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Items: 1 to 20 of 128

1.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction.

Yanover C, Singh M, Zaslavsky E.

Bioinformatics. 2009 Apr 1;25(7):868-74. doi: 10.1093/bioinformatics/btp090.

3.

More robust detection of motifs in coexpressed genes by using phylogenetic information.

Monsieurs P, Thijs G, Fadda AA, De Keersmaecker SC, Vanderleyden J, De Moor B, Marchal K.

BMC Bioinformatics. 2006 Mar 20;7:160.

4.

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.

PMID:
12627170
5.

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23.

7.

Transcription factor binding site identification using the self-organizing map.

Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.

Bioinformatics. 2005 May 1;21(9):1807-14.

8.

Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes.

McGuire AM, Hughes JD, Church GM.

Genome Res. 2000 Jun;10(6):744-57.

9.
10.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70.

11.

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.

12.

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Pierstorff N, Bergman CM, Wiehe T.

Bioinformatics. 2006 Dec 1;22(23):2858-64.

13.
14.

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. doi: 10.1371/journal.pcbi.1000299.

15.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67.

16.

MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.

Wijaya E, Yiu SM, Son NT, Kanagasabai R, Sung WK.

Bioinformatics. 2008 Oct 15;24(20):2288-95. doi: 10.1093/bioinformatics/btn420.

17.

PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.

Siddharthan R.

PLoS Comput Biol. 2008 Aug 29;4(8):e1000156. doi: 10.1371/journal.pcbi.1000156.

18.

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.

19.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

20.

A cluster refinement algorithm for motif discovery.

Li G, Chan TM, Leung KS, Lee KH.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):654-68. doi: 10.1109/TCBB.2009.25.

PMID:
21030733
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