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my_thesis.toc
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\babel
@toc
{
english
}{}
\babel
@toc
{
french
}{}
\babel
@toc
{
english
}{}
\contentsline
{
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
{
1.5.3
}
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
}
\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
}
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