Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
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* Corresponding author: Michael B Eisen mbeisen@lbl.gov
- † Equal contributors
Genome Biology 2004, 5:R61 doi:10.1186/gb-2004-5-9-r61
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BioMed Central: 19 citations
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Research article
Marc S Halfon, Qianqian Zhu, Elizabeth R Brennan, Yiyun Zhou BMC Genomics 2011, 12:578 (25 November 2011) |
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Research
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 Biology 2011, 12:R43 (11 May 2011) A map of the dynamically changing chromatin landscape throughout Drosophila development.
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Research
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 Biology 2009, 10:R80 (23 July 2009) Distinct developmental fates in |
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Research article
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 (1 August 2008) |
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Research article
Studying the functional conservation of cis-regulatory modules and their transcriptional output Denis C Bauer, Timothy L Bailey BMC Bioinformatics 2008, 9:220 (29 April 2008) |
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Method
Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen Genome Biology 2008, 9:R66 (7 April 2008) ModuleMiner detects |
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Minireview
A systems view of Drosophila segmentation Mike Levine Genome Biology 2008, 9:207 (11 February 2008) High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? |
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Research article
Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer BMC Bioinformatics 2007, 8:445 (15 November 2007) |
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Research article
Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian BMC Bioinformatics 2007, 8:437 (9 November 2007) Cis-regulatory regions can be found regardless of sequence conservation by grouping sets of interacting transcription factors, which can pin-point tissue-specific cis-regulatory modules.
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Research
Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg, Vsevolod J Makeev Algorithms for Molecular Biology 2007, 2:13 (10 October 2007) |
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Research
Anne Laurençon, Raphaëlle Dubruille, Evgeni Efimenko, Guillaume Grenier, Ryan Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Bénédicte Durand Genome Biology 2007, 8:R195 (17 September 2007) An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis. |
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Methodology article
A novel ensemble learning method for de novo computational identification of DNA binding sites Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross BMC Bioinformatics 2007, 8:249 (12 July 2007) |
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Research
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon Genome Biology 2007, 8:R101 (5 June 2007) Analysis of 280 experimentally-verified |
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Method
Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, Ward F Odenwald Genome Biology 2007, 8:R75 (9 May 2007) : The use of |
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Methodology article
Statistical significance of cis-regulatory modules Dustin E Schones, Andrew D Smith, Michael Q Zhang BMC Bioinformatics 2007, 8:19 (22 January 2007) |
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Research
Cris L Luengo Hendriks, Soile VE Keränen, Charless C Fowlkes, Lisa Simirenko, Gunther H Weber, Angela H DePace, Clara Henriquez, David W Kaszuba, Bernd Hamann, Michael B Eisen, Jitendra Malik, Damir Sudar, Mark D Biggin, David W Knowles Genome Biology 2006, 7:R123 (21 December 2006) A suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology with cellular resolution in whole |
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Research article
Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen BMC Bioinformatics 2006, 7:376 (14 August 2006) |
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Research
Stuart J Macdonald, Anthony D Long Genome Biology 2006, 7:R67 (27 July 2006) Comparative genomics reveals fine-scale structural variants, including microinversions, distinguishing two diverged Drosophila species |
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Research
Promoter features related to tissue specificity as measured by Shannon entropy Jonathan Schug, Winfried-Paul Schuller, Claudia Kappen, J Michael Salbaum, Maja Bucan, Christian J Stoeckert Genome Biology 2005, 6:R33 (29 March 2005) A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most genes show statistically significant tissue-dependent variations of expression level and identified components of promoters that distinguish tissue-specific from ubiquitous genes. |