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\babel@toc {english}{}
\babel@toc {french}{}
\babel@toc {english}{}
\contentsline {chapter}{Acknowledgements}{i}{chapter*.1}
\contentsline {chapter}{Preface}{iii}{chapter*.2}
\contentsline {chapter}{Abstract (English/Fran\IeC {\c c}ais/Deutsch)}{v}{chapter*.3}
\babel@toc {german}{}
\babel@toc {english}{}
\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}{1}{subsection.1.1.1}
\contentsline {subsection}{\numberline {1.1.2}The chromatin is dynamic}{3}{subsection.1.1.2}
\contentsline {subsection}{\numberline {1.1.3}Measuring nucleosome occupancy}{4}{subsection.1.1.3}
\contentsline {subsection}{\numberline {1.1.4}About nucleosome positioning}{5}{subsection.1.1.4}
\contentsline {subsection}{\numberline {1.1.5}Gene regulation in a nutshell}{7}{subsection.1.1.5}
\contentsline {subsection}{\numberline {1.1.6}Digital footprinting}{9}{subsection.1.1.6}
\contentsline {subsection}{\numberline {1.1.7}Pioneer factors}{11}{subsection.1.1.7}
\contentsline {section}{\numberline {1.2}About transcription factors}{12}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}TF co-binding}{13}{subsection.1.2.1}
\contentsline {subsection}{\numberline {1.2.2}Modeling sequence specificity}{14}{subsection.1.2.2}
\contentsline {subsubsection}{Position weight matrix}{14}{subsection.1.2.2}
\contentsline {subsubsection}{Predicting binding sites}{15}{equation.1.2.3}
\contentsline {subsubsection}{Aligning binding sites}{16}{equation.1.2.5}
\contentsline {subsection}{\numberline {1.2.3}The chromatin affects TF binding}{16}{subsection.1.2.3}
\contentsline {subsection}{\numberline {1.2.4}Measuring TF binding in vivo}{16}{subsection.1.2.4}
\contentsline {subsection}{\numberline {1.2.5}Measuring TF binding in vitro}{16}{subsection.1.2.5}
\contentsline {section}{\numberline {1.3}Data analysis}{16}{section.1.3}
\contentsline {chapter}{\numberline {2}Published laboratory projects}{19}{chapter.2}
\contentsline {chapter}{Published laboratory projects}{19}{chapter.2}
\contentsline {section}{\numberline {2.1}Mass Genome Annotation repository}{19}{section.2.1}
\contentsline {subsection}{\numberline {2.1.1}Introduction}{19}{subsection.2.1.1}
\contentsline {subsection}{\numberline {2.1.2}MGA content and organization}{19}{subsection.2.1.2}
\contentsline {subsection}{\numberline {2.1.3}Conclusions}{21}{subsection.2.1.3}
\contentsline {section}{\numberline {2.2}Eukaryotic Promoter Database}{22}{section.2.2}
\contentsline {subsection}{\numberline {2.2.1}Introduction}{23}{subsection.2.2.1}
\contentsline {subsection}{\numberline {2.2.2}EPDnew now annotates (some of) your mushrooms and vegetables}{23}{subsection.2.2.2}
\contentsline {subsection}{\numberline {2.2.3}Increased mapping precision in human}{23}{subsection.2.2.3}
\contentsline {subsection}{\numberline {2.2.4}Integration of EPDnew with other resources}{25}{subsection.2.2.4}
\contentsline {subsection}{\numberline {2.2.5}Conclusions}{26}{subsection.2.2.5}
\contentsline {subsection}{\numberline {2.2.6}Methods}{26}{subsection.2.2.6}
\contentsline {subsubsection}{Motif occurrence profiles}{26}{subsection.2.2.6}
\contentsline {section}{\numberline {2.3}PWMScan}{27}{section.2.3}
\contentsline {subsection}{\numberline {2.3.1}Introduction}{27}{subsection.2.3.1}
\contentsline {subsection}{\numberline {2.3.2}Data and methods}{29}{subsection.2.3.2}
\contentsline {subsection}{\numberline {2.3.3}Benchmark}{30}{subsection.2.3.3}
\contentsline {subsection}{\numberline {2.3.4}Conclusions}{32}{subsection.2.3.4}
\contentsline {section}{\numberline {2.4}SPar-K}{33}{section.2.4}
\contentsline {subsection}{\numberline {2.4.1}Introduction}{33}{subsection.2.4.1}
\contentsline {subsection}{\numberline {2.4.2}Methods}{33}{subsection.2.4.2}
\contentsline {subsection}{\numberline {2.4.3}Results}{37}{subsection.2.4.3}
\contentsline {subsection}{\numberline {2.4.4}Conclusion}{37}{subsection.2.4.4}
\contentsline {chapter}{\numberline {3}ENCODE peaks analysis}{39}{chapter.3}
\contentsline {chapter}{ENCODE peaks analysis}{39}{chapter.3}
\contentsline {section}{\numberline {3.1}Data}{39}{section.3.1}
\contentsline {section}{\numberline {3.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{41}{section.3.2}
\contentsline {subsection}{\numberline {3.2.1}Data realignment}{42}{subsection.3.2.1}
\contentsline {section}{\numberline {3.3}Nucleosome organization around transcription factor binding sites}{43}{section.3.3}
\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{45}{section.3.4}
\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{49}{section.3.5}
\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{53}{section.3.6}
