ignorespaces \textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }}{141}{figure.caption.54}} -\newlabel{suppl_atac_seq_emseq_auc_roc}{{A.16}{141}{\textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }{figure.caption.54}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.16}{\ignorespaces \textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }}{145}{figure.caption.54}} +\newlabel{suppl_atac_seq_emseq_auc_roc}{{A.16}{145}{\textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }{figure.caption.54}{}} \citation{nair_probabilistic_2014} -\@writefile{lof}{\contentsline {figure}{\numberline {A.17}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }}{142}{figure.caption.55}} -\newlabel{suppl_atac_seq_emseq_sp1_7class}{{A.17}{142}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }{figure.caption.55}{}} -\@writefile{toc}{\contentsline {subsubsection}{ChIPPartitioning}{142}{figure.caption.56}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.18}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. These sequences were classified by EMSequence to search for 10 different 30bp long motifs ($801 - 30 = 771$ of shifting freedom). The optimization was run for 20 iterations. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates head-to-tail arrangements of SP1 motifs.\relax }}{143}{figure.caption.56}} -\newlabel{suppl_atac_seq_emseq_sp1_10class}{{A.18}{143}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. These sequences were classified by EMSequence to search for 10 different 30bp long motifs ($801 - 30 = 771$ of shifting freedom). The optimization was run for 20 iterations. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates head-to-tail arrangements of SP1 motifs.\relax }{figure.caption.56}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.19}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{144}{figure.caption.57}} -\newlabel{suppl_atac_seq_emread_ctcf_noshift_flip}{{A.19}{144}{\textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.57}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.20}{\ignorespaces \textbf {Open chromatin classes around SP1 motifs :} EMRead was run without shifing (+/- 10bp) but with flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{145}{figure.caption.58}} -\newlabel{suppl_atac_seq_emread_sp1_noshift_flip}{{A.20}{145}{\textbf {Open chromatin classes around SP1 motifs :} EMRead was run without shifing (+/- 10bp) but with flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.58}{}} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.4}Other supplementary figures}{145}{subsection.A.4.4}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.23}{\ignorespaces \textbf {Extended sequence and chromatin models} found in monocytes regulatory regions. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{145}{figure.caption.61}} -\newlabel{suppl_atac_seq_23class}{{A.23}{145}{\textbf {Extended sequence and chromatin models} found in monocytes regulatory regions. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.61}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.21}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{146}{figure.caption.59}} -\newlabel{suppl_atac_seq_emread_ctcf_shift_flip}{{A.21}{146}{\textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.59}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.24}{\ignorespaces \textbf {PU.1 sub-classes} obtained by extracting PU.1 class data and subjecting them to a ChIPPartitioning classification into 2 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{146}{figure.caption.62}} -\newlabel{suppl_atac_seq_pu1_subclass}{{A.24}{146}{\textbf {PU.1 sub-classes} obtained by extracting PU.1 class data and subjecting them to a ChIPPartitioning classification into 2 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.62}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.22}{\ignorespaces \textbf {Open chromatin classes around SP1 motifs :} EMRead was run with shifing (+/- 10bp) flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{147}{figure.caption.60}} -\newlabel{suppl_atac_seq_emread_sp1_shift_flip}{{A.22}{147}{\textbf {Open chromatin classes around SP1 motifs :} EMRead was run with shifing (+/- 10bp) flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.60}{}} -\@writefile{lof}{\contentsline {figure}{\numberline {A.25}{\ignorespaces \textbf {AP1 sub-classes} obtained by extracting AP1 class data and subjecting them to a ChIPPartitioning classification into 3 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{147}{figure.caption.63}} -\newlabel{suppl_atac_seq_ap1_subclass}{{A.25}{147}{\textbf {AP1 sub-classes} obtained by extracting AP1 class data and subjecting them to a ChIPPartitioning classification into 3 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.63}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.17}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }}{146}{figure.caption.55}} +\newlabel{suppl_atac_seq_emseq_sp1_7class}{{A.17}{146}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }{figure.caption.55}{}} +\@writefile{toc}{\contentsline {subsubsection}{ChIPPartitioning}{146}{figure.caption.56}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.18}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. These sequences were classified by EMSequence to search for 10 different 30bp long motifs ($801 - 30 = 771$ of shifting freedom). The optimization was run for 20 iterations. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates head-to-tail arrangements of SP1 motifs.\relax }}{147}{figure.caption.56}} +\newlabel{suppl_atac_seq_emseq_sp1_10class}{{A.18}{147}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. These sequences were classified by EMSequence to search for 10 different 30bp long motifs ($801 - 30 = 771$ of shifting freedom). The optimization was run for 20 iterations. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates head-to-tail arrangements of SP1 motifs.\relax }{figure.caption.56}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.19}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{148}{figure.caption.57}} +\newlabel{suppl_atac_seq_emread_ctcf_noshift_flip}{{A.19}{148}{\textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.57}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.20}{\ignorespaces \textbf {Open chromatin classes around SP1 motifs :} EMRead was run without shifing (+/- 10bp) but with flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{149}{figure.caption.58}} +\newlabel{suppl_atac_seq_emread_sp1_noshift_flip}{{A.20}{149}{\textbf {Open chromatin classes around SP1 motifs :} EMRead was run without shifing (+/- 10bp) but with flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.58}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {A.4.4}Other supplementary figures}{149}{subsection.A.4.4}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.23}{\ignorespaces \textbf {Extended sequence and chromatin models} found in monocytes regulatory regions. Each read density and sequence pattern is a soft aggregation plot. The displayed logos correspond to the sequence class models found by EMSequence. