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Genome-wide prediction of transcription factor binding sites using an integrated model
Kyoung-Jae Won, Bing Ren, Wei Wang
Genome Biol. 2010; 11(1): R7. Published online 2010 January 22. doi: 10.1186/gb-2010-11-1-r7
PMCID:
PMC2847719
Abstract Full Text PDF–2.4M Supplementary Material

Is Cited by the Following 17 Articles in this Archive:

Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite
Elena Y Harris, Nadia Ponts, Karine G Le Roch, Stefano Lonardi
BMC Genomics. 2011; 12: 601. Published online 2011 December 13. doi: 10.1186/1471-2164-12-601
PMCID:
PMC3282892
Abstract Full Text PDF–951K 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
Epigenetic priors for identifying active transcription factor binding sites
Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey
Bioinformatics. 2012 January 1; 28(1): 56–62. Published online 2011 November 8. doi: 10.1093/bioinformatics/btr614
PMCID:
PMC3244768
Free in PMC on 2013/01/01
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors
Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein
Genome Biol. 2011; 12(11): R111. Published online 2011 November 7. doi: 10.1186/gb-2011-12-11-r111
PMCID:
PMC3334597
Abstract Full Text PDF–2.1M Supplementary Material
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles
Chao Cheng, Renqiang Min, Mark Gerstein
Bioinformatics. 2011 December 1; 27(23): 3221–3227. Published online 2011 October 29. doi: 10.1093/bioinformatics/btr552
PMCID:
PMC3223362
Free in PMC on 2012/12/01
Identifying functional single nucleotide polymorphisms in the human CArGome
Craig C. Benson, Qian Zhou, Xiaochun Long, Joseph M. Miano
Physiol Genomics. 2011 September; 43(18): 1038–1048. Published online 2011 July 19. doi: 10.1152/physiolgenomics.00098.2011
PMCID:
PMC3180741
Free in PMC on 2012/09/01
Tissue-specific prediction of directly regulated genes
Robert C. McLeay, Chris J. Leat, Timothy L. Bailey
Bioinformatics. 2011 September 1; 27(17): 2354–2360. Published online 2011 June 30. doi: 10.1093/bioinformatics/btr399
PMCID:
PMC3157924
Free in PMC on 2012/09/01
Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for the Arabidopsis LEAFY Transcription Factor
Edwige Moyroud, Eugenio Gómez Minguet, Felix Ott, Levi Yant, David Posé, Marie Monniaux, Sandrine Blanchet, Olivier Bastien, Emmanuel Thévenon, Detlef Weigel, Markus Schmid, François Parcy
Plant Cell. 2011 April; 23(4): 1293–1306. Published online 2011 April 22. doi: 10.1105/tpc.111.083329
PMCID:
PMC3101549
Abstract Full Text PDF–1014K
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin
Genome Biol. 2011; 12(4): R34. Published online 2011 April 7. doi: 10.1186/gb-2011-12-4-r34
PMCID:
PMC3218860
Abstract Full Text PDF–787K Supplementary Material
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
Junbai Wang
BMC Genomics. 2011; 12: 172. Published online 2011 April 1. doi: 10.1186/1471-2164-12-172
PMCID:
PMC3082246
Abstract Full Text PDF–860K Supplementary Material
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
Roger Pique-Regi, Jacob F. Degner, Athma A. Pai, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard
Genome Res. 2011 March; 21(3): 447–455. doi: 10.1101/gr.112623.110
PMCID:
PMC3044858
Abstract Full Text PDF–1.4M
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White, Peter J Park
BMC Genomics. 2011; 12: 134. Published online 2011 February 28. doi: 10.1186/1471-2164-12-134
PMCID:
PMC3053263
Abstract Full Text PDF–522K Supplementary Material
Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development
Tommy Kaplan, Xiao-Yong Li, Peter J. Sabo, Sean Thomas, John A. Stamatoyannopoulos, Mark D. Biggin, Michael B. Eisen
PLoS Genet. 2011 February; 7(2): e1001290. Published online 2011 February 3. doi: 10.1371/journal.pgen.1001290
PMCID:
PMC3033374
Abstract Full Text PDF–2.2M Supplementary Material
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 Biol. 2011; 12(1): R2. Published online 2011 January 13. doi: 10.1186/gb-2011-12-1-r2
PMCID:
PMC3091300
Abstract Full Text PDF–1.2M Supplementary Material
Assessing Computational Methods of Cis-Regulatory Module Prediction
Jing Su, Sarah A. Teichmann, Thomas A. Down
PLoS Comput Biol. 2010 December; 6(12): e1001020. Published online 2010 December 2. doi: 10.1371/journal.pcbi.1001020
PMCID:
PMC2996316
Abstract Full Text PDF–1.1M Supplementary Material
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
Stephen A. Ramsey, Theo A. Knijnenburg, Kathleen A. Kennedy, Daniel E. Zak, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Aaron E. Lampano, Vladimir Litvak, Garnet Navarro, Tetyana Stolyar, Alan Aderem, Ilya Shmulevich
Bioinformatics. 2010 September 1; 26(17): 2071–2075. Published online 2010 July 27. doi: 10.1093/bioinformatics/btq405
PMCID:
PMC2922897
Abstract Full Text PDF–314K Supplementary Material
Metamotifs - a generative model for building families of nucleotide position weight matrices
Matias Piipari, Thomas A Down, Tim JP Hubbard
BMC Bioinformatics. 2010; 11: 348. Published online 2010 June 25. doi: 10.1186/1471-2105-11-348
PMCID:
PMC2906491
Abstract Full Text PDF–1.4M Supplementary Material
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