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Items: 1 to 20 of 106


Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements.

Tharakaraman K, Mariño-Ramírez L, Sheetlin SL, Landsman D, Spouge JL.

BMC Bioinformatics. 2006 Sep 8;7:408.


Alignments anchored on genomic landmarks can aid in the identification of regulatory elements.

Tharakaraman K, Mariño-Ramírez L, Sheetlin S, Landsman D, Spouge JL.

Bioinformatics. 2005 Jun;21 Suppl 1:i440-8.


Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.


Searching for statistically significant regulatory modules.

Bailey TL, Noble WS.

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


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.


An improved Gibbs sampling method for motif discovery via sequence weighting.

Chen X, Jiang T.

Comput Syst Bioinformatics Conf. 2006:239-47.


PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.


MotifCut: regulatory motifs finding with maximum density subgraphs.

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

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


Adding sequence context to a Markov background model improves the identification of regulatory elements.

Kim NK, Tharakaraman K, Spouge JL.

Bioinformatics. 2006 Dec 1;22(23):2870-5. Epub 2006 Oct 26.


Motif Yggdrasil: sampling sequence motifs from a tree mixture model.

Andersson SA, Lagergren J.

J Comput Biol. 2007 Jun;14(5):682-97.


The Gibbs Centroid Sampler.

Thompson WA, Newberg LA, Conlan S, McCue LA, Lawrence CE.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W232-7. Epub 2007 May 5.


Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.

Narasimhan C, LoCascio P, Uberbacher E.

Bioinformatics. 2003 Oct 12;19(15):1952-63.


DNA motif alignment by evolving a population of Markov chains.

Bi C.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S13. doi: 10.1186/1471-2105-10-S1-S13.


Gibbs Recursive Sampler: finding transcription factor binding sites.

Thompson W, Rouchka EC, Lawrence CE.

Nucleic Acids Res. 2003 Jul 1;31(13):3580-5.


Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

Majoros WH, Ohler U.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001037. doi: 10.1371/journal.pcbi.1001037.


Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites.

Kim NK, Tharakaraman K, Mariño-Ramírez L, Spouge JL.

BMC Bioinformatics. 2008 Jun 4;9:262. doi: 10.1186/1471-2105-9-262.


Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D.

Methods Mol Biol. 2009;541:1-22. doi: 10.1007/978-1-59745-243-4_1. Review.


Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.


rMotifGen: random motif generator for DNA and protein sequences.

Rouchka EC, Hardin CT.

BMC Bioinformatics. 2007 Aug 7;8:292.

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