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{149}{figure.caption.61}} +\newlabel{suppl_atac_seq_23class}{{A.23}{149}{\textbf {Extended sequence and chromatin models} found in monocytes regulatory regions. Each read density and sequence pattern is a soft aggregation plot. The displayed logos correspond to the sequence class models found by EMSequence. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.61}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.21}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{150}{figure.caption.59}} +\newlabel{suppl_atac_seq_emread_ctcf_shift_flip}{{A.21}{150}{\textbf {Open chromatin classes around CTCF motifs} found by ChIPPartitioning with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.59}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.24}{\ignorespaces \textbf {PU.1 sub-classes} obtained by extracting PU.1 class data and subjecting them to a ChIPPartitioning classification into 2 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{150}{figure.caption.62}} +\newlabel{suppl_atac_seq_pu1_subclass}{{A.24}{150}{\textbf {PU.1 sub-classes} obtained by extracting PU.1 class data and subjecting them to a ChIPPartitioning classification into 2 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.62}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.22}{\ignorespaces \textbf {Open chromatin classes around SP1 motifs :} EMRead was run with shifing (+/- 10bp) flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{151}{figure.caption.60}} +\newlabel{suppl_atac_seq_emread_sp1_shift_flip}{{A.22}{151}{\textbf {Open chromatin classes around SP1 motifs :} EMRead was run with shifing (+/- 10bp) flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.60}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {A.25}{\ignorespaces \textbf {AP1 sub-classes} obtained by extracting AP1 class data and subjecting them to a ChIPPartitioning classification into 3 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }}{151}{figure.caption.63}} +\newlabel{suppl_atac_seq_ap1_subclass}{{A.25}{151}{\textbf {AP1 sub-classes} obtained by extracting AP1 class data and subjecting them to a ChIPPartitioning classification into 3 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.\relax }{figure.caption.63}{}} \@setckpt{tail/appendix}{ -\setcounter{page}{148} +\setcounter{page}{152} \setcounter{equation}{0} \setcounter{enumi}{8} \setcounter{enumii}{0} \setcounter{enumiii}{0} \setcounter{enumiv}{0} \setcounter{footnote}{0} \setcounter{mpfootnote}{0} \setcounter{part}{0} \setcounter{chapter}{1} \setcounter{section}{4} \setcounter{subsection}{4} \setcounter{subsubsection}{0} \setcounter{paragraph}{0} \setcounter{subparagraph}{0} \setcounter{figure}{25} \setcounter{table}{0} \setcounter{NAT@ctr}{0} \setcounter{FBcaption@count}{0} \setcounter{ContinuedFloat}{0} \setcounter{KVtest}{0} \setcounter{subfigure}{0} \setcounter{subfigure@save}{0} \setcounter{lofdepth}{1} \setcounter{subtable}{0} \setcounter{subtable@save}{0} \setcounter{lotdepth}{1} \setcounter{lips@count}{0} \setcounter{lstnumber}{1} \setcounter{Item}{8} \setcounter{Hfootnote}{0} \setcounter{bookmark@seq@number}{0} \setcounter{AM@survey}{0} \setcounter{ttlp@side}{0} \setcounter{myparts}{0} \setcounter{parentequation}{0} \setcounter{AlgoLine}{23} \setcounter{algocfline}{11} \setcounter{algocfproc}{11} \setcounter{algocf}{11} \setcounter{float@type}{8} \setcounter{nlinenum}{0} \setcounter{lstlisting}{0} \setcounter{section@level}{0} } diff --git a/tail/appendix.tex b/tail/appendix.tex index 19db916..6f046a2 100644 --- a/tail/appendix.tex +++ b/tail/appendix.tex @@ -1,718 +1,718 @@ \appendix % \beginsupplement \chapter{Supplementary material} % ===================================== encode peaks supplemental ===================================== \section{ENCODE peaks analysis supplementary material} % \begin{figure}[H] % \begin{center} % \includegraphics[scale=0.25]{images/ch_encode_peaks/em_examples.png} % \captionof{figure}{\textbf{Nucleosome architectures around TF binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. Partitions for \textbf{A} CTCF, \textbf{B} NRF1, \textbf{C} FOS and \textbf{D} max are displayed. The first row always contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} % \label{suppl_encode_peaks_em_examples} % % \end{center} % \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/wgEncodeAwgTfbsUwGm12878CtcfUniPk_MNase_GM12878_allpeaks_EM_4class_15shift_flip.png} \captionof{figure}{\textbf{Chromatine architectures around CTCF binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} \label{suppl_encode_peaks_em_ctcf} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/wgEncodeAwgTfbsSydhGm12878Nrf1IggmusUniPk_MNase_GM12878_allpeaks_EM_4class_15shift_flip.png} \captionof{figure}{\textbf{Chromatine architectures around NRF1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} \label{suppl_encode_peaks_em_nrf1} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/wgEncodeAwgTfbsSydhGm12878CfosUniPk_MNase_GM12878_allpeaks_EM_4class_15shift_flip.png} \captionof{figure}{\textbf{Chromatine architectures around cFOS binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} \label{suppl_encode_peaks_em_cfos} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/wgEncodeAwgTfbsSydhGm12878MaxIggmusUniPk_MNase_GM12878_allpeaks_EM_4class_15shift_flip.png} \captionof{figure}{\textbf{Chromatine architectures around max binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} \label{suppl_encode_peaks_em_max} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/wgEncodeAwgTfbsSydhGm12878Brca1a300IggmusUniPk_MNase_GM12878_allpeaks_EM_4class_15shift_flip.png} \captionof{figure}{\textbf{Chromatine architectures around BRCA1 binding sites} discovered using ChIPPartitioning. The partition was done with respect to the MNase reads (red), +/- 1kb around the peaks, in bins of 10bp, that were allowed to be shifted and flipped. DNaseI (blue), TSS density (violet) and sequence conservation (green) were realigned according to MNase classification and overlaid. The y-axis scale represent the proportion of the highest signal for each chromatin pattern. The first row contains the aggregated signal over all sites. The number of binding sites (peaks) is indicated in parenthesis. The following rows contains the 4 classes discovered. Their overall probability is indicated atop of the class signal, on the right. The y-axis indicates the min/max signal for all densities.} \label{suppl_encode_peaks_em_brca1} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.8]{images/ch_encode_peaks/ctcf_ndr.png} \captionof{figure}{\textbf{Nucleosome occupancy around CTCF peaks } measured by MNase-seq, in bins of 10bp. The nucleosome depleted region is displayed in blue.