My NCBISign In
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

Is Cited by the Following 271 Articles in this Archive:

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Julia Heisig, David Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Chia-Lin Wei, Manfred Gessler
PLoS Genet. 2012 May; 8(5): e1002728. Published online 2012 May 17. doi: 10.1371/journal.pgen.1002728
PMCID:
PMC3355086
Abstract Full Text PDF–1.4M Supplementary Material
ELK1 Uses Different DNA Binding Modes to Regulate Functionally Distinct Classes of Target Genes
Zaneta Odrowaz, Andrew D. Sharrocks
PLoS Genet. 2012 May; 8(5): e1002694. Published online 2012 May 10. doi: 10.1371/journal.pgen.1002694
PMCID:
PMC3349735
Abstract Full Text PDF–1.2M Supplementary Material
Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome
Heike Wollmann, Sarah Holec, Keith Alden, Neil D. Clarke, Pierre-Étienne Jacques, Frédéric Berger
PLoS Genet. 2012 May; 8(5): e1002658. Published online 2012 May 3. doi: 10.1371/journal.pgen.1002658
PMCID:
PMC3342937
Abstract Full Text PDF–805K Supplementary Material
YY1 Regulates Melanocyte Development and Function by Cooperating with MITF
Juying Li, Jun S. Song, Robert J. A. Bell, Thanh-Nga T. Tran, Rizwan Haq, Huifei Liu, Kevin T. Love, Robert Langer, Daniel G. Anderson, Lionel Larue, David E. Fisher
PLoS Genet. 2012 May; 8(5): e1002688. Published online 2012 May 3. doi: 10.1371/journal.pgen.1002688
PMCID:
PMC3342948
Abstract Full Text PDF–3.0M Supplementary Material
LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes
Karin Meier, Eve-Lyne Mathieu, Florian Finkernagel, L. Maximilian Reuter, Maren Scharfe, Gunther Doehlemann, Michael Jarek, Alexander Brehm
PLoS Genet. 2012 May; 8(5): e1002676. Published online 2012 May 3. doi: 10.1371/journal.pgen.1002676
PMCID:
PMC3342951
Abstract Full Text PDF–1.0M Supplementary Material
A DNA hypermethylation module for the stem/progenitor cell signature of cancer
Hariharan Easwaran, Sarah E. Johnstone, Leander Van Neste, Joyce Ohm, Tim Mosbruger, Qiuju Wang, Martin J. Aryee, Patrick Joyce, Nita Ahuja, Dan Weisenberger, Eric Collisson, Jingchun Zhu, Srinivasan Yegnasubramanian, William Matsui, Stephen B. Baylin
Genome Res. 2012 May; 22(5): 837–849. doi: 10.1101/gr.131169.111
PMCID:
PMC3337430
Abstract Full Text PDF–1.6M
Polycomb Repressive Complex 2-Dependent and -Independent Functions of Jarid2 in Transcriptional Regulation in Drosophila
Hans-Martin Herz, Man Mohan, Alexander S. Garrett, Caitlynn Miller, David Casto, Ying Zhang, Christopher Seidel, Jeffrey S. Haug, Laurence Florens, Michael P. Washburn, Masamitsu Yamaguchi, Ramin Shiekhattar, Ali Shilatifard
Mol Cell Biol. 2012 May; 32(9): 1683–1693. doi: 10.1128/MCB.06503-11
PMCID:
PMC3347239
Free in PMC on 2012/11/01
Downregulation of Integrin Receptor-Signaling Genes by Epstein-Barr Virus EBNA 3C via Promoter-Proximal and -Distal Binding Elements
Michael J. McClellan, Sarika Khasnis, C. David Wood, Richard D. Palermo, Sandra N. Schlick, Aditi S. Kanhere, Richard G. Jenner, Michelle J. West
J Virol. 2012 May; 86(9): 5165–5178. doi: 10.1128/JVI.07161-11
PMCID:
PMC3347391
Abstract Full Text PDF–1.6M Supplementary Material
Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment
Pratik Home, Biswarup Saha, Soma Ray, Debasree Dutta, Sumedha Gunewardena, Byunggil Yoo, Arindam Pal, Jay L. Vivian, Melissa Larson, Margaret Petroff, Patrick G. Gallagher, Vincent P. Schulz, Kenneth L. White, Thaddeus G. Golos, Barry Behr, Soumen Paul
Proc Natl Acad Sci U S A. 2012 May 8; 109(19): 7362–7367. Published online 2012 April 23. doi: 10.1073/pnas.1201595109
