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Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.

Dobrin R, Beg QK, Barabási AL, Oltvai ZN.

BMC Bioinformatics. 2004 Jan 30;5:10.PMID: 15018656 [PubMed - indexed for MEDLINE]Related articlesFree article

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach.

Ma HW, Buer J, Zeng AP.

BMC Bioinformatics. 2004 Dec 16;5:199.PMID: 15603590 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli.

Warren PB, ten Wolde PR.

J Mol Biol. 2004 Oct 1;342(5):1379-90.PMID: 15364567 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 19426448 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 15604458 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18565227 [PubMed - indexed for MEDLINE]Related articlesFree article

Bridge and brick network motifs: identifying significant building blocks from complex biological systems.

Huang CY, Cheng CY, Sun CT.

Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.PMID: 17825540 [PubMed - indexed for MEDLINE]Related articles

Ranking of network elements based on functional substructures.

Koschützki D, Schwöbbermeyer H, Schreiber F.

J Theor Biol. 2007 Oct 7;248(3):471-9. Epub 2007 Jun 6.PMID: 17644116 [PubMed - indexed for MEDLINE]Related articles

The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.

Brune I, Werner H, Hüser AT, Kalinowski J, Pühler A, Tauch A.

BMC Genomics. 2006 Feb 9;7:21.PMID: 16469103 [PubMed - indexed for MEDLINE]Related articlesFree article

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks.

Goemann B, Wingender E, Potapov AP.

BMC Syst Biol. 2009 May 19;3:53.PMID: 19454001 [PubMed - indexed for MEDLINE]Related articlesFree article

Homotypic regulatory clusters in Drosophila.

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

Genome Res. 2003 Apr;13(4):579-88.PMID: 12670999 [PubMed - indexed for MEDLINE]Related articlesFree article

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 [PubMed - indexed for MEDLINE]Related articles

Evolutionary dynamics of prokaryotic transcriptional regulatory networks.

Madan Babu M, Teichmann SA, Aravind L.

J Mol Biol. 2006 Apr 28;358(2):614-33. Epub 2006 Feb 28.PMID: 16530225 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

The topological relationship between the large-scale attributes and local interaction patterns of complex networks.

Vázquez A, Dobrin R, Sergi D, Eckmann JP, Oltvai ZN, Barabási AL.

Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):17940-5. Epub 2004 Dec 14.PMID: 15598746 [PubMed - indexed for MEDLINE]Related articlesFree article

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs.

Apte AA, Cain JW, Bonchev DG, Fong SS.

J Biol Eng. 2008 Feb 27;2:2.PMID: 18304325 [PubMed - in process]Related articlesFree article

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

Caselle M, Di Cunto F, Provero P.

BMC Bioinformatics. 2002;3:7. Epub 2002 Feb 14.PMID: 11876822 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.

Ward JJ, Thornton JM.

PLoS Comput Biol. 2007 Oct;3(10):1993-2002. Epub 2007 Aug 27.PMID: 17967049 [PubMed - indexed for MEDLINE]Related articlesFree article

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

Balázsi G, Barabási AL, Oltvai ZN.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7841-6. Epub 2005 May 20.PMID: 15908506 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17559662 [PubMed - indexed for MEDLINE]Related articlesFree article