} \label{suppl_encode_peaks_ctcf_ndr} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.4]{images/ch_encode_peaks/jund_motif_association.png} \captionof{figure}{\textbf{JunD motif association} measured around the binding sites of different TFs. For a each TF, its binding sites, +/- 500bp, were searched for the presence of i) the TF motif and ii) CTCF motif. For each TF, a 2x2 contingency table was created with the number of peaks having i) both motifs, ii) the TF motif only, iii) CTCF motif only and iv) no motif. \textbf{A} Odd ratio (OR) of the exact Fisher test performed on each TF contingency table. The ORs are displayed with their 95\% confidence interval (CI). ORs > 1 - that is, with 1 not part of the 95\%CI - are labeled in green and indicate an association of both motifs more frequent than expected by chance. ORs < 1 are labeled in red and indicate a repulsion of both motifs more frequence than expected by chance. The JunD and cFos dataset ORs are too high to be represented in this plot. \textbf{B} Density of JunD motif occurrence at the absolute distance of different TF binding sites (peak centers) which also have their own motif present (at distance 0). The rows were standardized and aggregated using the Euclidean distance. \textbf{C} Same as in (B) but for TF binding sites that does not have their own motif.} \label{suppl_encode_peaks_jund_association} \end{center} \end{figure} \begin{figure} \begin{center} \includegraphics[scale=0.4]{images/ch_encode_peaks/ebf1_haib_3.png} \captionof{figure}{\textbf{EBF1 binding sites} around the dyad of nucleosomes having an occupied EBF1 motif within 100bp (in red) and of all nucleosomes (in blue). The abrupt decrease of EBF1 motif frequency at +/- 100bp reflects the nucleosome selection process.} \label{suppl_encode_peaks_ebf1_nucl} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.5]{images/ch_encode_peaks/MA0154_3.png} \captionof{figure}{\textbf{EBF1 logo} from JASPAR binding model MA0154.3 \citep{khan_jaspar_2018}.} \label{suppl_encode_peaks_ebf1_logo} \end{center} \end{figure} \begin{figure} \begin{center} \includegraphics[scale=0.4]{images/ch_encode_peaks/ebf1_haib_2.png} \captionof{figure}{\textbf{EBF1 binding sites} chromatin features. \textbf{A} Chromatin accessibility around nucleosomes that have an EBF1 binding site within 100bp (red) and all nucleosomes (blue). \textbf{B} H3K4me2 deposition around nucleosomes that have an EBF1 binding site within 100bp (red) and all nucleosomes (blue). \textbf{C} Sequence conservation around nucleosomes that have an EBF1 binding site within 100bp (red) and all nucleosomes (blue).} \label{suppl_encode_peaks_ebf1_chrom} \end{center} \end{figure} % ======================================= SPar-K supplemental ======================================== \section{SPar-K supplementary material} \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{void SPar-K}% \begin{algorithm}[H] \label{algo_spark} \Fn{\Function{R, K, S, I}} { \KwData{$R$ a 2D matrix of numericals of dimension $N \times L$; $K$ the number clusters; $S$ the shifting allowed; $I$ the maximum number of iterations.} \KwResult{5 vectors of length $N$ with the cluster labels, the data shift values, the reference shift values, the data flip values and the distances to the cluster references.} $CLUSTER =$ vector of 0 of size $N$ \; $SHIFT\_DAT =$ vector of 0 of size $N$ \; $SHIFT\_REF =$ vector of 0 of size $N$ \; $FLIP\_DAT =$ vector of 0 of size $N$ \; $DISTANCE =$ vector of 0 of size $N$ \; \If{smoothing} { smoothOutliers($R$) \; } $REF = $ a matrix of $K$ rows and $L$ columns\; select $K$ rows of $R$ and copy them in $REF$ using seedingRandom($K$, $R$) or seedingKmeans++($K$, $R$) \; $n\_iter = 1$\; $converged = false$\; \While{$n\_iter != I$ or not $converged$} { \For{$i=0$ to $N-1$} { $D =$ a vector 0 of size $K$ \; $S\_REF =$ a vector 0 of size $K$ \; $S\_DAT =$ a vector 0 of size $K$ \; $F\_DAT =$ a vector 0 of size $K$ \; \For{$k=0$ to $K-1$} { $D_{k},S\_REF_{k},S\_DAT_{k}, F\_DAT_{k} =$ distanceFast($REF_{k,}$, $R{i,}$, $S$) \; } $j = $ index of minimum value in $REF$\; $CLUSTER_{i} = D_{j}$ \; $SHIFT\_REF_{i} = S\_REF_{j}$ \; $SHIFT\_DAT_{i} = S\_DAT_{j}$ \; $FLIP\_DAT_{i} = F\_DAT_{j}$ \; $DISTANCE\_{i} = D_{j}$ \; } $REF =$ computeClusterReferences($R$, $CLUSTER$, $SHIFT\_REF$, $SHIFT\_DAT$, $FLIP\_DAT$) \; \If{$n\_iter > 1$ and at least one value of $CLUSTER$ changed since last iteration} { $converged = false$ \; } \Else { $converged = true$ \; } $n\_iter = n\_iter + 1$ \; } \Return{$CLUSTER, SHIFT\_REF, SHIFT\_DAT, FLIP, DISTANCE$} } \caption{SPar-K algorithm.} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{MATRIX smoothOutliers}% \begin{algorithm}[H] \label{algo_smooth_outliers} \Fn{\Function{MATRIX}} { \KwData{$MATRIX$ a 2D matrix of numericals of dimensions $N \times L$.} \KwResult{a 2D matrix of numericals of dimensions $N \times L$. with outlier smoothed.} \ForEach{$ROW$ in MATRIX} { $m$ = mean of $ROW$ \; $s$ = standard deviation of $ROW$ \; $lower$ = $m$ - 3*$s$ \; $upper$ = $m$ + 3*$s$ \; \ForEach{$value$ in $ROW$} { \If{$value < lower$ or $value > upper$} { \If{$value$ has a left neighbor $l$ and a right neighbor $r$} { $value$ = ($l$ + $r$) / 2 \; } \ElseIf{$value$ has two left neighbors $l1$ and $l2$} { $value$ = ($l1$ + $l2$) / 2 \; } \ElseIf{$value$ has two right neighbors $r1$ and $r2$} { $value$ = ($r1$ + $r2$) / 2 \; } } } } \Return{$MATRIX$} } \caption{Smooth the data matrix by removing outliers.} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{d,s\_xf,s\_y,f\_y distanceFast}% \begin{algorithm}[H] \label{algo_distance_fast} \Fn{\Function{X,Y,S}} { \KwData{$X$ and $Y$ two vectors of size $L$ and $S$ the allowed shifting} \KwResult{the distance between $X$ and $Y$, the shift of $X$ and $Y$ and whether $Y$ was flipped in the alignment.} \tcc{initialize all variables and data structures} initialize() \; \For{$i=0$ to $n-1$} { $SUM\_X_0 \pluseq X_i $ \; $SUM\_X2_0 \pluseq X_i^2$ \; $SUM\_Y_0 \pluseq Y_i $ \; $SUM\_Y2_0 \pluseq Y_i^2$ \; } $i = n$ \; \For{$s=1$ to $s=S-1$ } { $SUM\_X_{s} = SUM\_X_{s-1} + X_{i-n} + X_{i} $ \; $SUM\_X2_{s} = SUM\_X2_{s-1} + X_{i-n}^{2} + X_{i}^{2}$ \; $SUM\_Y_{s} = SUM\_Y_{s-1} + Y_{i-n} + Y_{i} $ \; $SUM\_Y2_{s} = SUM\_Y2_{s-1} + Y_{i-n}^{2} + Y_{i}^{2}$ \; $i \pluseq 1$ \; } \tcc{compute all distances with $X$ having a shift of 0, $Y$ having a shift of 0 and all the remains ones. These functions can access and modify all variables and data structures in this function.