PMCID:
PMC3358889
Abstract Full Text PDF–1.1M Supplementary Material
Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis
Louis C. Doré, Timothy M. Chlon, Christopher D. Brown, Kevin P. White, John D. Crispino
Blood. 2012 April 19; 119(16): 3724–3733. Prepublished online 2012 March 1. doi: 10.1182/blood-2011-09-380634
PMCID:
PMC3335379
Free in PMC on 2013/04/19
Methylcap-Seq Reveals Novel DNA Methylation Markers for the Diagnosis and Recurrence Prediction of Bladder Cancer in a Chinese Population
Yangxing Zhao, Shicheng Guo, Jinfeng Sun, Zhaohui Huang, Tongyu Zhu, Hongyu Zhang, Jun Gu, Yinghua He, Wei Wang, Kelong Ma, Jina Wang, Jian Yu
PLoS One. 2012; 7(4): e35175. Published online 2012 April 17. doi: 10.1371/journal.pone.0035175
PMCID:
PMC3328468
Abstract Full Text PDF–2.4M Supplementary Material
Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis
Hong Hao, Douglas S. Kim, Bernward Klocke, Kory R. Johnson, Kairong Cui, Norimoto Gotoh, Chongzhi Zang, Janina Gregorski, Linn Gieser, Weiqun Peng, Yang Fann, Martin Seifert, Keji Zhao, Anand Swaroop
PLoS Genet. 2012 April; 8(4): e1002649. Published online 2012 April 12. doi: 10.1371/journal.pgen.1002649
PMCID:
PMC3325202
Abstract Full Text PDF–1.3M Supplementary Material
Essential role of EBF1 in the generation and function of distinct mature B cell types
Bojan Vilagos, Mareike Hoffmann, Abdallah Souabni, Qiong Sun, Barbara Werner, Jasna Medvedovic, Ivan Bilic, Martina Minnich, Elin Axelsson, Markus Jaritz, Meinrad Busslinger
J Exp Med. 2012 April 9; 209(4): 775–792. doi: 10.1084/jem.20112422
PMCID:
PMC3328360
Free in PMC on 2012/10/09
Nkx3.1 and Myc crossregulate shared target genes in mouse and human prostate tumorigenesis
Philip D. Anderson, Sydika A. McKissic, Monica Logan, Meejeon Roh, Omar E. Franco, Jie Wang, Irina Doubinskaia, Riet van Meer, Simon W. Hayward, Christine M. Eischen, Isam-Eldin Eltoum, Sarki A. Abdulkadir
J Clin Invest. 2012 May 1; 122(5): 1907–1919. Published online 2012 April 9. doi: 10.1172/JCI58540
PMCID:
PMC3336973
Abstract Full Text PDF–3.5M Supplementary Material
A Genome-Wide Screen for Genetic Variants That Modify the Recruitment of REST to Its Target Genes
Rory Johnson, Nadine Richter, Gireesh K. Bogu, Akshay Bhinge, Siaw Wei Teng, Siew Hua Choo, Lise O. Andrieux, Cinzia de Benedictis, Ralf Jauch, Lawrence W. Stanton
PLoS Genet. 2012 April; 8(4): e1002624. Published online 2012 April 5. doi: 10.1371/journal.pgen.1002624
PMCID:
PMC3320604
Abstract Full Text PDF–1.3M Supplementary Material
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
Ignacio Maeso, Manuel Irimia, Juan J. Tena, Esther González-Pérez, David Tran, Vydianathan Ravi, Byrappa Venkatesh, Sonsoles Campuzano, José Luis Gómez-Skarmeta, Jordi Garcia-Fernàndez
Genome Res. 2012 April; 22(4): 642–655. doi: 10.1101/gr.132233.111
PMCID:
PMC3317147
Free in PMC on 2012/10/01
MacroH2A1 Regulates the Balance between Self-Renewal and Differentiation Commitment in Embryonic and Adult Stem Cells
Catherine Creppe, Peggy Janich, Neus Cantariño, Marc Noguera, Vanesa Valero, Eva Musulén, Julien Douet, Melanija Posavec, Juan Martín-Caballero, Lauro Sumoy, Luciano Di Croce, Salvador A. Benitah, Marcus Buschbeck
Mol Cell Biol. 2012 April; 32(8): 1442–1452. doi: 10.1128/MCB.06323-11
PMCID:
PMC3318583
Free in PMC on 2012/10/01
Normalization, bias correction, and peak calling for ChIP-seq
Aaron Diaz, Kiyoub Park, Daniel A. Lim, Jun S. Song
Stat Appl Genet Mol Biol. Author manuscript; available in PMC 2012 May 3.
