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Items: 1 to 20 of 206

1.

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

Ng P, Nagarajan N, Jones N, Keich U.

Bioinformatics. 2006 Jul 15;22(14):e393-401.

PMID:
16873498
2.

SPACER: identification of cis-regulatory elements with non-contiguous critical residues.

Chakravarty A, Carlson JM, Khetani RS, DeZiel CE, Gross RH.

Bioinformatics. 2007 Apr 15;23(8):1029-31.

PMID:
17470480
3.

Finding motifs in the twilight zone.

Keich U, Pevzner PA.

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

PMID:
12376382
4.

MotifCut: regulatory motifs finding with maximum density subgraphs.

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

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

PMID:
16873465
5.

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
6.

Searching for statistically significant regulatory modules.

Bailey TL, Noble WS.

Bioinformatics. 2003 Oct;19 Suppl 2:ii16-25.

PMID:
14534166
7.
8.

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.

9.
10.

A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.

Liang KC, Wang X, Anastassiou D.

Bioinformatics. 2008 Jan 1;24(1):46-55. Epub 2007 Nov 17.

PMID:
18024972
11.

Computing the P-value of the information content from an alignment of multiple sequences.

Nagarajan N, Jones N, Keich U.

Bioinformatics. 2005 Jun;21 Suppl 1:i311-8. Erratum in: Bioinformatics. 2005 Sep 15;21(18):3700.

PMID:
15961473
12.

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.

Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ.

Bioinformatics. 2005 May 15;21(10):2240-5. Epub 2005 Feb 22.

PMID:
15728117
13.

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors.

Papatsenko D.

Bioinformatics. 2007 Apr 15;23(8):1032-4. Epub 2007 Feb 18.

PMID:
17308342
14.

Subtle motifs: defining the limits of motif finding algorithms.

Keich U, Pevzner PA.

Bioinformatics. 2002 Oct;18(10):1382-90.

PMID:
12376383
15.

Finding composite regulatory patterns in DNA sequences.

Eskin E, Pevzner PA.

Bioinformatics. 2002;18 Suppl 1:S354-63.

PMID:
12169566
16.

Randomized algorithms for motif detection.

Wang L, Dong L.

J Bioinform Comput Biol. 2005 Oct;3(5):1039-52.

PMID:
16278946
17.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

18.

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.

19.

BioOptimizer: a Bayesian scoring function approach to motif discovery.

Jensen ST, Liu JS.

Bioinformatics. 2004 Jul 10;20(10):1557-64. Epub 2004 Feb 12.

PMID:
14962923
20.

Tandem repeats over the edit distance.

Sokol D, Benson G, Tojeira J.

Bioinformatics. 2007 Jan 15;23(2):e30-5.

PMID:
17237101

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