} fillFirstRow() \; fillFirstColl() \; fillRemaining() \; \tcc{if more than one, find the minimal distance which also minimize the alignment score} $best_d = best\_s\_x = best\_s\_y = best\_f\_y = 0$ \; \For{$tripplet$ in $MIN\_DIST$} { $s\_x = tripplet_{0}$ \; $s\_y = tripplet_{1}$ \; $f\_y = tripplet_{2}$ \; $min\_score = \infty$ \; \If{$SCORES_{s\_x,s\_y} < min\_score$} { $min\_score = SCORES_{s\_x,s\_y}$ \; $best\_s\_x = s\_x$ \; $best\_s\_y = s\_y$ \; $best\_f\_y = f\_y$ \; $best\_d = DIST_{s\_x,s\_y,f\_y}$ \; } } \Return{$best\_d,best\_s\_x,best\_s\_y,best\_f\_y$} } \caption{Fast algorithm to compute the correlation distance with shift and flip} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{initialize}% \begin{algorithm}[H] \label{initialize_algo} \Fn{\Function{}} { $l\_half = L / 2$ \; $n = L - S + 1$ \; $n\_half = n / 2$ \; %\tcc{1-cor for each shift of $X$ (on rows) and each shift of $Y$ (on columns)} $DIST =$ 3D matrix of 3 of dimensions $S*S*2$ \; %\tcc{the sums of the pairwise products of the $X$ elements for each shift and $Y$ elements for each shift} $SUM\_XY =$ 3D matrix of 0 of dimensions $S*S*2$ \; %\tcc{the sums of the $X$ elements for each shift} $SUM\_X =$ a vector of 0 of size $S$ \; %\tcc{the sums of squares of the $X$ elements for each shift} $SUM\_X2 =$ a vector of 0 of size $S$ \; %\tcc{same for $Y$} $SUM\_Y =$ a vector of 0 of size $S$ \; $SUM\_Y2 =$ a vector of 0 of size $S$ \; %\tcc{a centrality score for each alignment, a forward and a reverse alignments have the same score} $SCORES =$ a 2D matrix of 0 of dimensions $S*S$ \; %\tcc{to track minimum distances in $DIST$} $MIN\_DIST =$ an empty list of triplets \; $min\_dist = 3$ \; } \caption{A routine of distanceFast() that initializes all the necessary variables. This function can access and modify variables in distanceFast().} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{void fillFirstRow}% \begin{algorithm}[H] \Fn{\Function{}} { % \tcc{fill first row of $DIST$, 1-cor with $X$ having a shift of 0} $from\_x = 0$ \; $to\_x = from\_x + n$ \; \For{$i = 0$ to $S-1$} { \tcc{forward orientation} $from\_y = i$ \; $to\_y = from\_y + n$ \; $SUM_XY{from\_x,from\_y,0} = 0$ \; \For{$j = 0$ to $n-1$} { $SUM\_XY_{from\_x,from\_y,0} \pluseq X_{from\_x+j} * Y_{from\_y+j}$ \; } % \tcc{correlation} $c = \frac{n* SUM\_XY_{from\_x,from\_y,0} - SUM\_X_{from\_x} * SUM\_Y_{from\_y}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^{2}} * \sqrt{n*SUM\_Y2_{from\_y} - SUM\_Y_{from\_y}^{2}}}$ \; \If{division by 0 occurred} { $c = 0$ \; } % \tcc{distance} $d = 1 - c$ \; $DIST_{from\_x,from\_y,0} = d$ \; % \tcc{alignment centrality score, this value is the same for forward and reverse alignments} $SCORES_{from\_x,from\_y} = \abs{l\_half - (n\_half + from\_x)} + \abs{l\_half - (n\_half + from\_y)}$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,from\_y, 0)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,from\_y, 0)$ to $MIN\_DIST$ \; } \tcc{reverse orientation} $SUM_XY{from\_x,from\_y,1} = 0$ \; \For{$j = 0$ to $n-1$} { $SUM\_XY_{from\_x,from\_y,1} \pluseq X_{from\_x+j} * Y_{to\_y-j-1}$ \; } % \tcc{correlation} $c = \frac{n* SUM\_XY_{from\_x,from\_y,1} - SUM\_X_{from\_x} * SUM\_Y_{from\_y}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^{2}} * \sqrt{n*SUM\_Y2_{from\_y} - SUM\_Y_{from\_y}^{2}}}$ \; \If{division by 0 occurred} { $c = 0$ \; } % \tcc{distance} $d = 1 - c$ \; $DIST_{from\_x,from\_y,1} = d$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,from\_y, 1)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,from\_y, 1)$ to $MIN\_DIST$ \; } } } \caption{A routine of distanceFast() computing all distances with $X$ having a shift of 0. This function can access and modify all variables declared in distanceFast().} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{void fillFirstCol}% \begin{algorithm}[H] \Fn{\Function{}} { % \tcc{fill first row of $DIST$, 1-cor with $X$ having a shift of 0} $from\_y = 0$ ; $to\_y = from\_y + n$ \; $from\_y\_rev = s - from\_y - 1$ \; $to\_y\_rev = from\_y\_rev + n$ \; \For{$i=0$ to $S-1$} { $from\_x = i$ \; $to\_x = from\_x + n$ \; \tcc{forward orientation} $SUM\_XY_{from\_x,from\_y,0} = 0 $ \; \For{$j=0$ to $n-1$} { $SUM\_XY{from\_x,from\_y,0} \pluseq X_{from\_x+j}*Y_{from\_y+j} $ \; } $c = \frac{n*SUM\_XY_{from\_x,from\_y,0} - SUM\_X_{from\_x}*SUM\_Y_{from\_y}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^{2}} * \sqrt{n*SUM\_Y2_{from\_y} - SUM\_Y_{from\_y}^{2}}}$ \; \If{division by 0 occurred} { $c = 0$ \; } % \tcc{distance} $d = 1 - c$ \; $DIST_{from\_x,from\_y,0} = d$ \; % \tcc{alignment centrality score, this value is the same for forward and reverse alignments} $SCORES_{from\_x,from\_y} = \abs{l\_half - (n\_half + from\_x)} + \abs{l\_half - (n\_half + from\_y)}$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,from\_y, 0)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,from\_y, 0)$ to $MIN\_DIST$ \; } \tcc{reverse orientation} $SUM\_XY_{from\_x,S-1,1} = 0$ \; \For{$j=0$ to $n-1$} { $SUM\_XY_{from\_x,S-1,1} \pluseq X_{from\_x+j} * Y_{to\_y\_rev-1-j}$ \; } $c = \frac{n*SUM\_XY_{from\_x,S-1,1} - SUM\_X_{from\_x}*SUM\_Y_{S-1}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^{2}} * \sqrt{n*SUM\_Y2_{S-1} - SUM\_Y_{S-1}^{2}}}$ \; \If{division by 0 occurred} { $c = 0$ \; } % \tcc{distance} $d = 1 - c$ \; $DIST_{from\_x,from\_y,1} = d$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,S-1, 1)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,S-1, 1)$ to $MIN\_DIST$ \; } } } \caption{A routine of distanceFast() computing all distances with $Y$ having a shift of 0. This function is can access and modify all variables declared in distanceFast().} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{void fillRemaining}% \begin{algorithm}[H] \Fn{\Function{}} { \For{$i=1$ to $S-1$} { $from\_x = i$ ; $to\_x = from\_x + n $ \; \For{$j=1$ to $S-1$} { $from\_y = j$ \; $to\_y = from\_y + n$ \; \tcc{forward orientation} $SUM\_XY_{from\_x,from\_y,0} = SUM\_XY_{from\_x-1,from\_y-1,1} - X_{from\_x-1} * Y_{from\_y-1} + X_{to\_x-1}*Y{to\_y-1}$ \; $c = \frac{n*SUM\_XY{from\_x,from\_y,0} - SUM\_X{from\_x}*SUM\_Y{from\_y}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^2} * \sqrt{n*SUM\_Y2_{from\_Y} - SUM\_Y_{from\_Y}^2}}$ \; \If{division by 0 occurred} { $c = 0$ \; } $d = 1 - c$ \; $DIST_{from\_x,from\_y,0} = d$ \; %\tcc{alignment centrality score, this value is the same for forward and reverse alignments} $SCORES_{from\_x,from\_y} = \abs{l\_half - (n\_half + from\_x)} + \abs{l\_half - (n\_half + from\_y)}$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,from\_y,0)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,from\_y,0)$ to $MIN\_DIST$ \; } \tcc{reverse orientation} $j\_rev = S - j - 1$ \; $from\_y\_rev = j\_rev$ \; $to\_y\_rev = from\_y\_rev + n$ \; $SUM\_XY_{from\_x,from\_y\_rev,1} = SUM\_XY_{from\_x-1,from\_y\_rev+1,1} - X_{from\_x-1}*Y_{to\_y\_rev} + X_{to\_x-1}*Y{from\_y\_rev}$ \; $c = \frac{n*SUM\_XY_{from\_x,from\_y\_rev,1} - SUM\_X_{from\_x}*SUM\_Y_{from\_y\_rev}} {\sqrt{n*SUM\_X2_{from\_x} - SUM\_X_{from\_x}^2} * \sqrt{n*SUM\_Y2_{from\_y\_rev} - SUM\_Y_{from\_y_rev}^2}}$ \; \If{division by 0 occurred} { $c = 0$ \; } $d = 1 - c$ \; $DIST_{from\_x,from\_y,1} = d$ \; \If{$d < min\_dist$} { $min\_distance = d$ \; append a triplet $(from\_x,from\_y\_rev,1)$ to $MIN\_DIST$ \; } \ElseIf{$d = min\_dist$} { append a triplet $(from\_x,from\_y\_rev,1)$ to $MIN\_DIST$ \; } } } } \caption{A routine of distanceFast() computing all remaining distances between $X$ and $Y$. This function can access and modify all variables declared in distanceFast().} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{REF seedingRandom}% \begin{algorithm}[H] \label{algo_seed_random} \Fn{\Function{K, R}} { \KwData{$K$ the number references to initialize from $R$, a 2D matrix of numericals of dimensions $N \times L$.} \KwResult{$REF$ a 2D matrix of numericals of dimensions $K \times L$.} $REF = $ a 2D matrix of dimensions $K*L$ \; \For{$i=0$ to $K-1$} { $j = $ sample a number from $0$ to $N-1$ with uniform probabilities \; \While{$j$ has already been sampled before} { $j = $ sample a number from $0$ to $N-1$ with uniform probabilities \; } $REF_{i,} = R_{j,}$ \; } \Return{$REF$} } \caption{Random seeding algorithm} \end{algorithm} \vspace{\baselineskip}% Insert a blank line \SetKwProg{Fn}{}{\{}{}\SetKwFunction{Function}{REF seedingKmeans++}% \begin{algorithm}[H] \label{algo_seed_kmeans++} \Fn{\Function{K, R, S}} { \KwData{$K$ the number references to initialize from $R$, a 2D matrix of numericals of dimensions $N \times L$, allowing a shifting of $S$.} \KwResult{$REF$ a 2D matrix of numericals of dimensions $K \times L$.} $REF = $ a 2D matrix of dimensions $K*L$ \; $DIST\_TO\_CLOSEST = $ a vector of size $N$\; \tcc{choose first reference, a standard deviation equals to 0 should be avoided otherwise computing a distance against this reference will always be equal to 1 (see how distance are computed).} $j = $ sample a number from $0$ to $N-1$ with uniform probabilities but for which $DATA_{j,}$ has a standard deviation different from $0$ \; $REF_{0,} = DATA_{j,}$ \; \tcc{choose next references} \For{$k=1$ to $K-1$} { \For{$i=0$ to $N-1$} { \tcc{distance to all current references for this region} $DIST\_TO\_CENTERS =$ a vector of size $k$ ; \For{$j=0$ to $k-1$} { $DIST\_TO\_CENTERS_{j,} =$ distanceFast($REF_{j,}$, $R_{i,}$, $S$) \; } \tcc{distance to closest current reference, for this region} $DIST\_TO\_CLOSEST{i,} =$ minimum value of $DIST\_TO\_CENTERS$\; } $j =$ sample a number from 0 to $N-1$ using $DIST\_TO\_CLOSEST$ as the probability/weight distribution for each point to be sample. \; \While{$j$ has already been sampled before} { $j =$ sample a number from 0 to $N-1$ using $DIST\_TO\_CLOSEST$ as the probability/weight distribution for each point to be sample. \; } $REF_{k,} = R{j,}$ \; } \Return{REF} } \caption{Kmeans++ seeding algorithm.} \end{algorithm} % ======================================= SMiLE-seq supplemental ======================================= \section{SMiLE-seq supplementary material} \begin{figure}[H] \begin{center} \includegraphics[scale=0.3]{images/ch_smile-seq/figure_s4_reproduced.png} \captionof{figure}{\textbf{Predictive power of SMiLE-seq :} \textbf{A} binding models were derived de novo from HT-SELEX 1st cycle data using the HMM discovery method (labelled HT-SELEX cycle 1 HMM) and their performances were assessed using the AUC-ROC. AUC-ROC values for the corresponding TF models derived from SMiLe-seq data (labelled SMiLE-seq) and reported by Jolma and colleagues (labelled HT-SELEX reported matrices, \cite{jolma_dna-binding_2013}) are also displayed. \textbf{B} the predictive performances of CEBPb, CTCF and TCF7 binding models were assessed using subsets of binding sites of decreasing affinities. Inside each peak list, the peaks were ranked by score and subsets of 500 peaks were selected. Peaks 1-500 have the highest affinity, then peaks 501-1000, and so on. The boxplots indicate the distribution of AUC-ROC obtained over all available peak-lists.} \label{suppl_smileseq_auc_2} \end{center} \end{figure} % ======================================= ATAC-seq supplemental ======================================== \section{Chromatin accessibility of monocytes supplementary material} \subsection{Fragment size analysis} \label{suppl_atac_seq_fragment_size} \begin{figure}[h] \begin{center} \includegraphics[scale=0.3]{images/ch_atac-seq/fragment_lengths.png} \captionof{figure}{\textbf{Fragment size analysis} \textbf{A} sequenced fragment size density. The three peaks, from left to right, indicate i) the open chromatin fragments, ii) the mono-nucleosome fragments and iii) the di-nucleosome fragments. A mixture model composed of three Gaussian distributions was fitted to the data in order to model the fragment sizes. The class fit is shown as dashed lines : open chromatin (red), mono-nucleosomes (blue) and di-nucleosomes (green). The violet dashed line show the sum of the three classes. \textbf{B :} probability that a fragment belongs to any of the three fragment classes, given its size i) open chromatin (red), ii) mono-nucleosomes (blue) and iii) di-nucleosomes (green). The vertical dashed lines indicates, for each class, the size limit at which the class probability drops below 0.9. With these limites, the class spans are i) 30-84bp for open chromatin (red), ii) 133-266bp for mono-nucleosomes (blue) and iii) 341-500bp for di-nucleosomes (green). The upper limit of the di-nucleosome class was arbitrarily set to 500bp. \textbf{C :} final fragment classes. Each fragments which size overlapped the size range spanned by a class, was assigned to that class. This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.} \label{atac_seq_fragment_size} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.4]{images/ch_atac-seq/ctcf_motifs_10e-6_aggregations.png} \captionof{figure}{\textbf{Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf{Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf{Middle row :} each position of the reads were used. \textbf{Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively.\\ The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).} \label{atac_seq_ctcf_all_data} \end{center} \end{figure} Nucleosomes fragments are expected to be large, as a nucleosome is wrapped by \~150bp of DNA whereas nucleosome free region fragments can be expected to be shorter. Long nucleosome free region fragments are unlikely. The longer an accessible region is, the most likely an insertion will happen resulting in the creation of two shorter fragments. A fragment size analysis allowed to identify different categories of fragments (Figure \ref{atac_seq_fragment_size}). In this figure, open regions, mono- and di-nucleosome fragments are clearly visible. Morever, a 10bp periodicity oscillations reflecting the DNA pitch is also visible. This pattern is expected and indicates a good data quality \citep{buenrostro_transposition_2013}. Rather than assigning arbitrary fragment size threshold to separate the categories, I preferred to use the approach developed by \citep{buenrostro_transposition_2013}. The fragment sizes were fitted by a mixture of three Gaussian distributions. Then, the limits for each fragment class was defined as the size at which the probability of assignment to that fragment class dropped under 0.9 (Figure \ref{atac_seq_fragment_size}B). This method ensured the classification of 134 millions of fragments, leaving ~46 millions reads unassigned (Figure \ref{atac_seq_fragment_size}C). However, this reduces drastically the risks of fragment mis-classification and protects the downstream analyses from a strong bias. \subsection{Measuring open chromatin and nucleosome occupancy} \label{suppl_atac_seq_measuring_signal} \begin{figure}[h] \begin{center} \includegraphics[scale=0.3]{images/ch_atac-seq/ctcf_sp1_myc_ebf1_footprint.png} \captionof{figure}{\textbf{Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with one PWM per TF to predict their binding sites (see section \ref{atac_seq_method_pwmscan}). For each TF, the open chromatin accessibility was measured (red) as well as and the nucleosome occupancy (blue) around their predicted binding sites. For the chromatin accessibility, the corrected read edges were considered and for nucleosomes, the center of the fragments. The motif location is indicated by the dashed lines.