FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845

Automated generation of heuristics for biological sequence comparison

Slater, G., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,959

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927

Dynamic Regulation of Nucleosome Positioning in the Human Genome

Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

Morin, R. D., O’Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M., et al. (2008) · Genome Research · doi:10.1101/gr.7179508 · Cited by 1,110

Genomic mapping by fingerprinting random clones: A mathematical analysis

Lander, E. S., & Waterman, M. S. (1988) · Genomics · doi:10.1016/0888-7543(88)90007-9 · Cited by 942

Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing

Taylor, K. H., Kramer, R. S., Davis, J. W., Guo, J., Duff, D. J., Xu, D. H., Caldwell, C. W., & Shi, H. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-1016 · Cited by 258

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217

Identifying ChIP-seq enrichment using MACS

Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.101 · Cited by 1,848

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Zhu, L. J., Gazin, C., Lawson, N. D., Pagès, H., Lin, S. M., Lapointe, D. S., & Green, M. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-237 · Cited by 1,159

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,072

Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways

Palmieri, M., Impey, S., Kang, H., di Ronza, A., Pelz, C., Sardiello, M., & Ballabio, A. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr306 · Cited by 1,022

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865

Next-Generation Sequencing: From Basic Research to Diagnostics

Voelkerding, K. V., Dames, S. A., & Durtschi, J. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.112789 · Cited by 903

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A. F., Smith, A. G., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.026 · Cited by 870

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, J. V., Hyman, A. A., Stunnenberg, H. G., et al. (2010) · Cell · doi:10.1016/j.cell.2010.08.020 · Cited by 806

Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

Malhotra, D., Portales-Casamar, É., Singh, A., Srivastava, S., Arenillas, D. J., Happel, C., Shyr, C., Wakabayashi, N., Kensler, T. W., Wasserman, W. W., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq212 · Cited by 812

Embryonic stem cell–specific microRNAs promote induced pluripotency

Judson, R. L., Babiarz, J., Venere, M., & Blelloch, R. H. (2009) · Nature Biotechnology · doi:10.1038/nbt.1535 · Cited by 702

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.04.004 · Cited by 535

Computation for ChIP-seq and RNA-seq studies

Pepke, S., Wold, B. J., & Mortazavi, A. (2009) · Nature Methods · doi:10.1038/nmeth.1371 · Cited by 568

Insights from genomic profiling of transcription factors

Farnham, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2636 · Cited by 519

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 530

Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesisPreprint

Nielsen, R., Pedersen, T. Å., Hagenbeek, D., Moulos, P., Siersbæk, R., Megens, E., Denissov, S., Børgesen, M., Françoijs, K., Mandrup, S., et al. (2008) · Genes & Development · doi:10.1101/gad.501108 · Cited by 520

Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis

Gou, L., Dai, P., Yang, J.-H., Xue, Y., Hu, Y.-P., Zhou, Y., Kang, J.-Y., Wang, X., Li, H., Hua, M.-M., et al. (2014) · Cell Research · doi:10.1038/cr.2014.41 · Cited by 428

ChIP‐Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

Welboren, W.-J., van Driel, M. A., Janssen‐Megens, E. M., van Heeringen, S. J., Sweep, F. C. G. J., Span, P. N., & Stunnenberg, H. G. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.88 · Cited by 395

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

Ernst, J., & Kellis, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3157 · Cited by 357

In the News

MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2122 · Cited by 320

Application of 'next-generation' sequencing technologies to microbial genetics

MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293

Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators

Tijssen, M. R., Cvejic, A., Joshi, A., Hannah, R., Ferreira, R., Forrai, A., Bellissimo, D. C., Oram, S. H., Smethurst, P. A., Wilson, N. K., et al. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.04.008 · Cited by 296

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

Wilbanks, E. G., & Facciotti, M. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011471 · Cited by 302

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

Kwon, A. T.-J., Arenillas, D. J., Worsley-Hunt, R., & Wasserman, W. W. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.003202 · Cited by 283

