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Items: 1 to 20 of 106

1.

What determines the assembly of transcriptional network motifs in Escherichia coli?

Camas FM, Poyatos JF.

PLoS One. 2008;3(11):e3657. doi: 10.1371/journal.pone.0003657. Epub 2008 Nov 6.

3.

Network motifs in the transcriptional regulation network of Escherichia coli.

Shen-Orr SS, Milo R, Mangan S, Alon U.

Nat Genet. 2002 May;31(1):64-8. Epub 2002 Apr 22.

PMID:
11967538
4.

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

BMC Syst Biol. 2009 Apr 14;3:39. doi: 10.1186/1752-0509-3-39.

5.

Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli.

Janga SC, Salgado H, Martínez-Antonio A, Collado-Vides J.

Nucleic Acids Res. 2007;35(20):6963-72. Epub 2007 Oct 12.

6.

Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli.

Gutierrez-Ríos RM, Freyre-Gonzalez JA, Resendis O, Collado-Vides J, Saier M, Gosset G.

BMC Microbiol. 2007 Jun 8;7:53.

7.

Structure and function of the feed-forward loop network motif.

Mangan S, Alon U.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):11980-5. Epub 2003 Oct 6.

8.

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.

Cho BK, Barrett CL, Knight EM, Park YS, Palsson BØ.

Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19462-7. doi: 10.1073/pnas.0807227105. Epub 2008 Dec 3.

9.

Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli.

Janga SC, Salgado H, Collado-Vides J, Martínez-Antonio A.

J Mol Biol. 2007 Apr 20;368(1):263-72. Epub 2007 Jan 12.

PMID:
17321548
10.

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps.

Veiga DF, Vicente FF, Nicolás MF, Vasconcelos AT.

BMC Microbiol. 2008 Jun 19;8:101. doi: 10.1186/1471-2180-8-101.

11.

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

Marr C, Theis FJ, Liebovitch LS, Hütt MT.

PLoS Comput Biol. 2010 Jul 1;6:e1000836. doi: 10.1371/journal.pcbi.1000836.

13.

Noise characteristics of feed forward loops.

Ghosh B, Karmakar R, Bose I.

Phys Biol. 2005 Mar;2(1):36-45.

PMID:
16204855
14.

Structure-function relations are subtle in genetic regulatory networks.

Wall ME.

Math Biosci. 2011 May;231(1):61-8. doi: 10.1016/j.mbs.2011.02.003. Epub 2011 Feb 15. Review.

PMID:
21329703
15.

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs.

Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP.

Nucleic Acids Res. 2004 Dec 16;32(22):6643-9. Print 2004.

16.

Modular analysis of the transcriptional regulatory network of E. coli.

Resendis-Antonio O, Freyre-González JA, Menchaca-Méndez R, Gutiérrez-Ríos RM, Martínez-Antonio A, Avila-Sánchez C, Collado-Vides J.

Trends Genet. 2005 Jan;21(1):16-20.

PMID:
15680508
17.

Evolutionary modelling of feed forward loops in gene regulatory networks.

Cooper MB, Loose M, Brookfield JF.

Biosystems. 2008 Jan;91(1):231-44. Epub 2007 Oct 5.

PMID:
18082936
18.

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors.

Österlund T, Bordel S, Nielsen J.

Integr Biol (Camb). 2015 May;7(5):560-8. doi: 10.1039/c4ib00247d. Epub 2015 Apr 9.

PMID:
25855217
19.

Functional organisation of Escherichia coli transcriptional regulatory network.

Martínez-Antonio A, Janga SC, Thieffry D.

J Mol Biol. 2008 Aug 1;381(1):238-47. doi: 10.1016/j.jmb.2008.05.054. Epub 2008 May 29.

20.

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.

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