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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

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.PMID: 17559676 [PubMed - indexed for MEDLINE]Related articlesFree article

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

Huber BR, Bulyk ML.

BMC Bioinformatics. 2006 Apr 27;7:229.PMID: 16643658 [PubMed - indexed for MEDLINE]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

Using PhyloCon to identify conserved regulatory motifs.

Wang T.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 2:Unit 2.12.PMID: 18428790 [PubMed - indexed for MEDLINE]Related articles

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.PMID: 16870937 [PubMed - indexed for MEDLINE]Related articlesFree article

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

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

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.PMID: 17893078 [PubMed - indexed for MEDLINE]Related articles

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

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9. Epub 2003 Mar 10.PMID: 12627170 [PubMed - indexed for MEDLINE]Related articles

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

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

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

Finding motifs in the twilight zone.

Keich U, Pevzner PA.

Bioinformatics. 2002 Oct;18(10):1374-81.PMID: 12376382 [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

A novel Bayesian DNA motif comparison method for clustering and retrieval.

Habib N, Kaplan T, Margalit H, Friedman N.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000010.PMID: 18463706 [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

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

MUSA: a parameter free algorithm for the identification of biologically significant motifs.

Mendes ND, Casimiro AC, Santos PM, Sá-Correia I, Oliveira AL, Freitas AT.

Bioinformatics. 2006 Dec 15;22(24):2996-3002. Epub 2006 Oct 26.PMID: 17068086 [PubMed - indexed for MEDLINE]Related articlesFree article