} \label{atac_seq_ctcf_sp1_myc_ebf1_footprint} \end{center} \end{figure} Once the different fragment populations have been identified, the next question to solve is how should each category of fragment be represented? First, for open chromatin fragment, it is clear that we want to know where the DNA is accessible. This information is provided by the fragment edges – the transpositions sites. However, to account for the fact that the Tn5 transposase acts as a homo-dimer and inserts two barcodes side by side \citep{adey_rapid_2010}, the fragment edges positions were modified by +4bp for reads mapping the + strand and -5bp for reads mapping the - strand, as done in other studies \citep{buenrostro_transposition_2013,li_identification_2019}. Second, for mono and di-nucleosome fragments, we are interested in knowing where the nucleosomes are sitting. For this, the fragment edges may not be the most informative. A better way to represent those fragments would be to use the center positions, which should correspond to the dyad for mono-nucleosomes or even to consider the entire reads or fragments. To test these hypotheses I investigated the different signal aggregations around predicted CTCF binding sites using. The signal, +/- 1kb around the motif, was aggregated inside bins of 1, 2 or 10bp size. CTCF predicted binding sites were good candidates because CTCF is know to bind mostly through its motif (\cite{neph_expansive_2012} and Figure \ref{encode_peaks_gm12878_motif_prop}). Additionally CTCF binding produces a really typical chromatin architecture with strongly positioned nucleosomes arrays \citep{fu_insulator_2008} and leaves a footprint \citep{neph_expansive_2012}. As seen in Figure \ref{atac_seq_ctcf_all_data}, entire open chromatin reads and fragments do not allow to visualize a footprint signature (upper and middle rows, red lines). Both of them, nonetheless highlight open chromatin regions. The footprint becomes visible when considering the edges of the open chromatin fragments (bottom row, red line). Increasing the bin size blurs it and eventually makes it disappear (10bp, lower right). Regarding nucleosomes, considering the entire fragments blurs the signal (upper row, blue and green lines) and the entire reads reveal the region upstream and downstream of the nucleosomes (middle row, blue and green lines). The only way to obtain a precise nucleosomes occupancy information was to use the middle position of the mono-nucleosome fragments (bottom row, blue line). Interesting enough, the middle position of di-nucleosome fragments indicates the DNA linker between two adjacent nucleosomes but does not accumulate in open chromatin regions (bottom row, green line). This suggested that di-nucleosome fragments could be separated in two mono-nucleosome fragments. I tested this hypothesis by simply dividing a di-nucleosome fragment in two smaller ones, at its center position. I then pooled these new fragments with the mono-nucleosome fragments to create a nucleosome fragment dataset. When looking at the middle of these fragments, they could perfectly reveal the nucleosomes directly adjacent to the CTCF motif. Additionally this nucleosome dataset was also able to reveal a second nucleosome in the arrays (bottom row, violet lines). To further support these results, I also measured the chromatin organization (+5/-4 corrected read edges for open chromatin and center of the nucleosome fragments from the nucleosome fragment dataset) around SP1, myc and EBF1 binding motifs as well. As shown in Figure \ref{atac_seq_ctcf_sp1_myc_ebf1_footprint}, the aggregation of the signal arount the CTCF and SP1 motifs show an enhanced accessibility on the motif as well as a clear footprint. Moreover, the footprint is in a nucleosome free region. The situation was different for myc and EBF1. Neither of the two aggregations showed a nucleosome free region, nor an increased accessibility around the motif. Regarding myc, even though its aggregation presented a signal compatible with a local protection of its motif, this was shallow in comparison of CTCF and SP1. Finally, EBF1 presented a somewhat decreased accessibility around its motif and a striking increase accessibility directly at the level of the motif. CTCF and SP1 motifs are supporting the fact that footprints and nucleosome occupancy can be revealed using this method. Together with myc and EBF1, they clearly show an heterogeneity of chromatin organizations, at least at the aggregation level. There are many possible explanations for these results. One of them is that the aggregation hides the variability of the individual regions and that SP1 and CTCF present a more conserved organization around their motif than myc and EBF1. Another would that the most visible and obvious footprint reflect an stronger TF activity. However, one should remain cautious on the interpretation of aggregation patterns as the individual sites signal may interfere with each other, creating an artificial aggregation that does not exist at any individual site \citep{kundaje_ubiquitous_2012}. In the light of these results, I decided to use the +5/-4 corrected edges of the open chromatin reads to investigate footprints and the fragment centers of the newly created nucleosome dataset to investigate nucleosome occupancy. If not explicitly stated otherwise, the reader should consider that any signal was measured using this procedure. \subsection{Evaluation of EMSequence and ChIPPartitioning} \label{suppl_eval_emseq_chippartitioning} It was important to assess the performances of the partitioning methods to discover sequence motifs and footprint classes. % To evaluate the behavior of each algorithm, a simple situation was considered. As in the previous section, a list of predicted CTCF, SP1, EBF1 and myc binding sites were compiled using a PWM genome scan. For each TF, the open chromatin read density, the nucleosome occupancy and the DNA sequences were extracted. % This case can be considered simple for two reasons. First, for a given TF, all the regions have a motif instance. Second, this motif instance is located exactly in the center of the region, in the same orientation. Thus no shifting nor flipping is required in order to reveal footprints. The only necessary thing may be to discover different types of footprints. \subsubsection{EMSequence} \begin{figure}[h] \begin{center} \includegraphics[scale=0.4]{images/ch_atac-seq/simulated_sequences_2class_flip_best_motifs.png} \captionof{figure}{\textbf{Simulated data motifs :} motifs used for the data generation (labeled "True motif") and the best scoring - based on the AUC - partition motifs (labeled "Found motif"). The partition with EMSequence was run such that it was searching for motifs of 11bp, slightly longer than those used for the data generation. "RC" stands for reverse complement. The motifs tree and alignment was build using the motifStack R package \citep{ou_motifstack_2018}.