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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 {section}{\numberline {1.2}About transcription factors}{5}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}TF co-binding}{6}{subsection.1.2.1}
\contentsline {subsection}{\numberline {1.2.2}Modeling sequence specificity}{7}{subsection.1.2.2}
\contentsline {subsubsection}{Position weight matrix}{7}{subsection.1.2.2}
\contentsline {subsubsection}{Predicting binding sites}{9}{equation.1.2.4}
\contentsline {subsubsection}{Aligning binding sites}{10}{equation.1.2.6}
\contentsline {subsection}{\numberline {1.2.3}Measuring TF binding in vivo}{10}{subsection.1.2.3}
\contentsline {subsection}{\numberline {1.2.4}Measuring TF binding in vitro}{11}{subsection.1.2.4}
\contentsline {section}{\numberline {1.3}About nucleosome positioning}{11}{section.1.3}
\contentsline {section}{\numberline {1.4}Gene regulation in a nutshell}{14}{section.1.4}
\contentsline {subsection}{\numberline {1.4.1}The chromatin barrier}{14}{subsection.1.4.1}
\contentsline {subsection}{\numberline {1.4.2}TFs cooperative binding}{14}{subsection.1.4.2}
\contentsline {subsection}{\numberline {1.4.3}Pioneer TFs}{15}{subsection.1.4.3}
\contentsline {subsection}{\numberline {1.4.4}Regulatory elements}{15}{subsection.1.4.4}
\contentsline {subsection}{\numberline {1.4.5}The genome goes 3D}{16}{subsection.1.4.5}
\contentsline {subsection}{\numberline {1.4.6}Digital footprinting}{17}{subsection.1.4.6}
\contentsline {chapter}{\numberline {2}Laboratory resources}{21}{chapter.2}
\contentsline {chapter}{Laboratory resources}{21}{chapter.2}
\contentsline {section}{\numberline {2.1}Mass Genome Annotation repository}{21}{section.2.1}
\contentsline {subsection}{\numberline {2.1.1}MGA content and organization}{22}{subsection.2.1.1}
\contentsline {subsection}{\numberline {2.1.2}Conclusions}{24}{subsection.2.1.2}
\contentsline {section}{\numberline {2.2}Eukaryotic Promoter Database}{25}{section.2.2}
\contentsline {subsection}{\numberline {2.2.1}EPDnew now annotates (some of) your mushrooms and vegetables}{26}{subsection.2.2.1}
\contentsline {subsection}{\numberline {2.2.2}Increased mapping precision in human}{27}{subsection.2.2.2}
\contentsline {subsection}{\numberline {2.2.3}Integration of EPDnew with other resources}{27}{subsection.2.2.3}
\contentsline {subsection}{\numberline {2.2.4}Conclusions}{28}{subsection.2.2.4}
\contentsline {subsection}{\numberline {2.2.5}Methods}{28}{subsection.2.2.5}
\contentsline {subsubsection}{Motif occurrence profiles}{28}{subsection.2.2.5}
\contentsline {chapter}{\numberline {3}ENCODE peaks analysis}{29}{chapter.3}
\contentsline {chapter}{ENCODE peaks analysis}{29}{chapter.3}
\contentsline {section}{\numberline {3.1}Data}{29}{section.3.1}
\contentsline {section}{\numberline {3.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{31}{section.3.2}
\contentsline {subsection}{\numberline {3.2.1}Data realignment}{32}{subsection.3.2.1}
\contentsline {section}{\numberline {3.3}Nucleosome organization around transcription factor binding sites}{33}{section.3.3}
\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{35}{section.3.4}
\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{39}{section.3.5}
\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{43}{section.3.6}
\contentsline {section}{\numberline {3.7}Discussion}{46}{section.3.7}
\contentsline {section}{\numberline {3.8}Methods}{46}{section.3.8}
\contentsline {subsection}{\numberline {3.8.1}Data and data processing}{46}{subsection.3.8.1}
\contentsline {subsection}{\numberline {3.8.2}Classification of MNase patterns}{47}{subsection.3.8.2}
\contentsline {subsection}{\numberline {3.8.3}Quantifying nucleosome array intensity from classification results}{48}{subsection.3.8.3}
\contentsline {subsection}{\numberline {3.8.4}Peak colocalization}{49}{subsection.3.8.4}
\contentsline {subsection}{\numberline {3.8.5}NDR detection}{50}{subsection.3.8.5}
\contentsline {subsection}{\numberline {3.8.6}CTCF and JunD interactors}{52}{subsection.3.8.6}
\contentsline {subsection}{\numberline {3.8.7}EBF1 and nucleosome}{53}{subsection.3.8.7}
\contentsline {chapter}{\numberline {4}SMiLE-seq data analysis}{55}{chapter.4}
\contentsline {chapter}{SMiLE-seq data analysis}{55}{chapter.4}
\contentsline {subsection}{\numberline {4.0.1}Introduction}{55}{subsection.4.0.1}
