PubMed

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

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

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

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

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.PMID: 17559640 [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

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

IEM: an algorithm for iterative enhancement of motifs using comparative genomics data.

Zeng E, Mathee K, Narasimhan G.

Comput Syst Bioinformatics Conf. 2007;6:227-35.PMID: 17951827 [PubMed - indexed for MEDLINE]Related articlesFree article

Discriminative discovery of transcription factor binding sites from location data.

Kawada Y, Sakakibara Y.

Proc IEEE Comput Syst Bioinform Conf. 2005:86-9.PMID: 16447966 [PubMed - indexed for MEDLINE]Related articles

BioOptimizer: a Bayesian scoring function approach to motif discovery.

Jensen ST, Liu JS.

Bioinformatics. 2004 Jul 10;20(10):1557-64. Epub 2004 Feb 12.PMID: 14962923 [PubMed - indexed for MEDLINE]Related articlesFree article

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.PMID: 15166027 [PubMed - indexed for MEDLINE]Related articlesFree article

A deterministic motif finding algorithm with application to the human genome.

Hon LS, Jain AN.

Bioinformatics. 2006 May 1;22(9):1047-54. Epub 2006 Feb 2.PMID: 16455748 [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

Discovering motifs in ranked lists of DNA sequences.

Eden E, Lipson D, Yogev S, Yakhini Z.

PLoS Comput Biol. 2007 Mar 23;3(3):e39.PMID: 17381235 [PubMed - indexed for MEDLINE]Related articlesFree article

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

Redhead E, Bailey TL.

BMC Bioinformatics. 2007 Oct 15;8:385.PMID: 17937785 [PubMed - indexed for MEDLINE]Related articlesFree article

Compo: composite motif discovery using discrete models.

Sandve GK, Abul O, Drabløs F.

BMC Bioinformatics. 2008 Dec 8;9:527.PMID: 19063744 [PubMed - indexed for MEDLINE]Related articlesFree article

STAMP: a web tool for exploring DNA-binding motif similarities.

Mahony S, Benos PV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W253-8. Epub 2007 May 3.PMID: 17478497 [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