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Items: 1 to 20 of 509


A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.


PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

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


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.


Localized motif discovery in gene regulatory sequences.

Narang V, Mittal A, Sung WK.

Bioinformatics. 2010 May 1;26(9):1152-9. doi: 10.1093/bioinformatics/btq106.


CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.

Ding Y, Lorenz WA, Chuang JH.

BMC Bioinformatics. 2012 Feb 14;13:32. doi: 10.1186/1471-2105-13-32.


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.


A fast weak motif-finding algorithm based on community detection in graphs.

Jia C, Carson MB, Yu J.

BMC Bioinformatics. 2013 Jul 17;14:227. doi: 10.1186/1471-2105-14-227.


MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Klepper K, Drabløs F.

BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9.


Finding motifs in the twilight zone.

Keich U, Pevzner PA.

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


A hybrid method for the exact planted (l, d) motif finding problem and its parallelization.

Abbas MM, Abouelhoda M, Bahig HM.

BMC Bioinformatics. 2012;13 Suppl 17:S10. doi: 10.1186/1471-2105-13-S17-S10.


Efficient motif search in ranked lists and applications to variable gap motifs.

Leibovich L, Yakhini Z.

Nucleic Acids Res. 2012 Jul;40(13):5832-47. doi: 10.1093/nar/gks206.


Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811.


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.


Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites.

Jajamovich GH, Wang X, Arkin AP, Samoilov MS.

Nucleic Acids Res. 2011 Nov;39(21):e146. doi: 10.1093/nar/gkr745.


Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.

Liseron-Monfils C, Lewis T, Ashlock D, McNicholas PD, Fauteux F, Strömvik M, Raizada MN.

BMC Plant Biol. 2013 Mar 15;13:42. doi: 10.1186/1471-2229-13-42.


SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.

Ding J, Hu H, Li X.

Nucleic Acids Res. 2014 Mar;42(5):e35. doi: 10.1093/nar/gkt1288.


A survey of DNA motif finding algorithms.

Das MK, Dai HK.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S21. Review.

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