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Items: 1 to 20 of 87

1.

A cost-aggregating integer linear program for motif finding.

Kingsford C, Zaslavsky E, Singh M.

J Discrete Algorithms (Amst). 2011 Dec 1;9(4):326-334.

2.

A combinatorial optimization approach for diverse motif finding applications.

Zaslavsky E, Singh M.

Algorithms Mol Biol. 2006 Aug 17;1:13.

3.

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. Epub 2009 Feb 17.

4.

Solving and analyzing side-chain positioning problems using linear and integer programming.

Kingsford CL, Chazelle B, Singh M.

Bioinformatics. 2005 Apr 1;21(7):1028-36. Epub 2004 Nov 16.

5.
6.

Voting algorithms for the motif finding problem.

Liu X, Ma B, Wang L.

Comput Syst Bioinformatics Conf. 2008;7:37-47.

7.

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.

8.

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
10.

MotifCut: regulatory motifs finding with maximum density subgraphs.

Fratkin E, Naughton BT, Brutlag DL, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e150-7.

11.

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.

12.

qPMS7: a fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences.

Dinh H, Rajasekaran S, Davila J.

PLoS One. 2012;7(7):e41425. doi: 10.1371/journal.pone.0041425. Epub 2012 Jul 24.

13.

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
14.

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.

15.

PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem.

Dinh H, Rajasekaran S, Kundeti VK.

BMC Bioinformatics. 2011 Oct 24;12:410. doi: 10.1186/1471-2105-12-410.

16.

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. doi: 10.1186/1471-2105-10-82.

17.

Direct vs 2-stage approaches to structured motif finding.

Federico M, Leoncini M, Montangero M, Valente P.

Algorithms Mol Biol. 2012 Aug 21;7(1):20. doi: 10.1186/1748-7188-7-20.

18.

A set-covering based heuristic algorithm for the periodic vehicle routing problem.

Cacchiani V, Hemmelmayr VC, Tricoire F.

Discrete Appl Math. 2014 Jan 30;163(Pt 1):53-64.

19.

Exact algorithms for haplotype assembly from whole-genome sequence data.

Chen ZZ, Deng F, Wang L.

Bioinformatics. 2013 Aug 15;29(16):1938-45. doi: 10.1093/bioinformatics/btt349. Epub 2013 Jun 18.

20.

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.

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