PubMed

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

Rajewsky N, Vergassola M, Gaul U, Siggia ED.

BMC Bioinformatics. 2002 Oct 24;3:30. Epub 2002 Oct 24.PMID: 12398796 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional control in the segmentation gene network of Drosophila.

Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U.

PLoS Biol. 2004 Sep;2(9):E271. Epub 2004 Aug 31.PMID: 15340490 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE.

Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20.PMID: 15345045 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62.PMID: 11805330 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

Grad YH, Roth FP, Halfon MS, Church GM.

Bioinformatics. 2004 Nov 1;20(16):2738-50. Epub 2004 May 14.PMID: 15145800 [PubMed - indexed for MEDLINE]Related articlesFree article

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M.

BMC Bioinformatics. 2005 May 2;6:110.PMID: 15865625 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.

Siddharthan R.

PLoS Comput Biol. 2008 Aug 29;4(8):e1000156.PMID: 18769735 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.

Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA.

Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10.PMID: 18332042 [PubMed - indexed for MEDLINE]Related articlesFree article

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.

Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED.

BMC Bioinformatics. 2004 Sep 9;5:129.PMID: 15357878 [PubMed - indexed for MEDLINE]Related articlesFree article

Conservation of regulatory elements between two species of Drosophila.

Emberly E, Rajewsky N, Siggia ED.

BMC Bioinformatics. 2003 Nov 20;4:57.PMID: 14629780 [PubMed - indexed for MEDLINE]Related articlesFree article

Stubb: a program for discovery and analysis of cis-regulatory modules.

Sinha S, Liang Y, Siggia E.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9.PMID: 16845069 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical significance of cis-regulatory modules.

Schones DE, Smith AD, Zhang MQ.

BMC Bioinformatics. 2007 Jan 22;8:19.PMID: 17241466 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes.

Narang V, Sung WK, Mittal A.

Genome Inform. 2006;17(2):14-24.PMID: 17503375 [PubMed - indexed for MEDLINE]Related articles

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U.

Nature. 2008 Jan 31;451(7178):535-40. Epub 2008 Jan 2.PMID: 18172436 [PubMed - indexed for MEDLINE]Related articles

Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

Abnizova I, te Boekhorst R, Walter K, Gilks WR.

BMC Bioinformatics. 2005 Apr 27;6:109.PMID: 15857505 [PubMed - indexed for MEDLINE]Related articlesFree article

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J.

Nat Protoc. 2008;3(10):1578-88.PMID: 18802439 [PubMed - indexed for MEDLINE]Related articles

Genome wide identification of regulatory motifs in Bacillus subtilis.

Mwangi MM, Siggia ED.

BMC Bioinformatics. 2003 May 16;4:18. Epub 2003 May 16.PMID: 12749771 [PubMed - indexed for MEDLINE]Related articlesFree article

Large-scale discovery of promoter motifs in Drosophila melanogaster.

Down TA, Bergman CM, Su J, Hubbard TJ.

PLoS Comput Biol. 2007 Jan 19;3(1):e7. Epub 2006 Dec 5.PMID: 17238282 [PubMed - indexed for MEDLINE]Related articlesFree article