PubMed

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.

Ivan A, Halfon MS, Sinha S.

Genome Biol. 2008 Jan 28;9(1):R22.PMID: 18226245 [PubMed - in process]Related articlesFree article

Assessment of composite motif discovery methods.

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F.

BMC Bioinformatics. 2008 Feb 26;9:123.PMID: 18302777 [PubMed - indexed for MEDLINE]Related articlesFree article

CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.

Zhou Q, Wong WH.

Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12114-9. Epub 2004 Aug 5.PMID: 15297614 [PubMed - indexed for MEDLINE]Related articlesFree article

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

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

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses.

Li L, Zhu Q, He X, Sinha S, Halfon MS.

Genome Biol. 2007;8(6):R101.PMID: 17550599 [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

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

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.

Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S.

Dev Cell. 2009 Oct;17(4):568-79.PMID: 19853570 [PubMed - indexed for MEDLINE]Related articles

A discriminative model for identifying spatial cis-regulatory modules.

Segal E, Sharan R.

J Comput Biol. 2005 Jul-Aug;12(6):822-34.PMID: 16108719 [PubMed - indexed for MEDLINE]Related articles

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

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Pierstorff N, Bergman CM, Wiehe T.

Bioinformatics. 2006 Dec 1;22(23):2858-64. Epub 2006 Oct 10.PMID: 17032682 [PubMed - indexed for MEDLINE]Related articlesFree article

MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.

Hu J, Hu H, Li X.

Nucleic Acids Res. 2008 Aug;36(13):4488-97. Epub 2008 Jul 7.PMID: 18606616 [PubMed - indexed for MEDLINE]Related articlesFree article

A cis-regulatory logic simulator.

Zeigler RD, Gertz J, Cohen BA.

BMC Bioinformatics. 2007 Jul 27;8:272.PMID: 17662143 [PubMed - indexed for MEDLINE]Related articlesFree article

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.

Halfon MS, Grad Y, Church GM, Michelson AM.

Genome Res. 2002 Jul;12(7):1019-28.PMID: 12097338 [PubMed - indexed for MEDLINE]Related articlesFree article

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Halfon MS, Gallo SM, Bergman CM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. Epub 2007 Nov 26.PMID: 18039705 [PubMed - indexed for MEDLINE]Related articlesFree article

ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.

Sun H, De Bie T, Storms V, Fu Q, Dhollander T, Lemmens K, Verstuyf A, De Moor B, Marchal K.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S30.PMID: 19208131 [PubMed - indexed for MEDLINE]Related articlesFree article

Combining sequence and time series expression data to learn transcriptional modules.

Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202.PMID: 17044183 [PubMed - indexed for MEDLINE]Related articles

[Bio-database literacy and its application with cis-regulatory modules to find novel drug target proteins]

Miyazaki S.

Yakugaku Zasshi. 2008 Nov;128(11):1525-35. Review. Japanese. PMID: 18981686 [PubMed - indexed for MEDLINE]Related articlesFree article

Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.

Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML.

PLoS Comput Biol. 2006 May;2(5):e53. Epub 2006 May 26.PMID: 16733548 [PubMed - indexed for MEDLINE]Related articlesFree article