The human transcription factors, Cell, vol.172, pp.650-665, 2018. ,
Identification of altered cis-regulatory elements in human disease, Trends Genet, vol.31, pp.67-76, 2015. ,
Genome-wide mapping of in vivo protein-DNA interactions, Science, vol.316, pp.1497-1502, 2007. ,
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.18602-18607, 2013. ,
Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments, Nucleic Acids Res, vol.43, pp.6959-6968, 2015. ,
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets, Genome Biol, vol.15, p.412, 2014. ,
Modeling the specificity of protein-DNA interactions, Quant Biol, vol.1, pp.115-130, 2013. ,
Evaluation of methods for modeling transcription factor sequence specificity, Nat. Biotechnol, vol.31, pp.126-134, 2013. ,
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites, J. Bioinform. Comput. Biol, vol.11, p.1340004, 2013. ,
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data, BMC Bioinformatics, vol.16, p.375, 2015. ,
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences, Nucleic Acids Res, vol.44, pp.6055-6069, 2016. ,
Absence of a simple code: how transcription factors read the genome, Trends Biochem. Sci, vol.39, pp.381-399, 2014. ,
Varying levels of complexity in transcription factor binding motifs, Nucleic Acids Res, vol.43, p.119, 2015. ,
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models, Mol. Syst. Biol, vol.13, p.910, 2017. ,
DNA shape features improve transcription factor binding site predictions in vivo, Cell Syst, vol.3, pp.278-286, 2016. ,
DOI : 10.1016/j.cels.2016.07.001
URL : https://doi.org/10.1016/j.cels.2016.07.001
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments, Nucleic Acids Res, vol.46, pp.267-275, 2018. ,
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments, Nucleic Acids Res, vol.45, pp.61-67, 2017. ,
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data, Nucleic Acids Res, vol.45, pp.43-50, 2017. ,
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse, Nucleic Acids Res, vol.45, pp.658-662, 2017. ,
The UCSC Genome Browser Database: update, Nucleic Acids Res, vol.34, pp.590-598, 2006. ,
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation, Bioinformatics, vol.22, pp.637-640, 2006. ,
DOI : 10.1093/bioinformatics/btk027
URL : https://academic.oup.com/bioinformatics/article-pdf/22/5/637/538215/btk027.pdf
The human genome browser at UCSC, Genome Res, vol.12, pp.996-1006, 2002. ,
MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations, Sci Data, vol.5, p.180141, 2018. ,
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework, Nucleic Acids Res, vol.46, p.1284, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01646126
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment, BMC Genomics, vol.15, p.472, 2014. ,
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints, PLoS Comput. Biol, vol.8, p.1002638, 2012. ,
DOI : 10.1371/journal.pcbi.1002638
URL : https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002638&type=printable
Inferring direct DNA binding from ChIP-seq, Nucleic Acids Res, vol.40, p.128, 2012. ,
Deep and wide digging for binding motifs in ChIP-Seq data, Bioinformatics, vol.26, pp.2622-2623, 2010. ,
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data, Nucleic Acids Res, vol.36, pp.5221-5231, 2008. ,
Evaluation of algorithm performance in ChIP-Seq peak detection, PLoS One, vol.5, p.11471, 2010. ,
The next generation of transcription factor binding site prediction, PLoS Comput. Biol, vol.9, p.1003214, 2013. ,
Improved models for transcription factor binding site identification using nonindependent interactions, Genetics, vol.191, pp.781-790, 2012. ,
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities, Nat. Biotechnol, vol.24, pp.1429-1435, 2006. ,
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution, Cell, vol.147, pp.1408-1419, 2011. ,
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors, Genome Biol, vol.13, p.48, 2012. ,
Applied bioinformatics for the identification of regulatory elements, Nat. Rev. Genet, vol.5, pp.276-287, 2004. ,
Discriminative motif optimization based on perceptron training, Bioinformatics, vol.30, pp.941-948, 2014. ,
GBshape: a genome browser database for DNA shape annotations, Nucleic Acids Res, vol.43, pp.103-109, 2015. ,
BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010. ,
, Modern Applied Statistics with, 2002.
A new method for gray-level picture thresholding using the entropy of the histogram, Comput. Vis. Graph. Image Process, vol.29, p.140, 1985. ,
A Mathematical Theory of Communication, Bell Syst. Tech. J, vol.27, pp.623-656, 1948. ,
NIH Image to ImageJ: 25 years of image analysis, Nat. Methods, vol.9, pp.671-675, 2012. ,
MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009. ,
Quantifying DNA-protein interactions by double-stranded DNA arrays, Nat. Biotechnol, vol.17, pp.573-577, 1999. ,
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.43, pp.117-122, 2015. ,
On a test of whether one of two random variables is stochastically larger than the other, Ann. Math. Stat, vol.18, pp.50-60, 1947. ,
Characterizing protein-DNA binding event subtypes in ChIP-exo data, Bioinformatics, 2018. ,
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities, Mol. Cell, vol.38, pp.576-589, 2010. ,
Genome-wide localization of protein-DNA binding, 2012. ,
, 13 Bayesian change-point method with ChIP-seq data, Nucleic Acids Research, vol.8, p.1002613, 2018.
Model-based analysis of ChIP-Seq (MACS), Genome Biol, vol.9, p.137, 2008. ,
More powerful procedures for multiple significance testing, Stat. Med, vol.9, pp.811-818, 1990. ,
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update, Nucleic Acids Res, vol.46, pp.537-544, 2018. ,
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function, Nucleic Acids Res, vol.38, pp.214-234, 2010. ,
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals, Bioinformatics, vol.32, pp.1214-1216, 2015. ,
The NCBI dbGaP database of genotypes and phenotypes, Nat. Genet, vol.39, pp.1181-1186, 2007. ,
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations, Nucleic Acids Res, vol.42, pp.1001-1006, 2014. ,
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Res, vol.15, pp.1034-1050, 2005. ,
BEDOPS: high-performance genomic feature operations, Bioinformatics, vol.28, pp.1919-1920, 2012. ,
bwtool: a tool for bigWig files, Bioinformatics, vol.30, pp.1618-1619, 2014. ,
Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins, Methods Mol. Biol, vol.338, pp.245-260, 2006. ,
Dynamic trans-Acting factor colocalization in human cells, Cell, vol.155, pp.713-724, 2013. ,
Comparative analysis of regulatory information and circuits across distant species, Nature, vol.512, pp.453-456, 2014. ,
Functional analysis of transcription factor binding sites in human promoters, Genome Biol, vol.13, p.50, 2012. ,
Super-enhancers in the control of cell identity and disease, Cell, vol.155, pp.934-947, 2013. ,
Dynamic CRM occupancy reflects a temporal map of developmental progression, 2010. ,
, Mol. Syst. Biol, vol.6, p.383
Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, vol.153, pp.307-319, 2013. ,
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species, Nat. Genet, vol.43, pp.414-420, 2011. ,
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.21330-21335, 2012. ,
Data sharing, N. Engl. J. Med, vol.374, pp.276-277, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01112977