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Dynamical pathway analysis.

Xiong H, Choe Y.

BMC Syst Biol. 2008 Jan 27;2:9.PMID: 18221557 [PubMed - indexed for MEDLINE]Related articlesFree article

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes.

Sotiropoulos V, Kaznessis YN.

BMC Syst Biol. 2007 Jan 9;1:7.PMID: 17408514 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring genetic networks and identifying compound mode of action via expression profiling.

Gardner TS, di Bernardo D, Lorenz D, Collins JJ.

Science. 2003 Jul 4;301(5629):102-5.PMID: 12843395 [PubMed - indexed for MEDLINE]Related articlesFree article

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response.

Samal A, Jain S.

BMC Syst Biol. 2008 Feb 29;2:21.PMID: 18312613 [PubMed - indexed for MEDLINE]Related articlesFree article

Threshold-dominated regulation hides genetic variation in gene expression networks.

Gjuvsland AB, Plahte E, Omholt SW.

BMC Syst Biol. 2007 Dec 6;1:57.PMID: 18062810 [PubMed - indexed for MEDLINE]Related articlesFree article

Elucidation of the relationships between LexA-regulated genes in the SOS response.

Aburatani S, Horimoto K.

Genome Inform. 2005;16(1):95-105.PMID: 16362911 [PubMed - indexed for MEDLINE]Related articles

Novel functional view of the crocidolite asbestos-treated A549 human lung epithelial transcriptome reveals an intricate network of pathways with opposing functions.

Hevel JM, Olson-Buelow LC, Ganesan B, Stevens JR, Hardman JP, Aust AE.

BMC Genomics. 2008 Aug 7;9:376.PMID: 18687144 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Guzmán-Vargas L, Santillán M.

BMC Syst Biol. 2008 Jan 31;2:13.PMID: 18237429 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18447957 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

Hegde SR, Manimaran P, Mande SC.

PLoS Comput Biol. 2008 Nov;4(11):e1000237. Epub 2008 Nov 28.PMID: 19043542 [PubMed - indexed for MEDLINE]Related articlesFree article

The TAO-Gen algorithm for identifying gene interaction networks with application to SOS repair in E. coli.

Yamanaka T, Toyoshiba H, Sone H, Parham FM, Portier CJ.

Environ Health Perspect. 2004 Nov;112(16):1614-21.PMID: 15598612 [PubMed - indexed for MEDLINE]Related articlesFree article

Genetic network identification using convex programming.

Julius A, Zavlanos M, Boyd S, Pappas GJ.

IET Syst Biol. 2009 May;3(3):155-66.PMID: 19449976 [PubMed - indexed for MEDLINE]Related articles

Structural systems identification of genetic regulatory networks.

Xiong H, Choe Y.

Bioinformatics. 2008 Feb 15;24(4):553-60. Epub 2008 Jan 5.PMID: 18175769 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics.

Ronen M, Rosenberg R, Shraiman BI, Alon U.

Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10555-60. Epub 2002 Jul 26.PMID: 12145321 [PubMed - indexed for MEDLINE]Related articlesFree article

Network legos: building blocks of cellular wiring diagrams.

Murali TM, Rivera CG.

J Comput Biol. 2008 Sep;15(7):829-44.PMID: 18707557 [PubMed - indexed for MEDLINE]Related articles

Autogenous and nonautogenous control of response in a genetic network.

Camas FM, Blázquez J, Poyatos JF.

Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12718-23. Epub 2006 Aug 14.PMID: 16908855 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstructing repressor protein levels from expression of gene targets in Escherichia coli.

Khanin R, Vinciotti V, Wit E.

Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18592-6. Epub 2006 Nov 22.PMID: 17121995 [PubMed - indexed for MEDLINE]Related articlesFree article

A data integration approach for cell cycle analysis oriented to model simulation in systems biology.

Alfieri R, Merelli I, Mosca E, Milanesi L.

BMC Syst Biol. 2007 Aug 1;1:35.PMID: 17678529 [PubMed - indexed for MEDLINE]Related articlesFree article

A method for the generation of standardized qualitative dynamical systems of regulatory networks.

Mendoza L, Xenarios I.

Theor Biol Med Model. 2006 Mar 16;3:13.PMID: 16542429 [PubMed - indexed for MEDLINE]Related articlesFree article