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., & Ule, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r67 · Cited by 234

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Salmon‐Divon, M., Dvinge, H., Koort, K., & Bertone, P. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-415 · Cited by 244

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

Seitan, V. C., Hao, B., Tachibana-Konwalski, K., Lavagnolli, T., Mira-Bontenbal, H., Brown, K. E., Teng, G., Carroll, T., Terry, A. V., Horan, K., et al. (2011) · Nature · doi:10.1038/nature10312 · Cited by 234

Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites

Boergesen, M., Pedersen, T. Å., Gross, B. S., van Heeringen, S. J., Hagenbeek, D., Bindesbøll, C., Caron, S., Lalloyer, F., Steffensen, K. R., Nebb, H. I., et al. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.06175-11 · Cited by 242

Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo

Rugg‐Gunn, P. J., Cox, B., Ralston, A., & Rossant, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914507107 · Cited by 240

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

Nix, D. A., Courdy, S., & Boucher, K. M. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-523 · Cited by 223

The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function

Guillon, N., Tirode, F., Boeva, V., Zynovyev, A., Barillot, E., & Delattre, O. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004932 · Cited by 218

Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia telangiectasia

Li, J., Chen, J., Ricupero, C. L., Hart, R. P., Schwartz, M. S., Kusnecov, A., & Herrup, K. (2012) · Nature Medicine · doi:10.1038/nm.2709 · Cited by 210

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

Markljung, E., Jiang, L., Jaffe, J. D., Mikkelsen, T. S., Wallerman, O., Larhammar, M., Zhang, X., Wang, L., Saenz-Vash, V., Gnirke, A., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000256 · Cited by 207

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

Saulière, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Tonquèze, O. L., Audic, Y., Paillard, L., Crollius, H. R., & Hir, H. L. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2420 · Cited by 216

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timingPreprint

Dellino, G. I., Cittaro, D., Piccioni, R., Luzi, L., Banfi, S., Segalla, S., Cesaroni, M., Mendoza-Maldonado, R., Giacca, M., & Pelicci, P. G. (2012) · Genome Research · doi:10.1101/gr.142331.112 · Cited by 190

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

Giresi, P. G., & Lieb, J. D. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.003 · Cited by 198

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells

Maksakova, I. A., Thompson, P. J., Goyal, P., Jones, S. J. M., Singh, P. B., Karimi, M. M., & Lorincz, M. C. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-15 · Cited by 189

Genomic location analysis by ChIP‐Seq

Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182

Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells

Weishi, Z., Prakash, C., Sum, C., Gong, Y., Li, Y., Kwok, J. J. T., Thiessen, N., Pettersson, S., Jones, S. J. M., Knapp, S., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.413047 · Cited by 185

KDM5B regulates embryonic stem cell self‐renewal and represses cryptic intragenic transcription

Xie, L., Pelz, C., Wang, W., Bashar, A., Varlamova, O., Shadle, S. C., & Impey, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.91 · Cited by 180

EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia

Li, J., Hart, R. P., Mallimo, E. M., Swerdel, M. R., Kusnecov, A. W., & Herrup, K. (2013) · Nature Neuroscience · doi:10.1038/nn.3564 · Cited by 177

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs

Zünd, D., Gruber, A. R., Zavolan, M., & Mühlemann, O. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2635 · Cited by 171

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

Horner, D. S., Pavesi, G., Castrignanò, T., Meo, P. D. D., Liuni, S., Sammeth, M., Picardi, E., & Pesole, G. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp046 · Cited by 183

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

Ing-Simmons, E., Seitan, V. C., Faure, A. J., Flicek, P., Carroll, T., Dekker, J., Fisher, A. G., Lenhard, B., & Merkenschlager, M. (2015) · Genome Research · doi:10.1101/gr.184986.114 · Cited by 167

Erk1/2 Activity Promotes Chromatin Features and RNAPII Phosphorylation at Developmental Promoters in Mouse ESCs

