% \bibitem{}Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime \textit{cis}-regulatory elements required for macrophage and B cell identities. \textit{Mol. Cell} \textbf{38}, 576--589 (2010).
% \bibitem{}Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime \textit{cis}-regulatory elements required for macrophage and B cell identities. \textit{Mol. Cell} \textbf{38}, 576--589 (2010).



\bibitem{Ren2000}Ren, B. et al. Genome-wide location and function of DNA binding proteins. \textit{Science} \textbf{290}, 2306--2309 (2000).

\bibitem{Barsk2007}Barski, A. et al. High-resolution profiling of histone methylations in the human genome. \textit{Cell} \textbf{129}, 823--837 (2007).

\bibitem{Marinov2014}Marinov, G. K., Kundaje, A., Park, P. J. \& Wold, B. J. Large-scale quality analysis of published ChIP-seq data. \textit{G3 (Bethesda)} \textbf{4}, 209--223 (2014).

\bibitem{Dreos2017}Dr\'eos R, et al. MGA repository: a curated data resource for ChIP-seq and other genome annotated data. \textit{Nucleic Acids Res.} \textbf{46}, D175--D180. % doi: 10.1093/nar/gkx995.

\bibitem{ENCODE2012}ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. \textit{Nature} \textbf{489}, 57--74 (2012).

\bibitem{modENCODE2010}modENCODE Consortium et al. Identification of functional elements and regulatory circuits by \textit{Drosophila} modENCODE. \textit{Science} \textbf{330}, 1787--1797 (2010).

\bibitem{Gerstein2010}Gerstein, M. B. et al. Integrative analysis of the \textit{Caenorhabditis elegans} genome by the modENCODE project. \textit{Science} \textbf{330}, 1775--1787 (2010).

\bibitem{Roadmap2015}Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. \textit{Nature} \textbf{518}, 317--330 (2015)

\bibitem{Park2009}Park, P. J. \& Park, P. J. ChIP–seq: advantages and challenges of a maturing technology. \textit{Nat Rev Genet} \textbf{10}, 669--680 (2009).

\bibitem{Pepke2009}Pepke, S., Wold, B. \& Mortazavi, A. Computation for ChIP-seq and RNA-seq studies. \textit{Nat. Meth.} \textbf{6}, S22--32 (2009).

\bibitem{Landt2012}Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. \textit{Genome Res.} \textbf{22}, 1813--1831 (2012).

\bibitem{Jung2014}Jung, Y. L. et al. Impact of sequencing depth in ChIP-seq experiments. \textit{Nucleic Acids Res.} \textbf{42}, e74 (2014).

\bibitem{Tyner2017}Tyner C, et al. The UCSC Genome Browser database: 2017 update. \textit{Nucleic Acids Res.} \textbf{45}, D626--D634. (2017)

\bibitem{Zhou2011}Zhou, X, et al. The Human Epigenome Browser at Washington University. \textit{Nat. Methods} \textbf{8}(12), 989--990. (2011)

\bibitem{Thorvaldsdottir2013}Thorvaldsdottir, H., Robinson, J. T. \& Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. \textit{Brief. Bioinform.} \textbf{14}, 178--192 (2013).

\bibitem{Zhang2008}Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). \textit{Genome Biol.}. \textbf{9}, R137 (2008).

\bibitem{Kharchenko2008}Kharchenko, P. V., Tolstorukov, M. Y. \& Park, P. J. Design and analysis of ChIP-seq experiments for DNA-binding proteins. \textit{Nat. Biotechnol.} \textbf{26}, 1351--1359 (2008).

\bibitem{Gerstein2012}Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. \textit{Nature} \textbf{489}, 91--100 (2012).

\bibitem{Li2011}Li, Q., Brown, J. B., Huang, H. \& Bickel, P. J. Measuring reproducibility of high-throughput experiments. \textit{Ann. Appl. Stat}. \textbf{5}, 1752--1779 (2011).

\bibitem{Kasowski2013}Kasowski, M. et al. Extensive Variation in Chromatin States Across Humans. \textit{Science} \textbf{342}, 750--752 (2013).

