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Tilescope: online analysis pipeline for high-density tiling microarray data

Zhengdong D Zhang, Joel Rozowsky, Hugo YK Lam, Jiang Du, Michael Snyder, Mark Gerstein

Genome Biol. 2007; 8(5): R81. Published online 2007 May 14. doi: 10.1186/gb-2007-8-5-r81

PMCID:: PMC1929149

Abstract Full Text PDF–473K Supplementary Material

Is Cited by the Following 20 Articles in this Archive:

The bZIP Transcription Factor Rca1p Is a Central Regulator of a Novel CO₂ Sensing Pathway in Yeast

Fabien Cottier, Martine Raymond, Oliver Kurzai, Marianne Bolstad, Worraanong Leewattanapasuk, Claudia Jiménez-López, Michael C. Lorenz, Dominique Sanglard, Libuše Váchová, Norman Pavelka, Zdena Palková, Fritz A. Mühlschlegel

PLoS Pathog. 2012 January; 8(1): e1002485. Published online 2012 January 12. doi: 10.1371/journal.ppat.1002485

PMCID:: PMC3257301

Abstract Full Text PDF–2.1M Supplementary Material

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, Aalt D. J. van Dijk

Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W524–W527. Published online 2011 May 24. doi: 10.1093/nar/gkr373

PMCID:: PMC3125775

Abstract Full Text PDF–241K

Regulation of Efflux Pump Expression and Drug Resistance by the Transcription Factors Mrr1, Upc2, and Cap1 in Candida albicans

Sabrina Schubert, Katherine S. Barker, Sadri Znaidi, Sabrina Schneider, Franziska Dierolf, Nico Dunkel, Malika Aïd, Geneviève Boucher, P. David Rogers, Martine Raymond, Joachim Morschhäuser

Antimicrob Agents Chemother. 2011 May; 55(5): 2212–2223. doi: 10.1128/AAC.01343-10

PMCID:: PMC3088179

Abstract Full Text PDF–1.4M Supplementary Material

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

Ghia M. Euskirchen, Raymond K. Auerbach, Eugene Davidov, Tara A. Gianoulis, Guoneng Zhong, Joel Rozowsky, Nitin Bhardwaj, Mark B. Gerstein, Michael Snyder

PLoS Genet. 2011 March; 7(3): e1002008. Published online 2011 March 3. doi: 10.1371/journal.pgen.1002008

PMCID:: PMC3048368

Abstract Full Text PDF–3.8M Supplementary Material

Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray

Jianti Zheng, Denghui Xing, Xiaohui Wu, Yingjia Shen, Diana M. Kroll, Guoli Ji, Qingshun Quinn Li

PLoS One. 2011; 6(2): e14719. Published online 2011 February 25. doi: 10.1371/journal.pone.0014719

PMCID:: PMC3045369

Abstract Full Text PDF–628K Supplementary Material

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu

Genome Biol. 2011; 12(2): R11. Published online 2011 February 1. doi: 10.1186/gb-2011-12-2-r11

PMCID:: PMC3188793

Abstract Full Text PDF–643K Supplementary Material

JAMIE: joint analysis of multiple ChIP-chip experiments

Hao Wu, Hongkai Ji

Bioinformatics. 2010 August 1; 26(15): 1864–1870. Published online 2010 June 15. doi: 10.1093/bioinformatics/btq314

PMCID:: PMC2905557

Abstract Full Text PDF–595K Supplementary Material

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

Ranjit Kumar, Pratik Shah, Edwin Swiatlo, Shane C Burgess, Mark L Lawrence, Bindu Nanduri

BMC Genomics. 2010; 11: 350. Published online 2010 June 3. doi: 10.1186/1471-2164-11-350

PMCID:: PMC2887815

Abstract Full Text PDF–1.3M Supplementary Material

TiArA: A Virtual Appliance for the Analysis of Tiling Array Data

Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven Head, Alessandro Sette, Bjoern Peters

PLoS One. 2010; 5(4): e9993. Published online 2010 April 1. doi: 10.1371/journal.pone.0009993

