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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker
Genome Biol. 2004; 5(9): R61. Published online 2004 August 20. doi: 10.1186/gb-2004-5-9-r61
PMCID:
PMC522868
Abstract Full Text PDF–1.2M Supplementary Material
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 Is Cited by the Following 75 Articles in this Archive:
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
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
Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences
Mark Rebeiz, Nick Jikomes, Victoria A. Kassner, Sean B. Carroll
Proc Natl Acad Sci U S A. 2011 June 21; 108(25): 10036–10043. Published online 2011 May 18. doi: 10.1073/pnas.1105937108
PMCID:
PMC3121811
Abstract Full Text PDF–1.0M Supplementary Material
Genome surveyor 2.0: cis-regulatory analysis in Drosophila
Majid Kazemian, Michael H. Brodsky, Saurabh Sinha
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W79–W85. Published online 2011 May 18. doi: 10.1093/nar/gkr291
PMCID:
PMC3125742
Abstract Full Text PDF–7.7M
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos
Genome Biol. 2011; 12(5): R43. Published online 2011 May 11. doi: 10.1186/gb-2011-12-5-r43
PMCID:
PMC3219966
Abstract Full Text PDF–1.5M Supplementary Material
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
Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila
Matthew Slattery, Lijia Ma, Nicolas Négre, Kevin P. White, Richard S. Mann
PLoS One. 2011; 6(4): e14686. Published online 2011 April 5. doi: 10.1371/journal.pone.0014686
PMCID:
PMC3071676
Abstract Full Text PDF–1.8M Supplementary Material
Nucleosome-mediated cooperativity between transcription factors
Leonid A. Mirny
Proc Natl Acad Sci U S A. 2010 December 28; 107(52): 22534–22539. Published online 2010 December 13. doi: 10.1073/pnas.0913805107
PMCID:
PMC3012490
Abstract Full Text PDF–814K Supplementary Material
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, Michael H. Brodsky
Nucleic Acids Res. 2011 January; 39(Database issue): D111–D117. Published online 2010 November 19. doi: 10.1093/nar/gkq858
PMCID:
PMC3013762
Abstract Full Text PDF–5.1M
The gap gene network
Johannes Jaeger
Cell Mol Life Sci. 2011 January; 68(2): 243–274. Published online 2010 October 8. doi: 10.1007/s00018-010-0536-y
PMCID:
PMC3016493
Abstract Full Text PDF–1.1M
Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials
Majid Kazemian, Charles Blatti, Adam Richards, Michael McCutchan, Noriko Wakabayashi-Ito, Ann S. Hammonds, Susan E. Celniker, Sudhir Kumar, Scot A. Wolfe, Michael H. Brodsky, Saurabh Sinha
PLoS Biol. 2010 August; 8(8): e1000456. Published online 2010 August 17. doi: 10.1371/journal.pbio.1000456
PMCID:
PMC2923081
Abstract Full Text PDF–1.3M Supplementary Material
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
Manonmani Arunachalam, Karthik Jayasurya, Pavel Tomancak, Uwe Ohler
Bioinformatics. 2010 September 1; 26(17): 2109–2115. Published online 2010 July 11. doi: 10.1093/bioinformatics/btq358
PMCID:
PMC2922894
Abstract Full Text PDF–304K Supplementary Material
Recombineering Hunchback identifies two conserved domains required to maintain neuroblast competence and specify early-born neuronal identity
Khoa D. Tran, Michael R. Miller, Chris Q. Doe
Development. 2010 May 1; 137(9): 1421–1430. doi: 10.1242/dev.048678
PMCID:
PMC2853844
Abstract Full Text Supplementary Material
Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances
Jaebum Kim, Ryan Cunningham, Brian James, Stefan Wyder, Joshua D. Gibson, Oliver Niehuis, Evgeny M. Zdobnov, Hugh M. Robertson, Gene E. Robinson, John H. Werren, Saurabh Sinha
PLoS Comput Biol. 2010 January; 6(1): e1000652. Published online 2010 January 29. doi: 10.1371/journal.pcbi.1000652
