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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}{Introduction}{1}{chapter*.7}
\contentsline {part}{I\hspace {1em}Body 1}{3}{part.1}
\contentsline {chapter}{\numberline {1}Published softwares}{5}{chapter.1}
\contentsline {chapter}{Published softwares}{5}{chapter.1}
\contentsline {section}{\numberline {1.1}PWMScan}{5}{section.1.1}
\contentsline {subsection}{\numberline {1.1.1}Introduction}{5}{subsection.1.1.1}
\contentsline {subsection}{\numberline {1.1.2}Data and methods}{7}{subsection.1.1.2}
\contentsline {subsection}{\numberline {1.1.3}Benchmark}{8}{subsection.1.1.3}
\contentsline {section}{\numberline {1.2}SPar-K}{10}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}Introduction}{10}{subsection.1.2.1}
\contentsline {subsection}{\numberline {1.2.2}Methods}{10}{subsection.1.2.2}
\contentsline {subsection}{\numberline {1.2.3}Results}{14}{subsection.1.2.3}
\contentsline {subsection}{\numberline {1.2.4}Conclusion}{14}{subsection.1.2.4}
\contentsline {chapter}{ENCODE peaks analysis}{15}{chapter*.14}
\contentsline {chapter}{SMiLE-seq data analysis}{17}{chapter*.15}
\contentsline {subsection}{\numberline {1.2.5}Introduction}{17}{subsection.1.2.5}
\contentsline {subsection}{\numberline {1.2.6}Hidden Markov Model motif discovery}{17}{subsection.1.2.6}
\contentsline {subsubsection}{Hidden Markov model motif discovery}{17}{figure.caption.17}
\contentsline {subsection}{\numberline {1.2.7}Binding motif evaluation}{20}{subsection.1.2.7}
\contentsline {subsection}{\numberline {1.2.8}Results}{22}{subsection.1.2.8}
\contentsline {chapter}{\numberline {2}Chromatin accessibility of monocytes}{25}{chapter.2}
\contentsline {section}{\numberline {2.1}ATAC-seq}{25}{section.2.1}
\contentsline {section}{\numberline {2.2}Monitoring TF binding}{27}{section.2.2}
\contentsline {section}{\numberline {2.3}The advent of single cell DGF}{28}{section.2.3}
\contentsline {section}{\numberline {2.4}A quick overview of scATAC-seq data analysis}{28}{section.2.4}
\contentsline {section}{\numberline {2.5}Open questions}{28}{section.2.5}
\contentsline {section}{\numberline {2.6}Data}{30}{section.2.6}
\contentsline {section}{\numberline {2.7}Identification of catalog of chromatin architectures}{30}{section.2.7}
\contentsline {subsection}{\numberline {2.7.1}EMRead : an algorithm to identify over-represented chromatin architecture}{31}{subsection.2.7.1}
\contentsline {subsection}{\numberline {2.7.2}EMSequence : an algorithm to identify over-represented sequences}{32}{subsection.2.7.2}
\contentsline {subsubsection}{without shift and flip}{33}{subsection.2.7.2}
\contentsline {subsubsection}{with shift and flip}{33}{equation.2.7.2}
\contentsline {subsection}{\numberline {2.7.3}EMJoint : an algorithm to identify over-represented sequences and chromatin architectures}{34}{subsection.2.7.3}
\contentsline {subsection}{\numberline {2.7.4}Further generalizing EMJoint}{35}{subsection.2.7.4}
\contentsline {subsection}{\numberline {2.7.5}Data realignment}{35}{subsection.2.7.5}
\contentsline {subsection}{\numberline {2.7.6}Implementations}{36}{subsection.2.7.6}
\contentsline {section}{\numberline {2.8}Results}{36}{section.2.8}
\contentsline {subsection}{\numberline {2.8.1}Fragment size analysis}{36}{subsection.2.8.1}
\contentsline {subsection}{\numberline {2.8.2}Measuring open chromatin and nucleosome occupancy}{39}{subsection.2.8.2}
\contentsline {subsection}{\numberline {2.8.3}Evaluation of EMRead and EMSequence}{42}{subsection.2.8.3}
\contentsline {subsubsection}{EMRead}{42}{subsection.2.8.3}
\contentsline {subsubsection}{EMSequence}{44}{figure.caption.26}
\contentsline {part}{II\hspace {1em}Body 2}{49}{part.2}
\contentsline {chapter}{\numberline {A}An appendix}{51}{appendix.A}
\contentsline {section}{\numberline {A.1}Supplementary figures}{51}{section.A.1}
\vspace {\normalbaselineskip }
\contentsline {chapter}{Bibliography}{55}{section*.33}
\contentsline {chapter}{Bibliography}{58}{appendix*.34}
\contentsline {chapter}{Curriculum Vitae}{59}{section*.35}

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