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Refining motifs by improving information content scores using neighborhood profile search.

Reddy CK, Weng YC, Chiang HD.

Algorithms Mol Biol. 2006 Nov 27;1:23.PMID: 17129371 [PubMed]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

TRUST-TECH-based expectation maximization for learning finite mixture models.

Reddy CK, Chiang HD, Rajaratnam B.

IEEE Trans Pattern Anal Mach Intell. 2008 Jul;30(7):1146-57.PMID: 18550899 [PubMed - indexed for MEDLINE]Related articles

A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences.

Bi C.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):370-86.PMID: 19644166 [PubMed - indexed for MEDLINE]Related articles

DNA motif alignment by evolving a population of Markov chains.

Bi C.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S13.PMID: 19208112 [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

DISCOVER: a feature-based discriminative method for motif search in complex genomes.

Fu W, Ray P, Xing EP.

Bioinformatics. 2009 Jun 15;25(12):i321-9.PMID: 19478006 [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

GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery.

Li L.

J Comput Biol. 2009 Feb;16(2):317-29.PMID: 19193149 [PubMed - indexed for MEDLINE]Related articlesFree article

A sequential Monte Carlo EM approach to the transcription factor binding site identification problem.

Jackson ES, Fitzgerald WJ.

Bioinformatics. 2007 Jun 1;23(11):1313-20. Epub 2007 Mar 25.PMID: 17387112 [PubMed - indexed for MEDLINE]Related articlesFree article

Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study.

Bi C.

J Proteome Res. 2008 Jan;7(1):192-201. Epub 2007 Dec 15.PMID: 18081244 [PubMed - indexed for MEDLINE]Related articles

fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control.

Li L, Bass RL, Liang Y.

Bioinformatics. 2008 Mar 1;24(5):629-36. Epub 2008 Feb 22.PMID: 18296465 [PubMed - indexed for MEDLINE]Related articlesFree article

Convergent algorithms for protein structural alignment.

Martínez L, Andreani R, Martínez JM.

BMC Bioinformatics. 2007 Aug 22;8:306.PMID: 17714583 [PubMed - indexed for MEDLINE]Related articlesFree article

An effective PSO-based memetic algorithm for flow shop scheduling.

Liu B, Wang L, Jin YH.

IEEE Trans Syst Man Cybern B Cybern. 2007 Feb;37(1):18-27.PMID: 17278555 [PubMed - indexed for MEDLINE]Related articles

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

An impatient evolutionary algorithm with probabilistic tabu search for unified solution of some NP-hard problems in graph and set theory via clique finding.

Guturu P, Dantu R.

IEEE Trans Syst Man Cybern B Cybern. 2008 Jun;38(3):645-66.PMID: 18558530 [PubMed - indexed for MEDLINE]Related articles

Efficient exact motif discovery.

Marschall T, Rahmann S.

Bioinformatics. 2009 Jun 15;25(12):i356-64.PMID: 19478010 [PubMed - indexed for MEDLINE]Related articlesFree article

Hybrid Simulated Annealing and Its Application to Optimization of Hidden Markov Models for Visual Speech Recognition.

Lee JS, Park CH.

IEEE Trans Syst Man Cybern B Cybern. 2010 Jan 8. [Epub ahead of print]PMID: 20064758 [PubMed - as supplied by publisher]Related articles

A multiresolution stochastic level set method for Mumford-Shah image segmentation.

Law YN, Lee HK, Yip AM.

IEEE Trans Image Process. 2008 Dec;17(12):2289-300.PMID: 19004702 [PubMed - indexed for MEDLINE]Related articles

Finding regulatory elements and regulatory motifs: a general probabilistic framework.

van Nimwegen E.

BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S4. Review.PMID: 17903285 [PubMed - indexed for MEDLINE]Related articlesFree article