} \label{suppl_atac_seq_emseq_best_motifs} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.4]{images/ch_atac-seq/simulated_sequences_2class_flip_auc_roc.png} \captionof{figure}{\textbf{Classification performances on simulated data :} \textbf{Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf{Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.} \label{suppl_atac_seq_emseq_auc_roc} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.35]{images/ch_atac-seq/sp1_motifs_7class.png} \captionof{figure}{\textbf{SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.} \label{suppl_atac_seq_emseq_sp1_7class} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.35]{images/ch_atac-seq/sp1_motifs_10class.png} \captionof{figure}{\textbf{SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. These sequences were classified by EMSequence to search for 10 different 30bp long motifs ($801 - 30 = 771$ of shifting freedom). The optimization was run for 20 iterations. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates head-to-tail arrangements of SP1 motifs.} \label{suppl_atac_seq_emseq_sp1_10class} \end{center} \end{figure} In order to measure the ability of EMSequence to retrieve over-represented motifs from a set of sequences, I simulated 2'000 synthetic DNA sequences of 100bp long. The sequences were separated in two classes. Each class was defined by a 8bp sequence motif (Figure \ref{suppl_atac_seq_emseq_best_motifs}). Each sequence had exactly one motif occurrence, anywhere in the sequence (with a uniform probability), on either strand (equiprobable). These sequences were partitioned with flipping into 2 classes by EMSequence in order to find 2 motifs of 11bp ($100bp - 11bp + 1 = 90$bp of shifting). The optimization was run for 200 iterations. To assert the quality of the motifs discovered, I set up a classification framework inspired by PWMEval-ChIP-peak (see section \ref{section_smileseq_pwmeval}). Using equation \ref{smile_seq_pwmeval_score}, each sequence was scored with both model of each partition and the area under the curve (AUC) of the receiver operator characteristic (ROC) value was computed for each partition. The same was done using the true motif models. Because EMSequence is sensitive to its initial state, 50 partitions were performed. As shown in Figure \ref{suppl_atac_seq_emseq_auc_roc}, the de-novo discovered models are as good as the actual sequence motifs to segregate both sequence classes. Additionally, a visual inspection of the discovered motif logo confirmed that most of the discovered motifs actually match the true sequence motifs (Figure \ref{suppl_atac_seq_emseq_best_motifs}). In order to further demonstrate the ability of EMSequence on a more significant biological case, I investigated SP1 sequence specificity. As for ChIPPartitioning, a list of 15'883 predicted SP1 binding sites were compiled using a PWM genome scan. The sequences +/- 400bp around the motif instance centers were extracted. Thus, all regions contained at least one SP1 site. Thus, retrieving the SP1 binding site is expected. Additionally, as SP1 tends to bind to promoters, we cannot exclude to see other motif being being discovered. These sequences were then given to EMSequence to search for several different 31bp long motifs ($801 - 31 + 1 = 771$ of shifting freedom). The optimization was run for 20 iterations. The motifs that were retrieved matched the expectations (Figure \ref{suppl_atac_seq_emseq_sp1_7class}). All classes retrieved an SP1 motif. Four classes (1,5,6,7) retrieved a single SP1 motif. Even though they are highly similar, they vary in term of flanking regions (class 6 versus 7 for instance). Class 3, which contained a surprisingly long motif, representing 24\% of the data, actually captured a LINE element. Indeed, the "GCAGCGAGGCTGGGGGAGGGGC" is characteristic of it (determined using BLAT \citep{kent_blatblast-like_2002} on the UCSC Genome Browser). Finally, and more interesting, classes 2 and 4 could capture two rare (about 1\% of the cases each) tandem repeats of SP1 motifs with two different spacers (1 and 9bp). Additionally, head-to-head SP1 motif repeats could be detected (\ref{suppl_atac_seq_emseq_sp1_10class}, classes 1 and 4). This suggested that SP1 binds as i) an homo-dimer or ii) as an hetero-dimer with another member of its family, binding a resembling motif. Moreover, the tandem and heat-to-head motif repeats suggested that different structural arrangement exist. According to BioGrid \citep{chatr-aryamontri_biogrid_2017}, SP1 has been reported to physically interact with SP1 (homo-dimer), SP3 and SP4 (hetero-dimer). According to JASPAR 2018 matrix clustering \citep{castro-mondragon_rsat_2017}, the KLF and EGR families recognizes similar motifs. Members of either families are also listed as SP1 interactors in Biogrid (KLF4, KLF6, KLF9, KLF10 and EGR1). The lack of non-SP1 motif discovered could be explained by at least one reason. The list of SP1 binding sites compiled was performed using a quite stringent threshold. The consequence is that the motif instances are highly similar to each other. This makes SP1 motifs strongly dominant within the dataset. Since EMSequence optimizes a set of models, it is highly sensitive to its starting state. In this experiment, EMSequence was initialised randomly. Because of the dominance of SP1 motifs within the data, it is likely that the different classes were attracted by them rather than allowed to diverge to detect other motifs. Together, these evidences support the fact that EMSequence is suited to perform a meaningful partition of DNA sequences and to retrieve biologically important DNA motifs. \subsubsection{ChIPPartitioning} \begin{figure}[h] \begin{center} \includegraphics[scale=0.30]{images/ch_atac-seq/ctcf_motifs_6class_noshift_flip.png} \captionof{figure}{\textbf{Open chromatin classes around CTCF motifs} found by ChIPPartitioning without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.