PMCID:: PMC2848623

Abstract Full Text PDF–735K Supplementary Material

EBNA1 regulates cellular gene expression by binding cellular promoters

Allon Canaan, Izhak Haviv, Alexander E. Urban, Vincent P. Schulz, Steve Hartman, Zhengdong Zhang, Dean Palejev, Albert B. Deisseroth, Jill Lacy, Michael Snyder, Mark Gerstein, Sherman M. Weissman

Proc Natl Acad Sci U S A. 2009 December 29; 106(52): 22421–22426. Published online 2009 December 22. doi: 10.1073/pnas.0911676106

PMCID:: PMC2799695

Abstract Full Text PDF–636K Supplementary Material

Dynamic and complex transcription factor binding during an inducible response in yeast

Li Ni, Can Bruce, Christopher Hart, Justine Leigh-Bell, Daniel Gelperin, Lara Umansky, Mark B. Gerstein, Michael Snyder

Genes Dev. 2009 June 1; 23(11): 1351–1363. doi: 10.1101/gad.1781909

PMCID:: PMC2701586

Abstract Full Text PDF–1.8M

Identification of the Candida albicans Cap1p Regulon

Sadri Znaidi, Katherine S. Barker, Sandra Weber, Anne-Marie Alarco, Teresa T. Liu, Geneviève Boucher, P. David Rogers, Martine Raymond

Eukaryot Cell. 2009 June; 8(6): 806–820. Published online 2009 April 24. doi: 10.1128/EC.00002-09

PMCID:: PMC2698309

Abstract Full Text PDF–550K Supplementary Material

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

Paul G. Giresi, Jason D. Lieb

Methods. Author manuscript; available in PMC 2010 July 1.

Published in final edited form as: Methods. 2009 July; 48(3): 233–239. Published online 2009 March 18. doi: 10.1016/j.ymeth.2009.03.003

PMCID:: PMC2710428

Abstract Full Text PDF–796K

Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data

Debayan Datta, Hongyu Zhao

BMC Bioinformatics. 2009; 10: 23. Published online 2009 January 19. doi: 10.1186/1471-2105-10-23

PMCID:: PMC2637844

Abstract Full Text PDF–788K

PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls

Joel Rozowsky, Ghia Euskirchen, Raymond K. Auerbach, Zhengdong D. Zhang, Theodore Gibson, Robert Bjornson, Nicholas Carriero, Michael Snyder, Mark B. Gerstein

Nat Biotechnol. Author manuscript; available in PMC 2010 August 20.

Published in final edited form as: Nat Biotechnol. 2009 January; 27(1): 66–75. Published online 2009 January 4. doi: 10.1038/nbt.1518

PMCID:: PMC2924752

Abstract Full Text PDF–965K Supplementary Material

An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong

Nat Biotechnol. Author manuscript; available in PMC 2009 May 1.

Published in final edited form as: Nat Biotechnol. 2008 November; 26(11): 1293–1300. Published online 2008 November 2. doi: 10.1038/nbt.1505

PMCID:: PMC2596672

Abstract Full Text PDF–1.7M Supplementary Material

Modeling ChIP Sequencing In Silico with Applications

Zhengdong D. Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, Mark Gerstein

PLoS Comput Biol. 2008 August; 4(8): e1000158. Published online 2008 August 22. doi: 10.1371/journal.pcbi.1000158

PMCID:: PMC2507756

Abstract Full Text PDF–482K Supplementary Material

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation

Zheng Lian, Alexander Karpikov, Jin Lian, Milind C. Mahajan, Stephen Hartman, Mark Gerstein, Michael Snyder, Sherman M. Weissman

Genome Res. 2008 August; 18(8): 1224–1237. doi: 10.1101/gr.075804.107

PMCID:: PMC2493437

Abstract Full Text PDF–991K

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson, Wei Li, D. Benjamin Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S. Carroll, Myles Brown, Paul Flicek, Christoph M. Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J. Farnham, Philipp Kapranov, David A. Nix, Thomas R. Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland D. Green, Jun S. Song, Scott A. McCuine, Elizabeth Anton, Loan Nguyen, Nathan D. Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C. Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P. Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M. Myers, Jason D. Lieb, X. Shirley Liu

Genome Res. 2008 March; 18(3): 393–403. doi: 10.1101/gr.7080508