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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu
Genome Biol. 2008; 9(9): R137. Published online 2008 September 17. doi: 10.1186/gb-2008-9-9-r137
PMCID:
PMC2592715
Abstract Full Text PDF–292K Supplementary Material
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 Is Cited by the Following 172 Articles in this Archive:
Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antonia Navarro, Diana Monsivais, John S. Coon V, J. Julie Kim, Yang Dai, Serdar E. Bulun
PLoS One. 2012; 7(1): e29021. Published online 2012 January 17. doi: 10.1371/journal.pone.0029021
PMCID:
PMC3260146
Abstract Full Text PDF–579K Supplementary Material
The Forkhead Transcription Factor FOXK2 Promotes AP-1-Mediated Transcriptional Regulation
Zongling Ji, Ian J. Donaldson, Jingru Liu, Andrew Hayes, Leo A. H. Zeef, Andrew D. Sharrocks
Mol Cell Biol. 2012 January; 32(2): 385–398. doi: 10.1128/MCB.05504-11
PMCID:
PMC3255788
Abstract Full Text PDF–1.3M Supplementary Material
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development
Jonathan Göke, Marc Jung, Sarah Behrens, Lukas Chavez, Sean O'Keeffe, Bernd Timmermann, Hans Lehrach, James Adjaye, Martin Vingron
PLoS Comput Biol. 2011 December; 7(12): e1002304. Published online 2011 December 22. doi: 10.1371/journal.pcbi.1002304
PMCID:
PMC3245296
Abstract Full Text PDF–1.1M Supplementary Material
Toward an Integrated Model of Capsule Regulation in Cryptococcus neoformans
Brian C. Haynes, Michael L. Skowyra, Sarah J. Spencer, Stacey R. Gish, Matthew Williams, Elizabeth P. Held, Michael R. Brent, Tamara L. Doering
PLoS Pathog. 2011 December; 7(12): e1002411. Published online 2011 December 8. doi: 10.1371/journal.ppat.1002411
PMCID:
PMC3234223
Abstract Full Text PDF–2.0M Supplementary Material
A co-ordinated interaction between CTCF and ER in breast cancer cells
Caryn S Ross-Innes, Gordon D Brown, Jason S Carroll
BMC Genomics. 2011; 12: 593. Published online 2011 December 5. doi: 10.1186/1471-2164-12-593
PMCID:
PMC3248577
Abstract Full Text PDF–3.4M Supplementary Material
NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression
Nicola Reynolds, Mali Salmon-Divon, Heidi Dvinge, Antony Hynes-Allen, Gayan Balasooriya, Donna Leaford, Axel Behrens, Paul Bertone, Brian Hendrich
EMBO J. 2012 February 1; 31(3): 593–605. Published online 2011 December 2. doi: 10.1038/emboj.2011.431
PMCID:
PMC3273378
Abstract Full Text PDF–1.6M Supplementary Material
Dual Function of Histone H3 Lysine 36 Methyltransferase ASH1 in Regulation of Hox Gene Expression
Yujiro Tanaka, Koji Kawahashi, Zen-Ichiro Katagiri, Yasuhiro Nakayama, Milind Mahajan, Dimitris Kioussis
PLoS One. 2011; 6(11): e28171. Published online 2011 November 28. doi: 10.1371/journal.pone.0028171
PMCID:
PMC3225378
Abstract Full Text PDF–595K Supplementary Material
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
Morten Rye, Pål Sætrom, Tony Håndstad, Finn Drabløs
BMC Biol. 2011; 9: 80. Published online 2011 November 24. doi: 10.1186/1741-7007-9-80
PMCID:
PMC3239327
Abstract Full Text PDF–536K Supplementary Material
Global Mapping of H3K4me1 and H3K4me3 Reveals the Chromatin State-Based Cell Type-Specific Gene Regulation in Human Treg Cells
Yi Tian, Zhengcai Jia, Jun Wang, Zemin Huang, Jun Tang, Yanhua Zheng, Yan Tang, Qinghong Wang, Zhiqiang Tian, Di Yang, Yi Zhang, Xiaolan Fu, Jianxun Song, Shunli Liu, Jennifer C. van Velkinburgh, Yuzhang Wu, Bing Ni
