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Results: 1 to 20 of 101

1.

The evolution of complex gene regulation by low-specificity binding sites.

Stewart AJ, Plotkin JB.

Proc Biol Sci. 2013 Aug 14;280(1768):20131313. doi: 10.1098/rspb.2013.1313. Print 2013 Oct 7.

PMID:
23945682
[PubMed - indexed for MEDLINE]
2.

The population genetics of cooperative gene regulation.

Stewart AJ, Seymour RM, Pomiankowski A, Plotkin JB.

BMC Evol Biol. 2012 Sep 6;12:173. doi: 10.1186/1471-2148-12-173.

PMID:
22954408
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

PMID:
19426448
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

BRNI: Modular analysis of transcriptional regulatory programs.

Nachman I, Regev A.

BMC Bioinformatics. 2009 May 20;10:155. doi: 10.1186/1471-2105-10-155.

PMID:
19457258
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.

Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S.

PLoS Biol. 2010 Aug 17;8(8). pii: e1000456. doi: 10.1371/journal.pbio.1000456. Erratum in: PLoS Biol. 2013 Oct;11(10). doi: 10.1371/annotation/e38f4ae8-0776-42e6-b912-50800f54436e.

PMID:
20808951
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A discriminative model for identifying spatial cis-regulatory modules.

Segal E, Sharan R.

J Comput Biol. 2005 Jul-Aug;12(6):822-34.

PMID:
16108719
[PubMed - indexed for MEDLINE]
7.

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
8.

Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: modeling and experiments reveal hierarchy in glucose repression.

Prasad V, Venkatesh KV.

BMC Syst Biol. 2008 Nov 17;2:97. doi: 10.1186/1752-0509-2-97.

PMID:
19014615
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells.

Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J.

BMC Genomics. 2012 Aug 31;13:437. doi: 10.1186/1471-2164-13-437.

PMID:
22938179
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Functional characterization of motif sequences under purifying selection.

Chen DH, Chang AY, Liao BY, Yeang CH.

Nucleic Acids Res. 2013 Feb 1;41(4):2105-20. doi: 10.1093/nar/gks1456. Epub 2013 Jan 8.

PMID:
23303791
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

PMID:
15166027
[PubMed - indexed for MEDLINE]
Free Article
12.

Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.

Gonçalves JP, Aires RS, Francisco AP, Madeira SC.

PLoS One. 2012;7(5):e35977. doi: 10.1371/journal.pone.0035977. Epub 2012 May 1.

PMID:
22563474
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Modular cis-regulatory organization of Endo16, a gut-specific gene of the sea urchin embryo.

Yuh CH, Davidson EH.

Development. 1996 Apr;122(4):1069-82.

PMID:
8620834
[PubMed - indexed for MEDLINE]
Free Article
14.

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.

PMID:
24042128
[PubMed - indexed for MEDLINE]
15.

Under-dominance constrains the evolution of negative autoregulation in diploids.

Stewart AJ, Seymour RM, Pomiankowski A, Reuter M.

PLoS Comput Biol. 2013;9(3):e1002992. doi: 10.1371/journal.pcbi.1002992. Epub 2013 Mar 21.

PMID:
23555226
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Evolution of transcriptional regulation in closely related bacteria.

Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS.

BMC Evol Biol. 2012 Oct 6;12:200. doi: 10.1186/1471-2148-12-200.

PMID:
23039862
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The smooth muscle myosin heavy chain gene exhibits smooth muscle subtype-selective modular regulation in vivo.

Manabe I, Owens GK.

J Biol Chem. 2001 Oct 19;276(42):39076-87. Epub 2001 Aug 6.

PMID:
11489897
[PubMed - indexed for MEDLINE]
Free Article
18.

Motif-guided sparse decomposition of gene expression data for regulatory module identification.

Gong T, Xuan J, Chen L, Riggins RB, Li H, Hoffman EP, Clarke R, Wang Y.

BMC Bioinformatics. 2011 Mar 22;12:82. doi: 10.1186/1471-2105-12-82.

PMID:
21426557
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns.

Martyanov V, Gross RH.

PLoS One. 2013;8(3):e59851. doi: 10.1371/journal.pone.0059851. Epub 2013 Mar 29.

PMID:
23555806
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules.

Halfon MS, Zhu Q, Brennan ER, Zhou Y.

BMC Genomics. 2011 Nov 25;12:578. doi: 10.1186/1471-2164-12-578.

PMID:
22115527
[PubMed - indexed for MEDLINE]
Free PMC Article

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