Model-based Analysis of ChIP-Seq (MACS)
-
* Corresponding authors: Wei Li wl1@bcm.edu - X Shirley Liu xsliu@jimmy.harvard.edu
- † Equal contributors
Genome Biology 2008, 9:R137 doi:10.1186/gb-2008-9-9-r137
Accesses
- Last 30 days: 853 accesses
- Last year: 11108 accesses
- All time: 34291 accesses
Cited by
BioMed Central: 25 citations
|
Proceedings
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data Zhi Han, Lu Tian, Thierry Pécot, Tim Huang, Raghu Machiraju, Kun Huang BMC Bioinformatics 2012, 13(Suppl 2):S2 (13 March 2012) |
|
Research article
Hansook Kim Chong, Jacob Biesinger, Young-Kyo Seo, Xiaohui Xie, Timothy F Osborne BMC Genomics 2012, 13:51 (1 February 2012) |
|
Research article
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynanen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg BMC Genomics 2012, 13:50 (31 January 2012) |
|
Proceedings
Hatice Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich, Xinghua Lu BMC Genomics 2012, 13(Suppl 1):S1 (17 January 2012) |
|
Research
Stefan Enroth, Claes R Andersson, Robin Andersson, Claes Wadelius, Mats G Gustafsson, Jan Komorowski Algorithms for Molecular Biology 2012, 7:2 (16 January 2012) |
|
Proceedings
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite Xi Wang, Xuegong Zhang BMC Systems Biology 2011, 5(Suppl 2):S3 (14 December 2011) |
|
Research article
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 (5 December 2011) |
|
Research article
Morten Rye, Pål Sætrom, Tony Håndstad, Finn Drabløs BMC Biology 2011, 9:80 (24 November 2011) |
|
Research
Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011) Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.
|
|
Software
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 Biology 2011, 12:R83 (22 August 2011) A Galaxy-based web application for integrative analysis of ChIP data
|
|
Research
Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) This article is part of a collection on The tammar wallaby genome... The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
|
|
Research highlight
Weiqun Peng, Keji Zhao Genome Biology 2011, 12:120 (25 July 2011) Keji Zhao discusses Genome Biology's method article on ZINBA, a novel peak-finding tool developed by Jason Lieb and colleagues
|
|
Method
Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011) ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
|
|
Software
An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou, Olivier Elemento BMC Bioinformatics 2011, 12:277 (7 July 2011) |
|
Research
Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Phillip WL Tai, Katherine I Fisher-Aylor, Charis L Himeda, Catherine L Smith, Alexandra P MacKenzie, Deri L Helterline, John C Angello, Robert E Welikson, Barbara J Wold, Stephen D Hauschka Skeletal Muscle 2011, 1:25 (7 July 2011) |
|
Research
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young, Hynek Wichterle, David K Gifford Genome Biology 2011, 12:R2 (13 January 2011) ChIP-seq for retinoic acid receptor binding during early neuronal differentiation reveals a complex landscape of transcriptional control.
|
|
Research article
Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells Igor Martianov, Mohamed-Amin Choukrallah, Arnaud Krebs, Tao Ye, Stephanie Legras, Erikjan Rijkers, Wilfred Van Ijcken, Bernard Jost, Paolo Sassone-Corsi, Irwin Davidson BMC Genomics 2010, 11:530 (29 September 2010) |
|
Method
Estimating enrichment of repetitive elements from high-throughput sequence data Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010) The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
|
|
Question & Answer
Q&A: ChIP-seq technologies and the study of gene regulation Edison T Liu, Sebastian Pott, Mikael Huss BMC Biology 2010, 8:56 (14 May 2010) Edison Liu and colleagues explain in Q&A format how ChIP-seq technology allows investigation of transcriptional regulation on a genomic scale, and what is next.
|
|
Software
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green BMC Bioinformatics 2010, 11:237 (11 May 2010) |
|
Method
Evidence-ranked motif identification Stoyan Georgiev, Alan P Boyle, Karthik Jayasurya, Xuan Ding, Sayan Mukherjee, Uwe Ohler Genome Biology 2010, 11:R19 (15 February 2010) A new computational method for the identification of regulatory motifs from large genomic datasets is presented here |
|
Research article
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, Dabing Zhang BMC Bioinformatics 2010, 11:81 (9 February 2010) |
|
Method
Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan Genome Biology 2009, 10:R142 (22 December 2009) CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites. |
|
Research article
Teemu D Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura L Elo BMC Genomics 2009, 10:618 (18 December 2009) |
|
Research article
Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq Yong Zhang, Hyunjin Shin, Jun S Song, Ying Lei, X Shirley Liu BMC Genomics 2008, 9:537 (13 November 2008) |