\contentsline {section}{\numberline {3.7}Methods}{56}{section.3.7}
\contentsline {subsection}{\numberline {3.7.1}Data and data processing}{56}{subsection.3.7.1}
\contentsline {subsection}{\numberline {3.7.2}Classification of MNase patterns}{57}{subsection.3.7.2}
\contentsline {subsection}{\numberline {3.7.3}Quantifying nucleosome array intensity from classification results}{57}{subsection.3.7.3}
\contentsline {subsection}{\numberline {3.7.4}Peak colocalization}{58}{subsection.3.7.4}
\contentsline {subsection}{\numberline {3.7.5}NDR detection}{59}{subsection.3.7.5}
\contentsline {subsection}{\numberline {3.7.6}CTCF and JunD interactors}{61}{subsection.3.7.6}
\contentsline {subsection}{\numberline {3.7.7}EBF1 and nucleosome}{62}{subsection.3.7.7}
\contentsline {chapter}{\numberline {4}SMiLE-seq data analysis}{65}{chapter.4}
\contentsline {chapter}{SMiLE-seq data analysis}{65}{chapter.4}
\contentsline {subsection}{\numberline {4.0.1}Introduction}{65}{subsection.4.0.1}
\contentsline {subsection}{\numberline {4.0.2}Hidden Markov Model Motif discovery}{67}{subsection.4.0.2}
\contentsline {subsection}{\numberline {4.0.3}Binding motif evaluation}{68}{subsection.4.0.3}
\contentsline {subsection}{\numberline {4.0.4}Results}{70}{subsection.4.0.4}
\contentsline {subsection}{\numberline {4.0.5}Conclusions}{72}{subsection.4.0.5}
\contentsline {chapter}{\numberline {5}Chromatin accessibility of monocytes}{73}{chapter.5}
\contentsline {section}{\numberline {5.1}Monitoring TF binding}{73}{section.5.1}
\contentsline {section}{\numberline {5.2}The advent of single cell DGF}{74}{section.5.2}
\contentsline {section}{\numberline {5.3}Open issues}{74}{section.5.3}
\contentsline {section}{\numberline {5.4}Data}{74}{section.5.4}
\contentsline {section}{\numberline {5.5}Identifying over-represented signals}{75}{section.5.5}
\contentsline {subsection}{\numberline {5.5.1}ChIPPartitioning : an algorithm to identify over-represented read patterns}{75}{subsection.5.5.1}
\contentsline {subsection}{\numberline {5.5.2}EMSequence : an algorithm to identify over-represented sequences}{75}{subsection.5.5.2}
\contentsline {subsubsection}{without shift and flip}{77}{figure.caption.33}
\contentsline {subsubsection}{with shift and flip}{77}{equation.5.5.2}
\contentsline {subsection}{\numberline {5.5.3}EMJoint : an algorithm to identify over-represented sequences and chromatin architectures}{79}{subsection.5.5.3}
\contentsline {subsection}{\numberline {5.5.4}Data realignment}{80}{subsection.5.5.4}
\contentsline {section}{\numberline {5.6}Results}{80}{section.5.6}
\contentsline {subsection}{\numberline {5.6.1}Fragment size analysis}{80}{subsection.5.6.1}
\contentsline {subsection}{\numberline {5.6.2}Measuring open chromatin and nucleosome occupancy}{83}{subsection.5.6.2}
\contentsline {subsection}{\numberline {5.6.3}Evaluation of EMSequence and ChIPPartitioning}{85}{subsection.5.6.3}
\contentsline {subsubsection}{EMSequence}{85}{subsection.5.6.3}
\contentsline {subsubsection}{ChIPPartitioning}{88}{figure.caption.38}
\contentsline {section}{\numberline {5.7}Aligning the binding sites}{90}{section.5.7}
\contentsline {section}{\numberline {5.8}Exploring individual TF classes}{93}{section.5.8}
\contentsline {section}{\numberline {5.9}Discussions}{94}{section.5.9}
\contentsline {section}{\numberline {5.10}Perspectives}{94}{section.5.10}
\contentsline {section}{\numberline {5.11}Methods}{95}{section.5.11}
\contentsline {subsection}{\numberline {5.11.1}Partitioning programs}{95}{subsection.5.11.1}
\contentsline {subsection}{\numberline {5.11.2}Fragment classes}{95}{subsection.5.11.2}
\contentsline {subsection}{\numberline {5.11.3}Simulated sequences}{96}{subsection.5.11.3}
\contentsline {subsection}{\numberline {5.11.4}Realignment using JASPAR motifs}{96}{subsection.5.11.4}
\contentsline {subsection}{\numberline {5.11.5}Model extension}{98}{subsection.5.11.5}
\contentsline {subsection}{\numberline {5.11.6}Extracting data assigned to a class}{98}{subsection.5.11.6}
\contentsline {subsection}{\numberline {5.11.7}Peak processing}{101}{subsection.5.11.7}
\contentsline {subsection}{\numberline {5.11.8}Per TF classes}{101}{subsection.5.11.8}
\contentsline {subsection}{\numberline {5.11.9}Per TF sub-classes}{101}{subsection.5.11.9}
\contentsline {chapter}{\numberline {A}An appendix}{103}{appendix.A}
\contentsline {section}{\numberline {A.1}Supplementary figures}{103}{section.A.1}
\vspace {\normalbaselineskip }
\contentsline {chapter}{Bibliography}{121}{section*.63}
\contentsline {chapter}{Bibliography}{132}{appendix*.64}
\contentsline {chapter}{Curriculum Vitae}{133}{section*.65}

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