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Items: 1 to 20 of 102


Assessing computational methods of cis-regulatory module prediction.

Su J, Teichmann SA, Down TA.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001020. doi: 10.1371/journal.pcbi.1001020.


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.


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.


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.


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.


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.


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.


CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.

Navarro C, Lopez FJ, Cano C, Garcia-Alcalde F, Blanco A.

PLoS One. 2014 Sep 30;9(9):e108065. doi: 10.1371/journal.pone.0108065. eCollection 2014.


Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.

Rouault H, Mazouni K, Couturier L, Hakim V, Schweisguth F.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14615-20. doi: 10.1073/pnas.1002876107. Epub 2010 Jul 29.


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.


Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.

Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F.

Genome Res. 2006 May;16(5):656-68. Epub 2006 Apr 10.


DISCOVER: a feature-based discriminative method for motif search in complex genomes.

Fu W, Ray P, Xing EP.

Bioinformatics. 2009 Jun 15;25(12):i321-9. doi: 10.1093/bioinformatics/btp230.


Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.

Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S.

Dev Cell. 2009 Oct;17(4):568-79. doi: 10.1016/j.devcel.2009.09.002.


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.


COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.

Ha N, Polychronidou M, Lohmann I.

PLoS One. 2012;7(12):e52055. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.


REDfly: a Regulatory Element Database for Drosophila.

Gallo SM, Li L, Hu Z, Halfon MS.

Bioinformatics. 2006 Feb 1;22(3):381-3. Epub 2005 Nov 22.


REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.

Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS.

Nucleic Acids Res. 2011 Jan;39(Database issue):D118-23. doi: 10.1093/nar/gkq999. Epub 2010 Oct 21.


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.


A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

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