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Items: 1 to 20 of 199

1.

Elementary network reconstruction: a framework for the analysis of regulatory networks in biological systems.

Dharmadi Y, Gonzalez R.

J Theor Biol. 2010 Apr 21;263(4):499-509. doi: 10.1016/j.jtbi.2009.12.007. Epub 2009 Dec 22.

PMID:
20004670
2.

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.

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6.

Functional states of the genome-scale Escherichia coli transcriptional regulatory system.

Gianchandani EP, Joyce AR, Palsson BØ, Papin JA.

PLoS Comput Biol. 2009 Jun;5(6):e1000403. doi: 10.1371/journal.pcbi.1000403. Epub 2009 Jun 5.

7.

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.

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.

Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks.

Egri-Nagy A, Nehaniv CL.

Artif Life. 2008 Summer;14(3):299-312. doi: 10.1162/artl.2008.14.3.14305.

PMID:
18489252
10.

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.

11.

A new model for investigating the evolution of transcription control networks.

Jenkins DJ, Stekel DJ.

Artif Life. 2009 Summer;15(3):259-91. doi: 10.1162/artl.2009.Stekel.006.

PMID:
19254178
12.

Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli.

Vázquez CD, Freyre-González JA, Gosset G, Loza JA, Gutiérrez-Ríos RM.

BMC Microbiol. 2009 Aug 24;9:176. doi: 10.1186/1471-2180-9-176.

13.

General organisational principles of the transcriptional regulation system: a tree or a circle?

Muskhelishvili G, Sobetzko P, Geertz M, Berger M.

Mol Biosyst. 2010 Apr;6(4):662-76. doi: 10.1039/b909192k. Epub 2010 Feb 8. Review.

PMID:
20237643
14.

Quantitative analysis of the dynamic signaling pathway involved in the cAMP mediated induction of l-carnitine biosynthesis in E. coli cultures.

Hormiga J, González-Alcón C, Sevilla A, Cánovas M, Torres NV.

Mol Biosyst. 2010 Apr;6(4):699-710. doi: 10.1039/b913063b. Epub 2010 Jan 27.

PMID:
20237648
15.

A copula method for modeling directional dependence of genes.

Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.

BMC Bioinformatics. 2008 May 1;9:225. doi: 10.1186/1471-2105-9-225.

16.

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS.

PLoS Comput Biol. 2005 Oct;1(5):e55. Epub 2005 Oct 28.

17.

A discrete mathematical model applied to genetic regulation and metabolic networks.

Asenjo AJ, Ramirez P, Rapaport I, Aracena J, Goles E, Andrews BA.

J Microbiol Biotechnol. 2007 Mar;17(3):496-510.

18.

List-decoding methods for inferring polynomials in finite dynamical gene network models.

Dingel J, Milenkovic O.

Bioinformatics. 2009 Jul 1;25(13):1686-93. doi: 10.1093/bioinformatics/btp281. Epub 2009 Apr 28.

PMID:
19401400
19.

Genetic regulation of fluxes: iron homeostasis of Escherichia coli.

Semsey S, Andersson AM, Krishna S, Jensen MH, Massé E, Sneppen K.

Nucleic Acids Res. 2006;34(17):4960-7. Epub 2006 Sep 18.

20.

Energetic methods to study bifunctional biotin operon repressor.

Beckett D.

Methods Enzymol. 1998;295:424-50.

PMID:
9750231

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