PMCID:
PMC2813253
Abstract Full Text PDF–898K Supplementary Material
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
The Complex Spatio-Temporal Regulation of the Drosophila Myoblast Attractant Gene duf/kirre
K. G. Guruharsha, Mar Ruiz-Gomez, H. A. Ranganath, Rahul Siddharthan, K. VijayRaghavan
PLoS One. 2009; 4(9): e6960. Published online 2009 September 9. doi: 10.1371/journal.pone.0006960
PMCID:
PMC2734059
Abstract Full Text PDF–2.3M 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
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen
Genome Biol. 2009; 10(7): R80. Published online 2009 July 23. doi: 10.1186/gb-2009-10-7-r80
PMCID:
PMC2728534
Abstract Full Text PDF–1.7M Supplementary Material
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets
Dennis J. Hazelett, Daniel L. Lakeland, Joseph B. Weiss
Bioinformatics. 2009 July 1; 25(13): 1617–1624. Published online 2009 April 28. doi: 10.1093/bioinformatics/btp282
PMCID:
PMC2732317
Abstract Full Text PDF–255K
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
Statistical detection of cooperative transcription factors with similarity adjustment
Utz J. Pape, Holger Klein, Martin Vingron
Bioinformatics. 2009 August 15; 25(16): 2103–2109. Published online 2009 March 13. doi: 10.1093/bioinformatics/btp143
PMCID:
PMC2722994
Abstract Full Text PDF–369K
Big Genomes Facilitate the Comparative Identification of Regulatory Elements
Brant K. Peterson, Emily E. Hare, Venky N. Iyer, Steven Storage, Laura Conner, Daniel R. Papaj, Rick Kurashima, Eric Jang, Michael B. Eisen
PLoS ONE. 2009; 4(3): e4688. Published online 2009 March 4. doi: 10.1371/journal.pone.0004688
PMCID:
PMC2650094
Abstract Full Text PDF–1.4M Supplementary Material
Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?
Antónia Monteiro, Ondrej Podlaha
PLoS Biol. 2009 February; 7(2): e1000037. Published online 2009 February 24. doi: 10.1371/journal.pbio.1000037
PMCID:
PMC2652386
Full Text PDF–397K
Identification of direct T-box target genes in the developing zebrafish mesoderm
Aaron T. Garnett, Tina M. Han, Michael J. Gilchrist, James C. Smith, Michael B. Eisen, Fiona C. Wardle, Sharon L. Amacher
Development. 2009 March 1; 136(5): 749–760. Published online 2009 January 21. doi: 10.1242/dev.024703
PMCID:
PMC2685943
Abstract Full Text Supplementary Material
Evolutionary Plasticity of Polycomb/Trithorax Response Elements in Drosophila Species
Arne Hauenschild, Leonie Ringrose, Christina Altmutter, Renato Paro, Marc Rehmsmeier
PLoS Biol. 2008 October; 6(10): e261. Published online 2008 October 28. doi: 10.1371/journal.pbio.0060261
PMCID:
PMC2573935
Abstract Full Text PDF–1.1M Supplementary Material
Computational Structural Analysis: Multiple Proteins Bound to DNA
Andrija Tomovic, Edward J. Oakeley
PLoS ONE. 2008; 3(9): e3243. Published online 2008 September 19. doi: 10.1371/journal.pone.0003243
PMCID:
PMC2532747
Abstract Full Text PDF–188K Supplementary Material
PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
Rahul Siddharthan
PLoS Comput Biol. 2008 August; 4(8): e1000156. Published online 2008 August 29. doi: 10.1371/journal.pcbi.1000156
PMCID:
PMC2518514
Abstract Full Text PDF–878K
PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
Rahul Siddharthan
PLoS Comput Biol. 2008 August; 4(8): e1000156. Published online 2008 August 29. doi: 10.1371/journal.pcbi.1000156
PMCID:
PMC2518514
Abstract Full Text PDF–878K
Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers
Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, Ward F Odenwald
BMC Genomics. 2008; 9: 371. Published online 2008 August 1. doi: 10.1186/1471-2164-9-371
PMCID:
PMC2529316
Abstract Full Text PDF–1.2M Supplementary Material
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