} \label{suppl_atac_seq_emread_ctcf_noshift_flip} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.3]{images/ch_atac-seq/sp1_motifs_6class_noshift_flip.png} \captionof{figure}{\textbf{Open chromatin classes around SP1 motifs :} EMRead was run without shifing (+/- 10bp) but with flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.} \label{suppl_atac_seq_emread_sp1_noshift_flip} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.35]{images/ch_atac-seq/ctcf_motifs_6class_shift_flip.png} \captionof{figure}{\textbf{Open chromatin classes around CTCF motifs} found by ChIPPartitioning with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.} \label{suppl_atac_seq_emread_ctcf_shift_flip} \end{center} \end{figure} \begin{figure}[h] \begin{center} \includegraphics[scale=0.3]{images/ch_atac-seq/sp1_motifs_6class_shift_flip.png} \captionof{figure}{\textbf{Open chromatin classes around SP1 motifs :} EMRead was run with shifing (+/- 10bp) flipping to identify different classes of footprints around 15'883 SP1 motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.} \label{suppl_atac_seq_emread_sp1_shift_flip} \end{center} \end{figure} A complete benchmark of the ChIPPartitioning has been performed in \citep{nair_probabilistic_2014}. In this paper, the authors have generated simulated ChIP-seq data with patterns to retrieve, at different coverages and compared the performances with other similar software. It turned out that ChIPPartitioning was the best performing method. For this reason, I did not repeat this benchmark. However, ChIPPartitioning ability to retrieve footprint classes from from ATAC-seq data has not been performed yet. To evaluate this, a simple situation was considered. As in the previous section, a list of predicted CTCF and SP1 binding sites were compiled using a genome scan with suited binding models. For each TF, the open chromatin read density around these sites was measured +/-400bp aroud the motif instances, at the single base pair resolution, and classified. As the motif instances were already aligned in the center of the regions, no shifting was used. However, the region orientations were not corrected based on the strand on which the motif instance appeared. To evaluate the capability of ChIPPartitioning to retrieve classes of footprints, these data were classified i) without shifting and with flip (Figure \ref{suppl_atac_seq_emread_ctcf_noshift_flip} and Figure \ref{suppl_atac_seq_emread_sp1_noshift_flip}) and ii) with shifting and flipping (Figure \ref{suppl_atac_seq_emread_ctcf_shift_flip} and \ref{suppl_atac_seq_emread_sp1_shift_flip}). First, in both conditions - with and without shifting - different open chromatin signal classes have been discovered. Second, in most cases, the chromatin accessibility is anti-correlated with the nucleosome occupancy, which is something expected. However this is not always the case, such as in Figure \ref{suppl_atac_seq_emread_ctcf_noshift_flip} classes 3 and 6. Such pattern may reflect a complex chromatin architecture, with variably positioned nucleosomes, that the partition cannot realign. But it is also likely to be an artifactual signal caused by the partition itself. Third, allowing the regions to be flipped based on the chromatin accessibility signature (Figure \ref{suppl_atac_seq_emread_ctcf_noshift_flip} and Figure \ref{suppl_atac_seq_emread_sp1_noshift_flip}) does not allow to resolve properly the orientation of the underlying CTCF and SP1 motif instances. Indeed, the sequence logos, in the center, are symetric indicating a superposition of +strand and -strand motif. Finally, allowing a moderated shifting freedom (+/- 10bp, Figure \ref{suppl_atac_seq_emread_ctcf_shift_flip} and \ref{suppl_atac_seq_emread_sp1_shift_flip}) results in blurred out sequence logo. This indicates that the chromatin accessibility signal realignment unphased the underlying CTCF and SP1 motif instances. Thus the signal that is observed does not represent classes of footprints. In this case, each the region contained a motif instance at its center. Nonetheless, even a limited shifting according to the open chromatin signal resulted in the dephasing the underlying motif instances. Trying to resolve the motif orientation by allowing flipping according to the open chromatin was not more successful. Thus, discovering footprint classes from a highly unaligned set of regions does not seem to be possible. Workaround strategies have to be found. \subsection{Other supplementary figures} \begin{figure}[H] \begin{center} \includegraphics[scale=0.35]{images/ch_atac-seq/peaks_rmsk_sampled_sequences_23class.png} - \captionof{figure}{\textbf{Extended sequence and chromatin models} found in monocytes regulatory regions. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.} + \captionof{figure}{\textbf{Extended sequence and chromatin models} found in monocytes regulatory regions. Each read density and sequence pattern is a soft aggregation plot. The displayed logos correspond to the sequence class models found by EMSequence. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.} \label{suppl_atac_seq_23class} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.30]{images/ch_atac-seq/data_classPU1_2class.png} \captionof{figure}{\textbf{PU.1 sub-classes} obtained by extracting PU.1 class data and subjecting them to a ChIPPartitioning classification into 2 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.} \label{suppl_atac_seq_pu1_subclass} \end{center} \end{figure} \begin{figure}[H] \begin{center} \includegraphics[scale=0.30]{images/ch_atac-seq/data_classjun_3class.png} \captionof{figure}{\textbf{AP1 sub-classes} obtained by extracting AP1 class data and subjecting them to a ChIPPartitioning classification into 3 classes. The displayed logos correspond to each class sequence aggregation. The corresponding chromatin accessibility (red) and nucleosome occupancy (blue) are displayed atop of the logos. The classes are displayed by overall decreasing probability. A zoom over the central part of each class aggregation is shown in the top right inlet.} \label{suppl_atac_seq_ap1_subclass} \end{center} \end{figure} diff --git a/tail/biblio.aux b/tail/biblio.aux index 6148726..86ad322 100644 --- a/tail/biblio.aux +++ b/tail/biblio.aux @@ -1,202 +1,202 @@ \relax \providecommand\hyper@newdestlabel[2]{} \bibstyle{apalike} \bibdata{tail/bibliography} \bibcite{adey_rapid_2010}{{1}{2010}{{Adey et~al.}}{{}}} \bibcite{aerts_toucan:_2003}{{2}{2003}{{Aerts et~al.}}{{}}} \bibcite{aibar_scenic:_2017}{{3}{2017}{{Aibar et~al.}}{{}}} \bibcite{ambrosini_chip-seq_2016}{{4}{2016a}{{Ambrosini et~al.}}{{}}} \bibcite{ambrosini_chip-seq_2016-1}{{5}{2016b}{{Ambrosini et~al.}}{{}}} \bibcite{ambrosini_pwmscan:_2018}{{6}{2018}{{Ambrosini et~al.}}{{}}} \bibcite{ambrosini_signal_2003}{{7}{2003}{{Ambrosini et~al.}}{{}}} \bibcite{angerer_single_2017}{{8}{2017}{{Angerer et~al.}}{{}}} \bibcite{arthur_k-means++:_2007}{{9}{2007}{{Arthur and Vassilvitskii}}{{}}} 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