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A combinatorial optimization approach for diverse motif finding applications.

Zaslavsky E, Singh M.

Algorithms Mol Biol. 2006 Aug 17;1:13.PMID: 16916460 [PubMed]Related articlesFree article

A correlated motif approach for finding short linear motifs from protein interaction networks.

Tan SH, Hugo W, Sung WK, Ng SK.

BMC Bioinformatics. 2006 Nov 16;7:502.PMID: 17107624 [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

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

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

A novel swarm intelligence algorithm for finding DNA motifs.

Lei C, Ruan J.

Int J Comput Biol Drug Des. 2009;2(4):323-39. doi: 10.1504/IJCBDD.2009.030764. Epub 2009 Jan 4.PMID: 20090174 [PubMed - in process]Related articles

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.

Wilczynski B, Dojer N, Patelak M, Tiuryn J.

BMC Bioinformatics. 2009 Mar 10;10:82.PMID: 19284541 [PubMed - indexed for MEDLINE]Related articlesFree article

Voting algorithms for the motif finding problem.

Liu X, Ma B, Wang L.

Comput Syst Bioinformatics Conf. 2008;7:37-47.PMID: 19642267 [PubMed - indexed for MEDLINE]Related articles

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

Detection of generic spaced motifs using submotif pattern mining.

Wijaya E, Rajaraman K, Yiu SM, Sung WK.

Bioinformatics. 2007 Jun 15;23(12):1476-85. Epub 2007 May 5.PMID: 17483509 [PubMed - indexed for MEDLINE]Related articlesFree article

Heterogeneity in DNA Multiple Alignments: Modeling, Inference, and Applications in Motif Finding.

Chen G, Zhou Q.

Biometrics. 2009 Nov 30. [Epub ahead of print]PMID: 19995355 [PubMed - as supplied by publisher]Related articles

Bases of motifs for generating repeated patterns with wild cards.

Pisanti N, Crochemore M, Grossi R, Sagot MF.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jan-Mar;2(1):40-50.PMID: 17044163 [PubMed - indexed for MEDLINE]Related articles

Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves.

Berendzen KW, Stüber K, Harter K, Wanke D.

BMC Bioinformatics. 2006 Nov 30;7:522.PMID: 17137509 [PubMed - indexed for MEDLINE]Related articlesFree article

HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.

Le T, Altman T, Gardiner K.

Bioinformatics. 2010 Feb 1;26(3):302-9. Epub 2009 Dec 8.PMID: 19996163 [PubMed - in process]Related articles

HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing.

Larsson E, Lindahl P, Mostad P.

BMC Bioinformatics. 2007 Oct 28;8:418.PMID: 17963524 [PubMed - indexed for MEDLINE]Related articlesFree article

rMotifGen: random motif generator for DNA and protein sequences.

Rouchka EC, Hardin CT.

BMC Bioinformatics. 2007 Aug 7;8:292.PMID: 17683637 [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

[Applications of the motif-programmed proteins in medical area]

Shiba K.

Yakugaku Zasshi. 2009 Nov;129(11):1295-302. Review. Japanese. PMID: 19881200 [PubMed - indexed for MEDLINE]Related articlesFree article

SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins.

Edwards RJ, Davey NE, Shields DC.

PLoS One. 2007 Oct 3;2(10):e967.PMID: 17912346 [PubMed - indexed for MEDLINE]Related articlesFree article

Finding linear motif pairs from protein interaction networks: a probabilistic approach.

Leung HC, Siu MH, Yiu SM, Chin FY, Sung KW.

Comput Syst Bioinformatics Conf. 2007;6:111-9.PMID: 17951817 [PubMed - indexed for MEDLINE]Related articlesFree article