PLoS One. 2011; 6(11): e27770. Published online 2011 November 23. doi: 10.1371/journal.pone.0027770
PMCID:
PMC3223197
Abstract Full Text PDF–2.5M Supplementary Material
PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer
Luca Magnani, Elizabeth B. Ballantyne, Xiaoyang Zhang, Mathieu Lupien
PLoS Genet. 2011 November; 7(11): e1002368. Published online 2011 November 17. doi: 10.1371/journal.pgen.1002368
PMCID:
PMC3219601
Abstract Full Text PDF–1.0M Supplementary Material
Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations
Melissa J. Fullwood, Joanne Lee, Lifang Lin, Guoliang Li, Mikael Huss, Patrick Ng, Wing-Kin Sung, Shirish Shenolikar
PLoS One. 2011; 6(11): e26054. Published online 2011 November 8. doi: 10.1371/journal.pone.0026054
PMCID:
PMC3210745
Abstract Full Text PDF–1.2M Supplementary Material
In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions
Simon Quenneville, Gaetano Verde, Andrea Corsinotti, Adamandia Kapopoulou, Johan Jakobsson, Sandra Offner, Ilaria Baglivo, Paolo V. Pedone, Giovanna Grimaldi, Andrea Riccio, Didier Trono
Mol Cell. 2011 November 4; 44(3): 361–372. doi: 10.1016/j.molcel.2011.08.032
PMCID:
PMC3210328
Abstract Full Text PDF–1.7M Supplementary Material
Optimized detection of transcription factor-binding sites in ChIP-seq experiments
Laura L. Elo, Aleksi Kallio, Teemu D. Laajala, R. David Hawkins, Eija Korpelainen, Tero Aittokallio
Nucleic Acids Res. 2012 January; 40(1): e1. Published online 2011 October 18. doi: 10.1093/nar/gkr839
PMCID:
PMC3245948
Abstract Full Text PDF–238K Supplementary Material
VDA, a Method of Choosing a Better Algorithm with Fewer Validations
Francesco Strino, Fabio Parisi, Yuval Kluger
PLoS One. 2011; 6(10): e26074. Published online 2011 October 12. doi: 10.1371/journal.pone.0026074
PMCID:
PMC3192143
Abstract Full Text PDF–447K Supplementary Material
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
Sonja Althammer, Juan González-Vallinas, Cecilia Ballaré, Miguel Beato, Eduardo Eyras
Bioinformatics. 2011 December 15; 27(24): 3333–3340. Published online 2011 October 12. doi: 10.1093/bioinformatics/btr570
PMCID:
PMC3232367
Abstract Full Text PDF–687K Supplementary Material
Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics
Marco A Mendoza-Parra, Mannu Walia, Martial Sankar, Hinrich Gronemeyer
Mol Syst Biol. 2011; 7: 538. Published online 2011 October 11. doi: 10.1038/msb.2011.73
PMCID:
PMC3261707
Abstract Full Text PDF–3.1M Supplementary Material
DNA Methylation Profiling of Embryonic Stem Cell Differentiation into the Three Germ Layers
Takayuki Isagawa, Genta Nagae, Nobuaki Shiraki, Takanori Fujita, Noriko Sato, Shumpei Ishikawa, Shoen Kume, Hiroyuki Aburatani
PLoS One. 2011; 6(10): e26052. Published online 2011 October 7. doi: 10.1371/journal.pone.0026052
PMCID:
PMC3189249
Abstract Full Text PDF–1.0M Supplementary Material
Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli
Biol Direct. 2011; 6: 51. Published online 2011 October 6. doi: 10.1186/1745-6150-6-51
PMCID:
PMC3201895
Abstract Full Text PDF–480K
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
Weisheng Wu, Yong Cheng, Cheryl A. Keller, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, Christine M. Dorman, Kuan-Bei Chen, Daniela Drautz, Belinda Giardine, Yoichiro Shibata, Lingyun Song, Max Pimkin, Gregory E. Crawford, Terrence S. Furey, Manolis Kellis, Webb Miller, James Taylor, Stephan C. Schuster, Yu Zhang, Francesca Chiaromonte, Gerd A. Blobel, Mitchell J. Weiss, Ross C. Hardison