Tee, W.-W., Shen, S. S., Oksuz, O., Narendra, V., & Reinberg, D. (2014) · Cell · doi:10.1016/j.cell.2014.01.009 · Cited by 165

Uniform, optimal signal processing of mapped deep-sequencing data

Kumar, V., Muratani, M., Rayan, N. A., Kraus, P., Lufkin, T., Ng, H., & Prabhakar, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2596 · Cited by 161

Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans

Ketel, C. S., Wang, H. S. W., McClellan, M., Bouchonville, K. J., Selmecki, A. M., Lahav, T., Gerami‐Nejad, M., & Berman, J. G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000400 · Cited by 170

Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications

O’Geen, H., Echipare, L., & Farnham, P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-316-5_20 · Cited by 174

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

DiGuistini, S., Liao, N., Platt, D., Robertson, G., Seidel, M. A., Chan, S. K., Docking, R., Birol, İ., Holt, R. A., Hirst, M., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-9-r94 · Cited by 161

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

Feng, X., Grossman, R. L., & Stein, L. D. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-139 · Cited by 158

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T., Jones, S. J. M., Hirst, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002301 · Cited by 165

Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming

Elo, L. L., Järvenpää, H., Tuomela, S., Raghav, S. K., Ahlfors, H., Laurila, K., Gupta, B., Lund, R., Tahvanainen, J., Hawkins, R. D., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.011 · Cited by 159

Deep and wide digging for binding motifs in ChIP-Seq data

Kulakovskiy, I. V., Boeva, V., Favorov, A. V., & Makeev, V. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq488 · Cited by 160

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

Boeva, V. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00024 · Cited by 163

AP4 is a mediator of epithelial–mesenchymal transition and metastasis in colorectal cancer

Jackstadt, R., Röh, S., Neumann, J. H. L., Jung, P., Hoffmann, R. F. G., Horst, D. A., Berens, C., Bornkamm, G. W., Kirchner, T., Menssen, A., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20120812 · Cited by 152

Harnessing genomics for evolutionary insights

Rokas, A., & Abbot, P. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.11.004 · Cited by 143

BayesPeak: Bayesian analysis of ChIP-seq data

Spyrou, C., Stark, R., Lynch, A. G., & Tavaré, S. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-299 · Cited by 132

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

Leddin, M., Perrod, C., Hoogenkamp, M., Ghani, S., Assi, S., Heinz, S., Wilson, N. K., Follows, G., Schönheit, J., Vockentanz, L., et al. (2011) · Blood · doi:10.1182/blood-2010-08-302976 · Cited by 131

Features that define the best ChIP-seq peak calling algorithms

Thomas, R., Thomas, S., Holloway, A. K., & Pollard, K. S. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw035 · Cited by 112

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

Waki, H., Nakamura, M., Yamauchi, T., Wakabayashi, K.-I., Yu, J., Hirose, L., Take, K., Sun, W., Iwabu, M., Okada‐Iwabu, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002311 · Cited by 129

The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development

Wilson, N. K., Miranda‐Saavedra, D., Kinston, S., Bonadies, N., Foster, S. D., Calero‐Nieto, F. J., Dawson, M. A., Donaldson, I. J., Dumon, S., Frampton, J., et al. (2009) · Blood · doi:10.1182/blood-2009-01-200048 · Cited by 126

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

Zhang, Y., Lin, Y.-H., Johnson, T. D., Rozek, L. S., & Sartor, M. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu372 · Cited by 120

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

Laajala, T. D., Raghav, S. K., Tuomela, S., Lahesmaa, R., Aittokallio, T. A., & Elo, L. L. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-618 · Cited by 124

Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation

Alder, O., Cullum, R., Lee, S., Kan, A. C., Wei, W., Yi, Y., Garside, V. C., Bilenky, M., Griffith, M., Morrissy, A. S., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.046 · Cited by 113

