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MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen
Genome Biol. 2004; 5(12): R98. Published online 2004 November 30. doi: 10.1186/gb-2004-5-12-r98
PMCID:
PMC545801
Abstract Full Text PDF–758K Supplementary Material
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 Is Cited by the Following 56 Articles in this Archive:
Formation of Regulatory Modules by Local Sequence Duplication
Armita Nourmohammad, Michael Lässig
PLoS Comput Biol. 2011 October; 7(10): e1002167. Published online 2011 October 6. doi: 10.1371/journal.pcbi.1002167
PMCID:
PMC3188502
Abstract Full Text PDF–412K Supplementary Material
Germline Fitness-Based Scoring of Cancer Mutations
Andrej Fischer, Chris Greenman, Ville Mustonen
Genetics. 2011 June; 188(2): 383–393. doi: 10.1534/genetics.111.127480
PMCID:
PMC3122307
Abstract Full Text PDF–1.0M
Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection
David S. Lawrie, Dmitri A. Petrov, Philipp W. Messer
Genome Biol Evol. 2011; 3: 383–395. Published online 2011 April 17. doi: 10.1093/gbe/evr032
PMCID:
PMC3101017
Abstract Full Text PDF–395K
Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
Georg Fuellen, Stephan Struckmann
Biol Direct. 2010; 5: 67. Published online 2010 December 29. doi: 10.1186/1745-6150-5-67
PMCID:
PMC3024949
Abstract Full Text PDF–819K Supplementary Material
PHAST and RPHAST: phylogenetic analysis with space/time models
Melissa J. Hubisz, Katherine S. Pollard, Adam Siepel
Brief Bioinform. 2011 January; 12(1): 41–51. Published online 2010 December 21. doi: 10.1093/bib/bbq072
PMCID:
PMC3030812
Abstract Full Text PDF–1.3M
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 identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny
Hervé Rouault, Khalil Mazouni, Lydie Couturier, Vincent Hakim, François Schweisguth
Proc Natl Acad Sci U S A. 2010 August 17; 107(33): 14615–14620. Published online 2010 July 29. doi: 10.1073/pnas.1002876107
PMCID:
PMC2930411
Abstract Full Text PDF–1.4M Supplementary Material
An effective model for natural selection in promoters
Michael M. Hoffman, Ewan Birney
Genome Res. 2010 May; 20(5): 685–692. doi: 10.1101/gr.096719.109
PMCID:
PMC2860170
Abstract Full Text PDF–564K
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data
Michael J. Palumbo, Lee A. Newberg
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W268–W274. Published online 2010 April 30. doi: 10.1093/nar/gkq330
PMCID:
PMC2896078
Abstract Full Text PDF–353K
A Systems Biology Approach to Transcription Factor Binding Site Prediction
Xiang Zhou, Pavel Sumazin, Presha Rajbhandari, Andrea Califano
PLoS One. 2010; 5(3): e9878. Published online 2010 March 26. doi: 10.1371/journal.pone.0009878
PMCID:
PMC2845628
Abstract Full Text PDF–487K Supplementary Material
Assigning roles to DNA regulatory motifs using comparative genomics
Fabian A. Buske, Mikael Bodén, Denis C. Bauer, Timothy L. Bailey
Bioinformatics. 2010 April 1; 26(7): 860–866. Published online 2010 February 10. doi: 10.1093/bioinformatics/btq049
PMCID:
PMC2844991
Abstract Full Text PDF–345K
Detection of nonneutral substitution rates on mammalian phylogenies
Katherine S. Pollard, Melissa J. Hubisz, Kate R. Rosenbloom, Adam Siepel
Genome Res. 2010 January; 20(1): 110–121. doi: 10.1101/gr.097857.109
PMCID:
PMC2798823
Abstract Full Text PDF–1.4M
Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila
Margaret C. W. Ho, Holly Johnsen, Sara E. Goetz, Benjamin J. Schiller, Esther Bae, Diana A. Tran, Andrey S. Shur, John M. Allen, Christoph Rau, Welcome Bender, William W. Fisher, Susan E. Celniker, Robert A. Drewell
PLoS Genet. 2009 November; 5(11): e1000709. Published online 2009 November 6. doi: 10.1371/journal.pgen.1000709
PMCID:
PMC2763271
Abstract Full Text PDF–673K Supplementary Material
Impact of DNA-binding position variants on yeast gene expression
Krishna B. S. Swamy, Chung-Yi Cho, Sufeng Chiang, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai
Nucleic Acids Res. 2009 November; 37(21): 6991–7001. Published online 2009 November. doi: 10.1093/nar/gkp743
PMCID:
PMC2790881
Abstract Full Text PDF–463K Supplementary Material
Assessing phylogenetic motif models for predicting transcription factor binding sites
John Hawkins, Charles Grant, William Stafford Noble, Timothy L. Bailey