\contentsline {subsection}{\numberline {4.0.2}Hidden Markov Model Motif discovery}{57}{subsection.4.0.2}
\contentsline {subsection}{\numberline {4.0.3}Binding motif evaluation}{58}{subsection.4.0.3}
\contentsline {subsection}{\numberline {4.0.4}Results}{60}{subsection.4.0.4}
\contentsline {subsection}{\numberline {4.0.5}Conclusions}{62}{subsection.4.0.5}
\contentsline {chapter}{\numberline {5}PWMScan}{63}{chapter.5}
\contentsline {section}{\numberline {5.1}Algorithms}{63}{section.5.1}
\contentsline {subsection}{\numberline {5.1.1}Scanner algorithm}{64}{subsection.5.1.1}
\contentsline {subsection}{\numberline {5.1.2}Matches enumeration and mapping}{64}{subsection.5.1.2}
\contentsline {section}{\numberline {5.2}PMWScan architecture}{65}{section.5.2}
\contentsline {section}{\numberline {5.3}Benchmark}{67}{section.5.3}
\contentsline {section}{\numberline {5.4}Conclusions}{69}{section.5.4}
\contentsline {chapter}{\numberline {6}Chromatin accessibility of monocytes}{71}{chapter.6}
\contentsline {section}{\numberline {6.1}Monitoring TF binding}{71}{section.6.1}
\contentsline {section}{\numberline {6.2}The advent of single cell DGF}{72}{section.6.2}
\contentsline {section}{\numberline {6.3}Open issues}{72}{section.6.3}
\contentsline {section}{\numberline {6.4}Data}{72}{section.6.4}
\contentsline {section}{\numberline {6.5}Identifying over-represented signals}{73}{section.6.5}
\contentsline {subsection}{\numberline {6.5.1}ChIPPartitioning : an algorithm to identify over-represented read patterns}{73}{subsection.6.5.1}
\contentsline {subsection}{\numberline {6.5.2}EMSequence : an algorithm to identify over-represented sequences}{73}{subsection.6.5.2}
\contentsline {subsubsection}{without shift and flip}{75}{figure.caption.30}
\contentsline {subsubsection}{with shift and flip}{75}{equation.6.5.2}
\contentsline {subsection}{\numberline {6.5.3}EMJoint : an algorithm to identify over-represented sequences and chromatin architectures}{76}{subsection.6.5.3}
\contentsline {subsection}{\numberline {6.5.4}Data realignment}{77}{subsection.6.5.4}
\contentsline {section}{\numberline {6.6}Results}{78}{section.6.6}
\contentsline {subsection}{\numberline {6.6.1}Fragment size analysis}{80}{subsection.6.6.1}
\contentsline {subsection}{\numberline {6.6.2}Measuring open chromatin and nucleosome occupancy}{80}{subsection.6.6.2}
\contentsline {subsection}{\numberline {6.6.3}Evaluation of EMSequence and ChIPPartitioning}{82}{subsection.6.6.3}
\contentsline {subsubsection}{EMSequence}{83}{subsection.6.6.3}
\contentsline {subsubsection}{ChIPPartitioning}{85}{figure.caption.35}
\contentsline {section}{\numberline {6.7}Aligning the binding sites}{87}{section.6.7}
\contentsline {section}{\numberline {6.8}Exploring individual TF classes}{91}{section.6.8}
\contentsline {section}{\numberline {6.9}Discussions}{91}{section.6.9}
\contentsline {section}{\numberline {6.10}Perspectives}{92}{section.6.10}
\contentsline {section}{\numberline {6.11}Methods}{93}{section.6.11}
\contentsline {subsection}{\numberline {6.11.1}Partitioning programs}{93}{subsection.6.11.1}
\contentsline {subsection}{\numberline {6.11.2}Fragment classes}{93}{subsection.6.11.2}
\contentsline {subsection}{\numberline {6.11.3}Simulated sequences}{94}{subsection.6.11.3}
\contentsline {subsection}{\numberline {6.11.4}Realignment using JASPAR motifs}{94}{subsection.6.11.4}
\contentsline {subsection}{\numberline {6.11.5}Model extension}{96}{subsection.6.11.5}
\contentsline {subsection}{\numberline {6.11.6}Extracting data assigned to a class}{96}{subsection.6.11.6}
\contentsline {subsection}{\numberline {6.11.7}Peak processing}{99}{subsection.6.11.7}
\contentsline {subsection}{\numberline {6.11.8}Per TF classes}{99}{subsection.6.11.8}
\contentsline {subsection}{\numberline {6.11.9}Per TF sub-classes}{99}{subsection.6.11.9}
\contentsline {chapter}{\numberline {7}Discussion}{101}{chapter.7}
\contentsline {chapter}{Discussions}{101}{chapter.7}
\vspace {\normalbaselineskip }
\contentsline {chapter}{\numberline {A}An appendix}{105}{appendix.A}
\contentsline {section}{\numberline {A.1}Supplementary figures}{105}{section.A.1}
\contentsline {chapter}{Bibliography}{123}{section*.60}
\contentsline {chapter}{Bibliography}{135}{appendix*.61}
\contentsline {chapter}{Curriculum Vitae}{137}{section*.62}

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