Genome Res. 2011 October; 21(10): 1659–1671. doi: 10.1101/gr.125088.111
PMCID:
PMC3202283
Abstract Full Text PDF–2.0M
Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data
Brandon M. Malone, Feng Tan, Susan M. Bridges, Zhaohua Peng
PLoS One. 2011; 6(9): e25260. Published online 2011 September 30. doi: 10.1371/journal.pone.0025260
PMCID:
PMC3184143
Abstract Full Text PDF–1.4M Supplementary Material
AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
Jiantao Shi, Wentao Yang, Mingjie Chen, Yanzhi Du, Ji Zhang, Kankan Wang
PLoS One. 2011; 6(9): e24576. Published online 2011 September 12. doi: 10.1371/journal.pone.0024576
PMCID:
PMC3171486
Abstract Full Text PDF–839K Supplementary Material
Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling
Bin Tang, Pietro Di Lena, Lana Schaffer, Steven R. Head, Pierre Baldi, Elizabeth A. Thomas
PLoS One. 2011; 6(9): e23691. Published online 2011 September 1. doi: 10.1371/journal.pone.0023691
PMCID:
PMC3164671
Abstract Full Text PDF–827K Supplementary Material
Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state
Say Li Kong, Guoliang Li, Siang Lin Loh, Wing-Kin Sung, Edison T Liu
Mol Syst Biol. 2011; 7: 526. Published online 2011 August 30. doi: 10.1038/msb.2011.59
PMCID:
PMC3202798
Abstract Full Text PDF–1.0M Supplementary Material
Systematic Clustering of Transcription Start Site Landscapes
Xiaobei Zhao, Eivind Valen, Brian J. Parker, Albin Sandelin
PLoS One. 2011; 6(8): e23409. Published online 2011 August 24. doi: 10.1371/journal.pone.0023409
PMCID:
PMC3160847
Abstract Full Text PDF–2.7M Supplementary Material
Cistrome: an integrative platform for transcriptional regulation studies
Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Genome Biol. 2011; 12(8): R83. Published online 2011 August 22. doi: 10.1186/gb-2011-12-8-r83
PMCID:
PMC3245621
Abstract Full Text PDF–2.1M Supplementary Material
Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy
Sami Heikkinen, Sami Väisänen, Petri Pehkonen, Sabine Seuter, Vladimir Benes, Carsten Carlberg
Nucleic Acids Res. 2011 November; 39(21): 9181–9193. Published online 2011 August 16. doi: 10.1093/nar/gkr654
PMCID:
PMC3241659
Abstract Full Text PDF–2.7M Supplementary Material
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
Gabriel E. Zentner, Paul J. Tesar, Peter C. Scacheri
Genome Res. 2011 August; 21(8): 1273–1283. doi: 10.1101/gr.122382.111
PMCID:
PMC3149494
Abstract Full Text PDF–2.0M
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
Ozren Bogdanović, Steven W. Long, Simon J. van Heeringen, Arie B. Brinkman, Jose Luis Gómez-Skarmeta, Hendrik G. Stunnenberg, Peter L. Jones, Gert Jan C. Veenstra
Genome Res. 2011 August; 21(8): 1313–1327. doi: 10.1101/gr.114843.110
PMCID:
PMC3149498
Abstract Full Text PDF–1.5M
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb
Genome Biol. 2011; 12(7): R67. Published online 2011 July 25. doi: 10.1186/gb-2011-12-7-r67
PMCID:
PMC3218829
Abstract Full Text PDF–1.5M Supplementary Material
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing
Eun-Joon Lee, Lirong Pei, Gyan Srivastava, Trupti Joshi, Garima Kushwaha, Jeong-Hyeon Choi, Keith D. Robertson, Xinguo Wang, John K. Colbourne, Lu Zhang, Gary P. Schroth, Dong Xu, Kun Zhang, Huidong Shi
Nucleic Acids Res. 2011 October; 39(19): e127. Published online 2011 July 23. doi: 10.1093/nar/gkr598
PMCID:
PMC3201883
Abstract Full Text PDF–16M Supplementary Material
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