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Items: 1 to 20 of 89


Using hexamers to predict cis-regulatory motifs in Drosophila.

Chan BY, Kibler D.

BMC Bioinformatics. 2005 Oct 27;6:262.


Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Pierstorff N, Bergman CM, Wiehe T.

Bioinformatics. 2006 Dec 1;22(23):2858-64. Epub 2006 Oct 10.


MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.

Hu J, Hu H, Li X.

Nucleic Acids Res. 2008 Aug;36(13):4488-97. doi: 10.1093/nar/gkn407. Epub 2008 Jul 7.


De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.


Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

Kazemian M, Zhu Q, Halfon MS, Sinha S.

Nucleic Acids Res. 2011 Dec;39(22):9463-72. doi: 10.1093/nar/gkr621. Epub 2011 Aug 5.


CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

Nikulova AA, Favorov AV, Sutormin RA, Makeev VJ, Mironov AA.

Nucleic Acids Res. 2012 Jul;40(12):e93. doi: 10.1093/nar/gks235. Epub 2012 Mar 15.


Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.

Girgis HZ, Ovcharenko I.

BMC Bioinformatics. 2012 Feb 7;13:25. doi: 10.1186/1471-2105-13-25.


Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila.

Ho MC, Johnsen H, Goetz SE, Schiller BJ, Bae E, Tran DA, Shur AS, Allen JM, Rau C, Bender W, Fisher WW, Celniker SE, Drewell RA.

PLoS Genet. 2009 Nov;5(11):e1000709. doi: 10.1371/journal.pgen.1000709. Epub 2009 Nov 6.


Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

Rajewsky N, Vergassola M, Gaul U, Siggia ED.

BMC Bioinformatics. 2002 Oct 24;3:30. Epub 2002 Oct 24.


A statistical thin-tail test of predicting regulatory regions in the Drosophila genome.

Shu JJ, Li Y.

Theor Biol Med Model. 2013 Feb 14;10:11. doi: 10.1186/1742-4682-10-11.


Computational methods for the detection of cis-regulatory modules.

Van Loo P, Marynen P.

Brief Bioinform. 2009 Sep;10(5):509-24. doi: 10.1093/bib/bbp025. Epub 2009 Jun 4. Review.


cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.

Yang TH, Wang CC, Hung PC, Wu WS.

BMC Syst Biol. 2014;8 Suppl 4:S8. doi: 10.1186/1752-0509-8-S4-S8. Epub 2014 Dec 8.


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.


The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.

Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4960-5. Epub 2005 Mar 25.


A statistical fat-tail test of predicting regulatory regions in the Drosophila genome.

Shu JJ, Li Y.

Comput Biol Med. 2012 Sep;42(9):935-41. doi: 10.1016/j.compbiomed.2012.07.007. Epub 2012 Aug 9.


MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

Sinha S, He X.

PLoS Comput Biol. 2007 Nov;3(11):e216. Epub 2007 Sep 24.


ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.

Sun H, De Bie T, Storms V, Fu Q, Dhollander T, Lemmens K, Verstuyf A, De Moor B, Marchal K.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S30. doi: 10.1186/1471-2105-10-S1-S30.

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