PubMed

Bounded search for de novo identification of degenerate cis-regulatory elements.

Carlson JM, Chakravarty A, Khetani RS, Gross RH.

BMC Bioinformatics. 2006 May 15;7:254.PMID: 16700920 [PubMed - indexed for MEDLINE]Related articlesFree article

SPACER: identification of cis-regulatory elements with non-contiguous critical residues.

Chakravarty A, Carlson JM, Khetani RS, DeZiel CE, Gross RH.

Bioinformatics. 2007 Apr 15;23(8):1029-31.PMID: 17470480 [PubMed - indexed for MEDLINE]Related articlesFree article

MotifCut: regulatory motifs finding with maximum density subgraphs.

Fratkin E, Naughton BT, Brutlag DL, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e150-7.PMID: 16873465 [PubMed - indexed for MEDLINE]Related articlesFree article

A novel ensemble learning method for de novo computational identification of DNA binding sites.

Chakravarty A, Carlson JM, Khetani RS, Gross RH.

BMC Bioinformatics. 2007 Jul 12;8:249.PMID: 17626633 [PubMed - indexed for MEDLINE]Related articlesFree article

SCOPE: a web server for practical de novo motif discovery.

Carlson JM, Chakravarty A, DeZiel CE, Gross RH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W259-64. Epub 2007 May 7.PMID: 17485471 [PubMed - indexed for MEDLINE]Related articlesFree article

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

Sinha S.

Bioinformatics. 2006 Jul 15;22(14):e454-63.PMID: 16873507 [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

Searching for statistically significant regulatory modules.

Bailey TL, Noble WS.

Bioinformatics. 2003 Oct;19 Suppl 2:ii16-25.PMID: 14534166 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.PMID: 17953763 [PubMed - indexed for MEDLINE]Related articlesFree article

A survey of DNA motif finding algorithms.

Das MK, Dai HK.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S21. Review.PMID: 18047721 [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

OSCAR: one-class SVM for accurate recognition of cis-elements.

Jiang B, Zhang MQ, Zhang X.

Bioinformatics. 2007 Nov 1;23(21):2823-8. Epub 2007 Oct 5.PMID: 17921174 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.PMID: 16716228 [PubMed - indexed for MEDLINE]Related articlesFree article

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. Epub 2009 Mar 13.PMID: 19293946 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of cis-regulatory elements: from high-information content analysis to motif identification.

Li G, Lu J, Olman V, Xu Y.

J Bioinform Comput Biol. 2007 Aug;5(4):817-38.PMID: 17787058 [PubMed - indexed for MEDLINE]Related articles

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

Yu X, Lin J, Zack DJ, Qian J.

BMC Bioinformatics. 2007 Nov 9;8:437.PMID: 17996093 [PubMed - indexed for MEDLINE]Related articlesFree article

Informative priors based on transcription factor structural class improve de novo motif discovery.

Narlikar L, Gordân R, Ohler U, Hartemink AJ.

Bioinformatics. 2006 Jul 15;22(14):e384-92.PMID: 16873497 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

Mao L, Zheng WJ.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S21.PMID: 17217514 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical modeling of transcription factor binding affinities predicts regulatory interactions.

Manke T, Roider HG, Vingron M.

PLoS Comput Biol. 2008 Mar 21;4(3):e1000039.PMID: 18369429 [PubMed - indexed for MEDLINE]Related articlesFree article