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Results: 1 to 20 of 445

1.

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
[PubMed - indexed for MEDLINE]
Free Article
2.

Searching for statistically significant regulatory modules.

Bailey TL, Noble WS.

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

PMID:
14534166
[PubMed - indexed for MEDLINE]
Free Article
3.

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.

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

Nucleic Acids Res. 2006;34(20):5730-9. Epub 2006 Oct 13.

PMID:
17041233
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.

PMID:
16870937
[PubMed - indexed for MEDLINE]
Free Article
5.

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]
6.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

PMID:
16716228
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects.

Noto K, Craven M.

Bioinformatics. 2007 Jan 15;23(2):e156-62.

PMID:
17237085
[PubMed - indexed for MEDLINE]
Free Article
8.

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

Sinha S.

Bioinformatics. 2006 Jul 15;22(14):e454-63.

PMID:
16873507
[PubMed - indexed for MEDLINE]
Free Article
9.

Predicting genetic regulatory response using classification.

Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.

PMID:
15262804
[PubMed - indexed for MEDLINE]
Free Article
10.

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
[PubMed - indexed for MEDLINE]
Free Article
11.

Informative priors based on transcription factor structural class improve de novo motif discovery.

Narlikar L, Gordân R, Ohler U, Hartemink AJ.

Bioinformatics. 2006 Jul 15;22(14):e384-92.

PMID:
16873497
[PubMed - indexed for MEDLINE]
Free Article
12.

Bounded search for de novo identification of degenerate cis-regulatory elements.

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

BMC Bioinformatics. 2006 May 15;7:254.

PMID:
16700920
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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. Epub 2009 Mar 13.

PMID:
19293946
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Assessment of composite motif discovery methods.

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F.

BMC Bioinformatics. 2008 Feb 26;9:123. doi: 10.1186/1471-2105-9-123.

PMID:
18302777
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
Free Article
16.

Finding optimal degenerate patterns in DNA sequences.

Shinozaki D, Akutsu T, Maruyama O.

Bioinformatics. 2003 Oct;19 Suppl 2:ii206-14.

PMID:
14534191
[PubMed - indexed for MEDLINE]
Free Article
17.

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

Chen X, Hughes TR, Morris Q.

Bioinformatics. 2007 Jul 1;23(13):i72-9.

PMID:
17646348
[PubMed - indexed for MEDLINE]
Free Article
18.

Statistical modeling of transcription factor binding affinities predicts regulatory interactions.

Manke T, Roider HG, Vingron M.

PLoS Comput Biol. 2008 Mar 21;4(3):e1000039. doi: 10.1371/journal.pcbi.1000039.

PMID:
18369429
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A graph-based approach to systematically reconstruct human transcriptional regulatory modules.

Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XJ.

Bioinformatics. 2007 Jul 1;23(13):i577-86.

PMID:
17646346
[PubMed - indexed for MEDLINE]
Free Article
20.

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
[PubMed - indexed for MEDLINE]
Free Article

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