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Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
Genome Biol. 2007; 8(6): R101. Published online 2007 June 5. doi: 10.1186/gb-2007-8-6-r101
PMCID:
PMC2394749
Abstract Full Text PDF–1.1M Supplementary Material

Is Cited by the Following 22 Articles in this Archive:

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis
Brian W. Busser, Leila Taher, Yongsok Kim, Terese Tansey, Molly J. Bloom, Ivan Ovcharenko, Alan M. Michelson
PLoS Genet. 2012 March; 8(3): e1002531. Published online 2012 March 8. doi: 10.1371/journal.pgen.1002531
PMCID:
PMC3297574
Abstract Full Text PDF–2.8M Supplementary Material
Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar
Jun Ding, Haiyan Hu, Xiaoman Li
Plant Physiol. 2012 January; 158(1): 145–155. doi: 10.1104/pp.111.186080
PMCID:
PMC3252106
Abstract Full Text PDF–493K
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules
Marc S Halfon, Qianqian Zhu, Elizabeth R Brennan, Yiyun Zhou
BMC Genomics. 2011; 12: 578. Published online 2011 November 25. doi: 10.1186/1471-2164-12-578
PMCID:
PMC3235160
Abstract Full Text PDF–1.7M Supplementary Material
Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness
Michael Z. Ludwig, Manu, Ralf Kittler, Kevin P. White, Martin Kreitman
PLoS Genet. 2011 November; 7(11): e1002364. Published online 2011 November 10. doi: 10.1371/journal.pgen.1002364
PMCID:
PMC3213169
Abstract Full Text PDF–1.4M Supplementary Material
Evolutionary Origins of Transcription Factor Binding Site Clusters
Xin He, Thyago S.P.C. Duque, Saurabh Sinha
Mol Biol Evol. 2012 March; 29(3): 1059–1070. Published online 2011 November 10. doi: 10.1093/molbev/msr277
PMCID:
PMC3278477
Free in PMC on 2013/03/01
Manduca sexta Moricin Promoter Elements can Increase Promoter Activities of Drosophila melanogaster Antimicrobial Peptide Genes
Xiang-Jun Rao, Xiao-Xia Xu, Xiao-Qiang Yu
Insect Biochem Mol Biol. Author manuscript; available in PMC 2012 December 1.
Published in final edited form as: Insect Biochem Mol Biol. 2011 December; 41(12): 982–992. Published online 2011 October 12. doi: 10.1016/j.ibmb.2011.09.007
PMCID:
PMC3210862
Free in PMC on 2012/12/01
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
Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer
Christina I. Swanson, David B. Schwimmer, Scott Barolo
Curr Biol. Author manuscript; available in PMC 2012 July 26.
Published in final edited form as: Curr Biol. 2011 July 26; 21(14): 1186–1196. Published online 2011 July 7. doi: 10.1016/j.cub.2011.05.056
PMCID:
PMC3143281
Free in PMC on 2012/07/26
Notch regulates numb: integration of conditional and autonomous cell fate specification
Mark Rebeiz, Steven W. Miller, James W. Posakony
Development. 2011 January 15; 138(2): 215–225. doi: 10.1242/dev.050161
PMCID:
PMC3005598
Abstract Full Text 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
Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers
Justin Crocker, Nathan Potter, Albert Erives
Nat Commun. 2010 October; 1(7): 99. doi: 10.1038/ncomms1102
PMCID:
PMC2963808
Abstract Full Text PDF–1.2M Supplementary Material
Dynamic CRM occupancy reflects a temporal map of developmental progression
Bartek Wilczyński, Eileen E M Furlong
Mol Syst Biol. 2010; 6: 383. Published online 2010 June 22. doi: 10.1038/msb.2010.35
PMCID:
PMC2913398
Abstract Full Text PDF–1.3M Supplementary Material
Systems Biology of Embryogenesis
Lucas B. Edelman, Sriram Chandrasekaran, Nathan D. Price
Reprod Fertil Dev. Author manuscript; available in PMC 2010 August 13.
Published in final edited form as: Reprod Fertil Dev. 2010; 22(1): 98–105. doi: 10.1071/RD09215
PMCID:
PMC2921326
Abstract Full Text PDF–735K
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse
Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha
Dev Cell. Author manuscript; available in PMC 2010 October 1.
Published in final edited form as: Dev Cell. 2009 October; 17(4): 568–579. doi: 10.1016/j.devcel.2009.09.002
PMCID:
PMC2768654
Abstract Full Text PDF–1.6M Supplementary Material
Identifying Cis-Regulatory Sequences by Word Profile Similarity
Garmay Leung, Michael B. Eisen
PLoS One. 2009; 4(9): e6901. Published online 2009 September 4. doi: 10.1371/journal.pone.0006901
PMCID:
PMC2731932
Abstract Full Text PDF–546K Supplementary Material
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn
BMC Bioinformatics. 2009; 10: 82. Published online 2009 March 10. doi: 10.1186/1471-2105-10-82
PMCID:
PMC2669485
Abstract Full Text PDF–685K 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
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster
Qianqian Zhu, Marc S Halfon
BMC Genomics. 2009; 10: 9. Published online 2009 January 7. doi: 10.1186/1471-2164-10-9
PMCID:
PMC2631479
Abstract Full Text PDF–1.7M Supplementary Material
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
Steven G. Kuntz, Erich M. Schwarz, John A. DeModena, Tristan De Buysscher, Diane Trout, Hiroaki Shizuya, Paul W. Sternberg, Barbara J. Wold
Genome Res. 2008 December; 18(12): 1955–1968. doi: 10.1101/gr.085472.108
PMCID:
PMC2593573
Abstract Full Text PDF–1.3M
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
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
Andra Ivan, Marc S Halfon, Saurabh Sinha
Genome Biol. 2008; 9(1): R22. Published online 2008 January 28. doi: 10.1186/gb-2008-9-1-r22
PMCID:
PMC2395258
Abstract Full Text PDF–1.0M Supplementary Material
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
Marc S. Halfon, Steven M. Gallo, Casey M. Bergman
Nucleic Acids Res. 2008 January; 36(Database issue): D594–D598. Published online 2008 January. doi: 10.1093/nar/gkm876
PMCID:
PMC2238825
Abstract Full Text PDF–345K
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