Bioinformatics. 2009 June 15; 25(12): i339–i347. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp201
PMCID:
PMC2687955
Abstract Full Text PDF–271K
Multiple whole-genome alignments without a reference organism
Inna Dubchak, Alexander Poliakov, Andrey Kislyuk, Michael Brudno
Genome Res. 2009 April; 19(4): 682–689. doi: 10.1101/gr.081778.108
PMCID:
PMC2665786
Abstract Full Text PDF–1.0M
Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution
Xin He, Xu Ling, Saurabh Sinha
PLoS Comput Biol. 2009 March; 5(3): e1000299. Published online 2009 March 13. doi: 10.1371/journal.pcbi.1000299
PMCID:
PMC2657044
Abstract Full Text PDF–657K Supplementary Material
Evolution of Regulatory Sequences in 12 Drosophila Species
Jaebum Kim, Xin He, Saurabh Sinha
PLoS Genet. 2009 January; 5(1): e1000330. Published online 2009 January 9. doi: 10.1371/journal.pgen.1000330
PMCID:
PMC2607023
Abstract Full Text PDF–262K Supplementary Material
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
Tom Whitington, Andrew C. Perkins, Timothy L. Bailey
Nucleic Acids Res. 2009 January; 37(1): 14–25. Published online 2009 January. doi: 10.1093/nar/gkn866
PMCID:
PMC2662491
Abstract Full Text PDF–2.0M Supplementary Material
Exact Calculation of Distributions on Integers, with Application to Sequence Alignment
Lee A. Newberg, Charles E. Lawrence
J Comput Biol. 2009 January; 16(1): 1–18. doi: 10.1089/cmb.2008.0137
PMCID:
PMC2858568
Abstract Full Text PDF–393K Supplementary Material
MotifMap: a human genome-wide map of candidate regulatory motif sites
Xiaohui Xie, Paul Rigor, Pierre Baldi
Bioinformatics. 2009 January 15; 25(2): 167–174. Published online 2008 November 18. doi: 10.1093/bioinformatics/btn605
PMCID:
PMC2732295
Abstract Full Text PDF–255K Supplementary Material
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
Avinash Varadarajan, Robert K Bradley, Ian H Holmes
Genome Biol. 2008; 9(10): R147. Published online 2008 October 8. doi: 10.1186/gb-2008-9-10-r147
PMCID:
PMC2760874
Abstract Full Text PDF–425K
A Catalog of Neutral and Deleterious Polymorphism in Yeast
Scott W. Doniger, Hyun Seok Kim, Devjanee Swain, Daniella Corcuera, Morgan Williams, Shiaw-Pyng Yang, Justin C. Fay
PLoS Genet. 2008 August; 4(8): e1000183. Published online 2008 August 29. doi: 10.1371/journal.pgen.1000183
PMCID:
PMC2515631
Abstract Full Text PDF–405K Supplementary Material
xREI: a phylo-grammar visualization webserver
Lars Barquist, Ian Holmes
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W65–W69. Published online 2008 July 1. doi: 10.1093/nar/gkn283
PMCID:
PMC2447789
Abstract Full Text PDF–598K
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
Lucas D. Ward, Harmen J. Bussemaker
Bioinformatics. 2008 July 1; 24(13): i165–i171. doi: 10.1093/bioinformatics/btn154
PMCID:
PMC2718632
Abstract Full Text PDF–283K Supplementary Material
CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P. Xing
PLoS Comput Biol. 2008 June; 4(6): e1000090. Published online 2008 June 6. doi: 10.1371/journal.pcbi.1000090
PMCID:
PMC2396503
Abstract Full Text PDF–1.1M Supplementary Material
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J Siezen
BMC Genomics. 2008; 9: 145. Published online 2008 March 27. doi: 10.1186/1471-2164-9-145
PMCID:
PMC2329647
Abstract Full Text PDF–739K Supplementary Material
Systematic identification of mammalian regulatory motifs' target genes and functions
Jason B. Warner, Anthony A. Philippakis, Savina A. Jaeger, Fangxue Sherry He, Jolinta Lin, Martha L. Bulyk
Nat Methods. Author manuscript; available in PMC 2009 July 10.
Published in final edited form as: Nat Methods. 2008 April; 5(4): 347–353. Published online 2008 March 2. doi: 10.1038/nmeth.1188
PMCID:
PMC2708972
Abstract Full Text PDF–1.6M Supplementary Material
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L. Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin
PLoS Biol. 2008 February; 6(2): e27. Published online 2008 February 12. doi: 10.1371/journal.pbio.0060027
Correction in:
PLoS Biol. 2008 July; 6(7): e190.
PMCID:
PMC2235902
Abstract Full Text PDF–1.9M Supplementary Material Correction
Universal patterns of purifying selection at noncoding positions in bacteria
Nacho Molina, Erik van Nimwegen
Genome Res. 2008 January; 18(1): 148–160. doi: 10.1101/gr.6759507
PMCID:
PMC2134783
Abstract Full Text PDF–591K
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