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Results: 1 to 20 of 110

1.

Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.

Rouault H, Santolini M, Schweisguth F, Hakim V.

Nucleic Acids Res. 2014 Jun;42(10):6128-45. doi: 10.1093/nar/gku209. Epub 2014 Mar 25.

PMID:
24682824
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
20671200
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23272209
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
18606616
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.

Xie D, Cai J, Chia NY, Ng HH, Zhong S.

Genome Res. 2008 Aug;18(8):1325-35. doi: 10.1101/gr.072769.107. Epub 2008 May 15.

PMID:
18490265
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22313678
[PubMed - indexed for MEDLINE]
Free PMC Article
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(1):1047. doi: 10.1186/1471-2164-15-1047.

PMID:
25442502
[PubMed - in process]
Free PMC Article
8.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

PMID:
18950538
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19853570
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
19208131
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

INSECT: IN-silico SEarch for Co-occurring Transcription factors.

Rohr CO, Parra RG, Yankilevich P, Perez-Castro C.

Bioinformatics. 2013 Nov 15;29(22):2852-8. doi: 10.1093/bioinformatics/btt506. Epub 2013 Sep 4.

PMID:
24008418
[PubMed - indexed for MEDLINE]
Free Article
12.

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Klepper K, Drabløs F.

BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9.

PMID:
23323883
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

Yu X, Lin J, Zack DJ, Qian J.

BMC Bioinformatics. 2007 Nov 9;8:437.

PMID:
17996093
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21821659
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22422836
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

Grad YH, Roth FP, Halfon MS, Church GM.

Bioinformatics. 2004 Nov 1;20(16):2738-50. Epub 2004 May 14.

PMID:
15145800
[PubMed - indexed for MEDLINE]
Free Article
17.

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.

Sun H, Guns T, Fierro AC, Thorrez L, Nijssen S, Marchal K.

Nucleic Acids Res. 2012 Jul;40(12):e90. doi: 10.1093/nar/gks237. Epub 2012 Mar 15.

PMID:
22422841
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
17032682
[PubMed - indexed for MEDLINE]
Free Article
19.

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs.

Starr MO, Ho MC, Gunther EJ, Tu YK, Shur AS, Goetz SE, Borok MJ, Kang V, Drewell RA.

Dev Biol. 2011 Nov 15;359(2):290-302. doi: 10.1016/j.ydbio.2011.07.028. Epub 2011 Jul 28.

PMID:
21821017
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

Makeev VJ, Lifanov AP, Nazina AG, Papatsenko DA.

Nucleic Acids Res. 2003 Oct 15;31(20):6016-26.

PMID:
14530449
[PubMed - indexed for MEDLINE]
Free PMC Article

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