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Efficient and accurate P-value computation for Position Weight Matrices.

Touzet H, Varré JS.

Algorithms Mol Biol. 2007 Dec 11;2:15.PMID: 18072973 [PubMed]Related articlesFree article

Computing exact P-values for DNA motifs.

Zhang J, Jiang B, Li M, Tromp J, Zhang X, Zhang MQ.

Bioinformatics. 2007 Mar 1;23(5):531-7. Epub 2007 Jan 18.PMID: 17237046 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast index based algorithms and software for matching position specific scoring matrices.

Beckstette M, Homann R, Giegerich R, Kurtz S.

BMC Bioinformatics. 2006 Aug 24;7:389.PMID: 16930469 [PubMed - indexed for MEDLINE]Related articlesFree article

Faster exact Markovian probability functions for motif occurrences: a DFA-only approach.

Ribeca P, Raineri E.

Bioinformatics. 2008 Dec 15;24(24):2839-48. Epub 2008 Oct 9.PMID: 18845582 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast probabilistic analysis of sequence function using scoring matrices.

Wu TD, Nevill-Manning CG, Brutlag DL.

Bioinformatics. 2000 Mar;16(3):233-44.PMID: 10869016 [PubMed - indexed for MEDLINE]Related articlesFree article

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.

Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ.

Algorithms Mol Biol. 2007 Oct 10;2:13.PMID: 17927813 [PubMed]Related articlesFree article

fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control.

Li L, Bass RL, Liang Y.

Bioinformatics. 2008 Mar 1;24(5):629-36. Epub 2008 Feb 22.PMID: 18296465 [PubMed - indexed for MEDLINE]Related articlesFree article

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.

Chen X, Guo L, Fan Z, Jiang T.

Bioinformatics. 2008 May 1;24(9):1121-8. Epub 2008 Mar 5.PMID: 18325926 [PubMed - indexed for MEDLINE]Related articlesFree article

An efficient method for statistical significance calculation of transcription factor binding sites.

Qian Z, Lu L, Qi L, Li Y.

Bioinformation. 2007 Dec 30;2(5):169-74.PMID: 18305824 [PubMed - in process]Related articlesFree article

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series.

Madeira SC, Oliveira AL.

Algorithms Mol Biol. 2009 Jun 4;4:8.PMID: 19497096 [PubMed]Related articlesFree article

Efficient representation and P-value computation for high-order Markov motifs.

da Fonseca PG, Guimarães KS, Sagot MF.

Bioinformatics. 2008 Aug 15;24(16):i160-6.PMID: 18689819 [PubMed - indexed for MEDLINE]Related articlesFree article

Matching isotopic distributions from metabolically labeled samples.

McIlwain S, Page D, Huttlin EL, Sussman MR.

Bioinformatics. 2008 Jul 1;24(13):i339-47.PMID: 18586733 [PubMed - indexed for MEDLINE]Related articlesFree article

An efficient voting algorithm for finding additive biclusters with random background.

Xiao J, Wang L, Liu X, Jiang T.

J Comput Biol. 2008 Dec;15(10):1275-93.PMID: 19040364 [PubMed - indexed for MEDLINE]Related articles

Voting algorithms for the motif finding problem.

Liu X, Ma B, Wang L.

Comput Syst Bioinformatics Conf. 2008;7:37-47.PMID: 19642267 [PubMed - indexed for MEDLINE]Related articles

Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'.

Dai Q, Wang T.

BMC Bioinformatics. 2008 Sep 23;9:394.PMID: 18811946 [PubMed - indexed for MEDLINE]Related articlesFree article

A combinatorial optimization approach for diverse motif finding applications.

Zaslavsky E, Singh M.

Algorithms Mol Biol. 2006 Aug 17;1:13.PMID: 16916460 [PubMed]Related articlesFree article

Species tree inference by minimizing deep coalescences.

Than C, Nakhleh L.

PLoS Comput Biol. 2009 Sep;5(9):e1000501. Epub 2009 Sep 11.PMID: 19749978 [PubMed - indexed for MEDLINE]Related articlesFree article

Visual MRI: merging information visualization and non-parametric clustering techniques for MRI dataset analysis.

Castellani U, Cristani M, Combi C, Murino V, Sbarbati A, Marzola P.

Artif Intell Med. 2008 Nov;44(3):183-99. Epub 2008 Sep 4.PMID: 18775655 [PubMed - indexed for MEDLINE]Related articles

An efficient algorithm for finding short approximate non-tandem repeats.

Adebiyi EF, Jiang T, Kaufmann M.

Bioinformatics. 2001;17 Suppl 1:S5-S12.PMID: 11472987 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

Bastien O, Maréchal E.

BMC Bioinformatics. 2008 Aug 7;9:332.PMID: 18687111 [PubMed - indexed for MEDLINE]Related articlesFree article