Published in final edited form as: Stat Appl Genet Mol Biol. 2012 March 31; 11(3): 10.1515/1544-6115.1750 /j/sagmb.2012.11.issue-3/1544-6115.1750/1544-6115.1750.xml. doi: 10.1515/1544-6115.1750
PMCID:
PMC3342857
Abstract Full Text PDF–1.6M
Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo
Michael J. Guertin, André L. Martins, Adam Siepel, John T. Lis
PLoS Genet. 2012 March; 8(3): e1002610. Published online 2012 March 29. doi: 10.1371/journal.pgen.1002610
PMCID:
PMC3315474
Abstract Full Text PDF–1.4M Supplementary Material
TWIST Represses Estrogen Receptor-alpha Expression by Recruiting the NuRD Protein Complex in Breast Cancer Cells
Junjiang Fu, Lianmei Zhang, Tao He, Xiuli Xiao, Xiaoyan Liu, Li Wang, Luquan Yang, Manman Yang, Tiandan Zhang, Rui Chen, Jianming Xu
Int J Biol Sci. 2012; 8(4): 522–532. Published online 2012 March 22. doi: 10.7150/ijbs.4164
PMCID:
PMC3314193
Abstract Full Text PDF–1010K
Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
Huaishun Shen, Hang He, Jigang Li, Wei Chen, Xuncheng Wang, Lan Guo, Zhiyu Peng, Guangming He, Shangwei Zhong, Yijun Qi, William Terzaghi, Xing Wang Deng
Plant Cell. 2012 March; 24(3): 875–892. Published online 2012 March 20. doi: 10.1105/tpc.111.094870
PMCID:
PMC3336129
Free in PMC on 2013/03/01
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
Andrew E Jaffe, Peter Murakami, Hwajin Lee, Jeffrey T Leek, M Daniele Fallin, Andrew P Feinberg, Rafael A Irizarry
Int J Epidemiol. 2012 February; 41(1): 200–209. Published online 2012 March 14. doi: 10.1093/ije/dyr238
PMCID:
PMC3304533
Free in PMC on 2013/02/01
A unique role of cohesin-SA1 in gene regulation and development
Silvia Remeseiro, Ana Cuadrado, Gonzalo Gómez-López, David G Pisano, Ana Losada
EMBO J. 2012 May 2; 31(9): 2090–2102. Published online 2012 March 13. doi: 10.1038/emboj.2012.60
PMCID:
PMC3343463
Free in PMC on 2013/05/02
“Calling Cards” for DNA-Binding Proteins in Mammalian Cells
Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston, Robi David Mitra
Genetics. 2012 March; 190(3): 941–949. doi: 10.1534/genetics.111.137315
PMCID:
PMC3296256
Free in PMC on 2013/03/01
R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters
Paul A. Ginno, Paul L. Lott, Holly C. Christensen, Ian Korf, Frédéric Chédin
Mol Cell. Author manuscript; available in PMC 2013 March 30.
Published in final edited form as: Mol Cell. 2012 March 30; 45(6): 814–825. Published online 2012 March 1. doi: 10.1016/j.molcel.2012.01.017
PMCID:
PMC3319272
Free in PMC on 2013/03/30
Distinct regulatory mechanisms and functions of p53-activated and p53-repressed DNA damage response genes in embryonic stem cells
Mangmang Li, Yunlong He, Wendy Dubois, Xiaolin Wu, Jianxin Shi, Jing Huang
Mol Cell. Author manuscript; available in PMC 2013 April 13.
Published in final edited form as: Mol Cell. 2012 April 13; 46(1): 30–42. Published online 2012 March 1. doi: 10.1016/j.molcel.2012.01.020
PMCID:
PMC3327774
Free in PMC on 2013/04/13
Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response
Maria Jesus Iglesias, Sarah-Jayne Reilly, Olof Emanuelsson, Bengt Sennblad, Mohammad Pirmoradian Najafabadi, Lasse Folkersen, Anders Mälarstig, Jens Lagergren, Per Eriksson, Anders Hamsten, Jacob Odeberg
PLoS One. 2012; 7(2): e32306. Published online 2012 February 27. doi: 10.1371/journal.pone.0032306
Correction in:
PLoS One. 2012; 7(4): 10.1371/annotation/689ae222-9eb1-4f80-8ebe-6b80e8ad45ce.
PMCID:
PMC3288078
Abstract Full Text PDF–971K Supplementary Material Correction
Gain-of-function p53 mutants have widespread genomic locations partially overlapping with p63
Elena Martynova, Silvia Pozzi, Valentina Basile, Diletta Dolfini, Federico Zambelli, Carol Imbriano, Giulio Pavesi, Roberto Mantovani
Oncotarget. 2012 February; 3(2): 132–143. Published online 2012 February 22.
PMCID:
PMC3326644
Abstract Full Text PDF–1.0M Supplementary Material
RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3
Lígia Tavares, Emilia Dimitrova, David Oxley, Judith Webster, Raymond Poot, Jeroen Demmers, Karel Bezstarosti, Stephen Taylor, Hiroki Ura, Hiroshi Koide, Anton Wutz, Miguel Vidal, Sarah Elderkin, Neil Brockdorff
Cell. 2012 February 17; 148(4): 664–678. doi: 10.1016/j.cell.2011.12.029
PMCID:
PMC3281992
Abstract Full Text Supplementary Material
High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Satish Sati, Vinay Singh Tanwar, K. Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, S. Umakar Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
PLoS One. 2012; 7(2): e31621. Published online 2012 February 15. doi: 10.1371/journal.pone.0031621
PMCID:
PMC3280313
Abstract Full Text PDF–688K Supplementary Material
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