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Items: 1 to 20 of 205

1.

Recognition of cis-regulatory elements with vombat.

Posch S, Grau J, Gohr A, Ben-Gal I, Kel AE, Grosse I.

J Bioinform Comput Biol. 2007 Apr;5(2B):561-77.

PMID:
17636862
2.

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees.

Grau J, Ben-Gal I, Posch S, Grosse I.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W529-33.

3.
4.

Searching for statistically significant regulatory modules.

Bailey TL, Noble WS.

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

PMID:
14534166
5.

In silico modelling of hormone response elements.

Stepanova M, Lin F, Lin VC.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S27.

7.

Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.

Dalevi D, Dubhashi D, Hermansson M.

Bioinformatics. 2006 Mar 1;22(5):517-22. Epub 2006 Jan 10.

PMID:
16403797
8.

Transcription binding site prediction using Markov models.

Abnizova I, Rust AG, Robinson M, Te Boekhorst R, Gilks WR.

J Bioinform Comput Biol. 2006 Apr;4(2):425-41.

PMID:
16819793
9.

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.

Wong WS, Nielsen R.

Bioinformatics. 2007 Aug 15;23(16):2031-7. Epub 2007 Jun 5.

PMID:
17550911
10.

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
11.

A hidden Markov model approach for determining expression from genomic tiling micro arrays.

Munch K, Gardner PP, Arctander P, Krogh A.

BMC Bioinformatics. 2006 May 3;7:239.

12.
13.

Computational detection of cis -regulatory modules.

Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B.

Bioinformatics. 2003 Oct;19 Suppl 2:ii5-14.

PMID:
14534164
14.

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
15.

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.

16.

Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures.

Chowdhary R, Tan SL, Ali RA, Boerlage B, Wong L, Bajic VB.

Bioinformatics. 2006 Sep 15;22(18):2310-2. Epub 2006 Apr 13.

PMID:
16613910
17.

Computational approaches to finding and analyzing cis-regulatory elements.

Brown CT.

Methods Cell Biol. 2008;87:337-65. doi: 10.1016/S0091-679X(08)00218-5. Review.

PMID:
18485306
18.

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.

19.

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.

PMID:
17068091
20.

Markov encoding for detecting signals in genomic sequences.

Rajapakse JC, Ho LS.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Apr-Jun;2(2):131-42.

PMID:
17044178

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