\bibitem{Motamedi2014}Motamedi, F. J. et al. WT1 controls antagonistic FGF and BMP-pSMAD pathways in early renal progenitors. \textit{Nat. Commun.} \textbf{5}, 4444 (2014).

\bibitem{Crawford2006}Crawford, G. E. et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). \textit{Genome Res.} \textbf{16}, 123--131 (2006).

\bibitem{Giresi2007}Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R. \& Lieb, J. D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. \textit{Genome Res.} \textbf{17}, 877--885 (2007).

\bibitem{Buenrostro2013}Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. \& Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. \textit{Nat. Meth.} \textbf{10}, 1213--1218 (2013).

\bibitem{Patel2012}Patel, R. K. \& Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. \textit{PLoS ONE} \textbf{7}, e30619 (2012).

\bibitem{Daley2013}Daley, T. \& Smith, A. D. Predicting the molecular complexity of sequencing libraries. \textit{Nat. Meth.} \textbf{10}, 325--327 (2013).

\bibitem{Yang2013}Yang, X. et al. HTQC: a fast quality control toolkit for Illumina sequencing data. \textit{BMC Bioinform.} \textbf{14}, 33 (2013).

\bibitem{Diaz2012}Diaz, A., Nellore, A. \& Song, J. S. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. \textit{Genome Biol.} \textbf{13}, R98 (2012).

\bibitem{Planet2012}Planet, E., Attolini, C. S.-O., Reina, O., Flores, O. \& Rossell, D. htSeqTools: high-throughput sequencing quality control, processing and visualization in R. \textit{Bioinformatics} \textbf{28}, 589--590 (2012).

\bibitem{Mendoza2013}Mendoza-Parra, M.-A., Van Gool, W., Mohamed Saleem, M. A., Ceschin, D. G. \& Gronemeyer, H. A quality control system for profiles obtained by ChIP sequencing. \textit{Nucleic Acids Res.} \textbf{41}, e196 (2013).

\bibitem{Bardet2012}Bardet, A. F., He, Q., Zeitlinger, J. \& Stark, A. A computational pipeline for comparative ChIP-seq analyses. \textit{Nat. Protoc.} \textbf{7}, 45--61 (2012).

\bibitem{Li2009}Li, H. \& Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. \textit{Bioinformatics} \textbf{25}, 1754--1760 (2009).

\bibitem{Langmead2009}Langmead, B., Trapnell, C., Pop, M. \& Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. \textit{Genome Biol.} \textbf{10}, R25 (2009).

\bibitem{Langmead2012}Langmead, B. \& Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. \textit{Nat. Methods} \textbf{9}, 357--359 (2012)

\bibitem{Sasaki2009}Sasaki, S. et al. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. \textit{Science} \textbf{323}, 401--404 (2009).

\bibitem{Diaz2012b}Diaz, A., et al. Normalization, bias correction, and peak calling for ChIP-seq. \textit{Stat Appl Genet Mol Biol} \textbf{11}, Article 9 (2012). 

\bibitem{Ramirez2016}Ram\'irez F, Ryan DP, Gr\"uning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, D\"undar F, Manke T. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. \textit{Nucleic Acids Res} \textbf{44}(W1):W160--165. % doi: 10.1093/nar/gkw257. 

\bibitem{Bailey2013}Bailey, T. et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. \textit{PLoS Comput. Biol.} \textbf{9}, e1003326 (2013).

\bibitem{Schmidl2015}Schmidl, C., et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. \textit{Nat Methods} \textbf{12}, 963--965 (2015).

\bibitem{Zarnegar2017}Zarnegar, M.A., et al. Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers. \textit{Nucleic Acids Res} \textbf{45}< e153 (2017).

\bibitem{Rhee2011}Rhee, H.S., \& B.F. Pugh. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. \textit{Cell} \textbf{147}, 1408--1419 (2011).

\bibitem{He2015}He, Q., et al. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. \textit{Nat Biotechnol} \textbf{33}, 395--401 (2015)

\bibitem{Zentner2015}Zentner, G.E., et al. ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. \textit{Nat Commun} \textbf{6}, 8733 (2015).

\bibitem{Skene2017}Skene, P.J., \& S. Henikoff. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. \textit{Elife} \textbf{6}, pii: e21856 (2017).