Histone deacetylase inhibitors induce apoptosis, histone hyperacetylation and up-regulation of gene transcription in Schistosoma mansoni

Dubois, F., Caby, S., Oger, F., Cosseau, C., Capron, M., Grunau, C., Dissous, C., & Pierce, R. J. (2009) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2009.06.001 · Cited by 119

Polycomb Group Gene OsFIE2 Regulates Rice (Oryza sativa) Seed Development and Grain Filling via a Mechanism Distinct from Arabidopsis

Nallamilli, B. R. R., Zhang, J., Mujahid, H., Malone, B., Bridges, S. M., & Peng, Z. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003322 · Cited by 112

Extracting transcription factor targets from ChIP-Seq data

Tuteja, G., White, P., Schug, J., & Kaestner, K. H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp536 · Cited by 108

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

Hu, M., Yu, J., Taylor, J. M. G., Chinnaiyan, A. M., & Qin, Z. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1180 · Cited by 104

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

Schwartz, S., Ram, O., & Ast, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016685 · Cited by 101

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Sundaram, S. K., Yu, J., & Chinnaiyan, A. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-369 · Cited by 104

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

Paris, O., Ferraro, L., Grober, O. M. V., Ravo, M., Filippo, M. R. D., Giurato, G., Nassa, G., Tarallo, R., Cantarella, C., Rizzo, F. M., et al. (2012) · Oncogene · doi:10.1038/onc.2011.583 · Cited by 99

Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset

Zhu, L. J. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-607-8_8 · Cited by 98

An integrated ChIP-seq analysis platform with customizable workflows

Γιαννοπούλου, Ε., & Elemento, O. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-277 · Cited by 91

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

Althammer, S., González‐Vallinas, J., Ballaré, C., Beato, M., & Eyras, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr570 · Cited by 90

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Chung, D., Kuan, P. F., Li, B., Sanalkumar, R., Liang, K., Bresnick, E. H., Dewey, C. N., & Keleş, S. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002111 · Cited by 89

Research Resource: Interplay between the Genomic and Transcriptional Networks of Androgen Receptor and Estrogen Receptor α in Luminal Breast Cancer Cells

Need, E. F., Selth, L. A., Harris, T. J., Birrell, S. N., Tilley, W. D., & Buchanan, G. (2012) · Molecular Endocrinology · doi:10.1210/me.2011-1314 · Cited by 87

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Lan, X., Adams, C., Landers, M. A., Dudas, M., Krissinger, D., Marnellos, G., Bonneville, R., Xu, M., Wang, J., Huang, T. H. ‐., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022226 · Cited by 82

Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors

O’Geen, H., Frietze, S. E., & Farnham, P. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-753-2_27 · Cited by 77

MACE: model based analysis of ChIP-exo

Wang, L., Chen, J., Wang, C., Uusküla-Reimand, L., Chen, K., Medina-Rivera, A., Young, E. J., Zimmermann, M. T., Yan, H., Sun, Z., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku846 · Cited by 74

A Genome-Wide Screen of CREB Occupancy Identifies the RhoA Inhibitors Par6C and Rnd3 as Regulators of BDNF-Induced Synaptogenesis

Lesiak, A. J., Pelz, C., Ando, H., Zhu, M., Davare, M. A., Lambert, T. J., Hansen, K. F., Obrietan, K. H., Appleyard, S. M., Impey, S., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064658 · Cited by 77

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets

Worsley Hunt, R., & Wasserman, W. W. (2014) · Genome Biology · doi:10.1186/s13059-014-0412-4 · Cited by 73

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

Boeva, V., Surdez, D., Guillon, N., Tirode, F., Fejes, A. P., Delattre, O., & Barillot, E. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq217 · Cited by 75

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

Liu, H.-W., Zhang, J., Heine, G. F., Arora, M., Özer, H. G., Onti-Srinivasan, R., Huang, K., & Parvin, J. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks819 · Cited by 78

