How does DNA sequence motif discovery work? [Nat Biotechnol. 2006] - PubMed

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A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. [Bioinformatics. 2008]
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.
Discovery of regulatory elements in vertebrates through comparative genomics. [Nat Biotechnol. 2005]
Discovery of regulatory elements in vertebrates through comparative genomics.
Prakash A, Tompa M. Nat Biotechnol. 2005 Oct; 23(10):1249-56.
A novel ensemble learning method for de novo computational identification of DNA binding sites. [BMC Bioinformatics. 2007]
A novel ensemble learning method for de novo computational identification of DNA binding sites.
Chakravarty A, Carlson JM, Khetani RS, Gross RH. BMC Bioinformatics. 2007 Jul 12; 8:249. Epub 2007 Jul 12.
Review Homology assessment and molecular sequence alignment. [J Biomed Inform. 2006]
Review Homology assessment and molecular sequence alignment.
Phillips AJ. J Biomed Inform. 2006 Feb; 39(1):18-33. Epub 2005 Dec 9.
Review The many faces of sequence alignment. [Brief Bioinform. 2005]
Review The many faces of sequence alignment.
Batzoglou S. Brief Bioinform. 2005 Mar; 6(1):6-22.

One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses. [Nucleic Acids Res. 2013]
One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses.
Narlikar L, Mehta N, Galande S, Arjunwadkar M. Nucleic Acids Res. 2013 Feb 1; 41(3):1416-24. Epub 2012 Dec 24.
Direct vs 2-stage approaches to structured motif finding. [Algorithms Mol Biol. 2012]
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. Epub 2012 Aug 21.
Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. [BMC Plant Biol. 2012]
Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.
Wang S, Yin Y, Ma Q, Tang X, Hao D, Xu Y. BMC Plant Biol. 2012 Aug 9; 12:138. Epub 2012 Aug 9.

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How does DNA sequence motif discovery work?
How does DNA sequence motif discovery work?
Nat Biotechnol. 2006 Aug ;24(8):959-61.

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