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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 {chapter}{\numberline {1}Published laboratory projects}{3}{chapter.1}
\contentsline {chapter}{Published laboratory projects}{3}{chapter.1}
\contentsline {section}{\numberline {1.1}Mass Genome Annotation repository}{3}{section.1.1}
\contentsline {subsection}{\numberline {1.1.1}Introduction}{3}{subsection.1.1.1}
\contentsline {subsection}{\numberline {1.1.2}MGA content and organization}{3}{subsection.1.1.2}
\contentsline {subsection}{\numberline {1.1.3}Conclusions}{5}{subsection.1.1.3}
\contentsline {section}{\numberline {1.2}Eukaryotic Promoter Database}{6}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}Introduction}{7}{subsection.1.2.1}
\contentsline {subsection}{\numberline {1.2.2}EPDnew now annotates (some of) your mushrooms and vegetables}{7}{subsection.1.2.2}
\contentsline {subsection}{\numberline {1.2.3}Increased mapping precision in human}{7}{subsection.1.2.3}
\contentsline {subsection}{\numberline {1.2.4}Integration of EPDnew with other resources}{9}{subsection.1.2.4}
\contentsline {subsection}{\numberline {1.2.5}Conclusions}{10}{subsection.1.2.5}
\contentsline {subsection}{\numberline {1.2.6}Methods}{10}{subsection.1.2.6}
\contentsline {subsubsection}{Motif occurrence profiles}{10}{subsection.1.2.6}
\contentsline {section}{\numberline {1.3}PWMScan}{10}{section.1.3}
\contentsline {subsection}{\numberline {1.3.1}Introduction}{10}{subsection.1.3.1}
\contentsline {subsection}{\numberline {1.3.2}Data and methods}{12}{subsection.1.3.2}
\contentsline {subsection}{\numberline {1.3.3}Benchmark}{13}{subsection.1.3.3}
\contentsline {subsection}{\numberline {1.3.4}Conclusions}{15}{subsection.1.3.4}
\contentsline {section}{\numberline {1.4}SPar-K}{17}{section.1.4}
\contentsline {subsection}{\numberline {1.4.1}Introduction}{17}{subsection.1.4.1}
\contentsline {subsection}{\numberline {1.4.2}Methods}{17}{subsection.1.4.2}
\contentsline {subsection}{\numberline {1.4.3}Results}{21}{subsection.1.4.3}
\contentsline {subsection}{\numberline {1.4.4}Conclusion}{21}{subsection.1.4.4}
\contentsline {chapter}{\numberline {2}ENCODE peaks analysis}{23}{chapter.2}
\contentsline {chapter}{ENCODE peaks analysis}{23}{chapter.2}
\contentsline {chapter}{\numberline {3}SMiLE-seq data analysis}{25}{chapter.3}
\contentsline {chapter}{SMiLE-seq data analysis}{25}{chapter.3}
\contentsline {subsection}{\numberline {3.0.1}Introduction}{25}{subsection.3.0.1}
\contentsline {subsection}{\numberline {3.0.2}Hidden Markov Model Motif discovery}{27}{subsection.3.0.2}
\contentsline {subsection}{\numberline {3.0.3}Binding motif evaluation}{28}{subsection.3.0.3}
\contentsline {subsection}{\numberline {3.0.4}Results}{30}{subsection.3.0.4}
\contentsline {subsection}{\numberline {3.0.5}Conclusions}{32}{subsection.3.0.5}
\contentsline {chapter}{\numberline {4}Chromatin accessibility of monocytes}{33}{chapter.4}
\contentsline {section}{\numberline {4.1}ATAC-seq}{33}{section.4.1}
\contentsline {section}{\numberline {4.2}Monitoring TF binding}{35}{section.4.2}
\contentsline {section}{\numberline {4.3}The advent of single cell DGF}{36}{section.4.3}
\contentsline {section}{\numberline {4.4}A quick overview of scATAC-seq data analysis}{36}{section.4.4}
\contentsline {section}{\numberline {4.5}Open questions}{36}{section.4.5}
\contentsline {section}{\numberline {4.6}Data}{38}{section.4.6}
\contentsline {section}{\numberline {4.7}Identification of catalog of chromatin architectures}{38}{section.4.7}
\contentsline {subsection}{\numberline {4.7.1}EMRead : an algorithm to identify over-represented chromatin architecture}{39}{subsection.4.7.1}
\contentsline {subsection}{\numberline {4.7.2}EMSequence : an algorithm to identify over-represented sequences}{40}{subsection.4.7.2}
\contentsline {subsubsection}{without shift and flip}{41}{subsection.4.7.2}
\contentsline {subsubsection}{with shift and flip}{41}{equation.4.7.2}
\contentsline {subsection}{\numberline {4.7.3}EMJoint : an algorithm to identify over-represented sequences and chromatin architectures}{42}{subsection.4.7.3}
\contentsline {subsection}{\numberline {4.7.4}Data realignment}{43}{subsection.4.7.4}
\contentsline {subsection}{\numberline {4.7.5}Implementations}{44}{subsection.4.7.5}
\contentsline {section}{\numberline {4.8}Results}{44}{section.4.8}
\contentsline {subsection}{\numberline {4.8.1}Fragment size analysis}{44}{subsection.4.8.1}
\contentsline {subsection}{\numberline {4.8.2}Measuring open chromatin and nucleosome occupancy}{48}{subsection.4.8.2}
\contentsline {subsection}{\numberline {4.8.3}Evaluation of EMRead and EMSequence}{49}{subsection.4.8.3}
\contentsline {subsubsection}{EMRead}{51}{subsection.4.8.3}
\contentsline {subsubsection}{EMSequence}{52}{figure.caption.29}
\contentsline {chapter}{\numberline {A}An appendix}{55}{appendix.A}
\contentsline {section}{\numberline {A.1}Supplementary figures}{55}{section.A.1}
\vspace {\normalbaselineskip }
\contentsline {chapter}{Bibliography}{61}{section*.38}
\contentsline {chapter}{Bibliography}{67}{appendix*.39}
\contentsline {chapter}{Curriculum Vitae}{69}{section*.40}

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