Epigenetic and transcriptional determinants of the human breast

Gascard, P. D., Bilenky, M., Sigaroudinia, M., Zhao, J., Li, L., Carles, A., Delaney, A. D., Tam, A., Kamoh, B., Cho, S. H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7351 · Cited by 73

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b

Ebata, K. T., Mesh, K., Liu, S., Bilenky, M., Fekete, A., Acker, M. G., Hirst, M., Garcia, B. A., & Ramalho‐Santos, M. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0143-3 · Cited by 72

PICS: Probabilistic Inference for ChIP-seq

Zhang, X., Robertson, G., Krzywinski, M. I., Ning, K., Droit, A., Jones, S. J. M., & Gottardo, R. (2010) · Biometrics · doi:10.1111/j.1541-0420.2010.01441.x · Cited by 72

Next generation sequencing based approaches to epigenomics

Hirst, M., & Marra, M. A. (2010) · Briefings in Functional Genomics · doi:10.1093/bfgp/elq035 · Cited by 70

PPARalpha regulates the production of serum Vanin‐1 by liver

Rommelaere, S., Millet, V., Gensollen, T., Bourges, C., Eeckhoute, J., Hennuyer, N., Baugé, E., Chasson, L., Cacciatore, I., Staels, B., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.09.046 · Cited by 69

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

Micsinai, M., Parisi, F., Strino, F., Asp, P., Dynlacht, B. D., & Kluger, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks048 · Cited by 66

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Lun, D. S., Sherrid, A. M., Weiner, B., Sherman, D. R., & Galagan, J. E. (2009) · Genome biology · doi:10.1186/gb-2009-10-12-r142 · Cited by 65

Next‐generation technologies and data analytical approaches for epigenomics

Mensaert, K., Denil, S. L. I. J., Trooskens, G., Criekinge, W. V., Thas, O., & Meyer, T. D. (2013) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21841 · Cited by 68

The p53/microRNA Network in Cancer: Experimental and Bioinformatics Approaches

Hünten, S., Siemens, H., Kaller, M., & Hermeking, H. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-94-007-5590-1_5 · Cited by 66

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

Rye, M. B., Sætrom, P., & Drabløs, F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1187 · Cited by 67

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

Schmid, C. D., & Bücher, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011425 · Cited by 67

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

Baker, K., Dhillon, T., Colas, I., Cook, N., Milne, I., Milne, L., Bayer, M., & Flavell, A. J. (2015) · The Plant Journal · doi:10.1111/tpj.12963 · Cited by 62

“Calling Cards” for DNA-Binding Proteins in Mammalian Cells

Wang, H., Mayhew, D. N., Chen, X., Johnston, M., & Mitra, R. D. (2012) · Genetics · doi:10.1534/genetics.111.137315 · Cited by 61

Three Distinct Patterns of Histone H3Y41 Phosphorylation Mark Active Genes

Dawson, M. A., Foster, S. D., Bannister, A. J., Robson, S. C., Hannah, R., Wang, X., Xhemalçe, B., Wood, A. D., Green, A. R., Göttgens, B., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.016 · Cited by 60

Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data

Malone, B., Tan, F., Bridges, S. M., & Peng, Z. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025260 · Cited by 61

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

Blahnik, K. R., Dou, L., O’Geen, H., McPhillips, T., Xu, X., Cao, A. R., Iyengar, S., Nicolet, C. M., Ludäscher, B., Korf, I. F., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1012 · Cited by 117

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data

Lan, X., Bonneville, R., Apostolos, J., Wu, W., & Jin, V. X. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq669 · Cited by 45

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Sundaram, S. K., Yu, J., & Chinnaiyan, A. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-369 · Cited by 104

read-enriched regions in ChIP-Seq data Open Access

Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Sundaram, S. K., Yu, J., & Chinnaiyan, A. M. (2013)

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Salmon‐Divon, M., Dvinge, H., Koort, K., & Bertone, P. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-415 · Cited by 244