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Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools
Weichun Huang, Joseph R Nevins, Uwe Ohler
Genome Biol. 2007; 8(10): R225. Published online 2007 October 24. doi: 10.1186/gb-2007-8-10-r225
PMCID:
PMC2246299
Abstract Full Text PDF–1.3M Supplementary Material
 Is Cited by the Following 10 Articles in this Archive:
Genome-wide identification of conserved regulatory function in diverged sequences
Leila Taher, David M. McGaughey, Samantha Maragh, Ivy Aneas, Seneca L. Bessling, Webb Miller, Marcelo A. Nobrega, Andrew S. McCallion, Ivan Ovcharenko
Genome Res. 2011 July; 21(7): 1139–1149. doi: 10.1101/gr.119016.110
PMCID:
PMC3129256
Abstract Full Text PDF–645K
Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs
William H. Majoros, Uwe Ohler
PLoS Comput Biol. 2010 December; 6(12): e1001037. Published online 2010 December 16. doi: 10.1371/journal.pcbi.1001037
PMCID:
PMC3002982
Abstract Full Text PDF–1007K Supplementary Material
Towards realistic benchmarks for multiple alignments of non-coding sequences
Jaebum Kim, Saurabh Sinha
BMC Bioinformatics. 2010; 11: 54. Published online 2010 January 26. doi: 10.1186/1471-2105-11-54
PMCID:
PMC2823711
Abstract Full Text PDF–2.3M Supplementary Material
A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data
Xin He, Chieh-Chun Chen, Feng Hong, Fang Fang, Saurabh Sinha, Huck-Hui Ng, Sheng Zhong
PLoS One. 2009; 4(12): e8155. Published online 2009 December 1. doi: 10.1371/journal.pone.0008155
PMCID:
PMC2780727
Abstract Full Text PDF–524K Supplementary Material
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
Sacha A. F. T. van Hijum, Marnix H. Medema, Oscar P. Kuipers
Microbiol Mol Biol Rev. 2009 September; 73(3): 481–509. doi: 10.1128/MMBR.00037-08
PMCID:
PMC2738135
Abstract Full Text PDF–4.4M
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler
Genome Biol. 2009; 10(7): R73. Published online 2009 July 9. doi: 10.1186/gb-2009-10-7-r73
PMCID:
PMC2728527
Abstract Full Text PDF–1.6M Supplementary Material
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
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
Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolf Meier, Michael B. Eisen
PLoS Genet. 2008 June; 4(6): e1000106. Published online 2008 June 27. doi: 10.1371/journal.pgen.1000106
PMCID:
PMC2430619
Abstract Full Text PDF–434K 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
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