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Exploiting the pathway structure of metabolism to reveal high-order epistasis.

Imielinski M, Belta C.

BMC Syst Biol. 2008 Apr 30;2:40.PMID: 18447928 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of genome-scale metabolic network models using experimentally measured flux profiles.

Herrgård MJ, Fong SS, Palsson BØ.

PLoS Comput Biol. 2006 Jul 7;2(7):e72. Epub 2006 May 10.PMID: 16839195 [PubMed - indexed for MEDLINE]Related articlesFree article

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.

Mol Syst Biol. 2007;3:121. Epub 2007 Jun 26.PMID: 17593909 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15.PMID: 19175927 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting synthetic rescues in metabolic networks.

Motter AE, Gulbahce N, Almaas E, Barabási AL.

Mol Syst Biol. 2008;4:168. Epub 2008 Feb 12.PMID: 18277384 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.

Puchałka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA.

PLoS Comput Biol. 2008 Oct;4(10):e1000210. Epub 2008 Oct 31.PMID: 18974823 [PubMed - indexed for MEDLINE]Related articlesFree article

Essential genes on metabolic maps.

Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A.

Curr Opin Biotechnol. 2006 Oct;17(5):448-56. Epub 2006 Sep 15. Review.PMID: 16978855 [PubMed - indexed for MEDLINE]Related articles

Phenotype prediction in regulated metabolic networks.

Kaleta C, Centler F, di Fenizio PS, Dittrich P.

BMC Syst Biol. 2008 Apr 25;2:37.PMID: 18439260 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

Wang Q, Chen X, Yang Y, Zhao X.

Appl Microbiol Biotechnol. 2006 Dec;73(4):887-94. Epub 2006 Aug 23.PMID: 16927085 [PubMed - indexed for MEDLINE]Related articles

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.

Lee J, Yun H, Feist AM, Palsson BØ, Lee SY.

Appl Microbiol Biotechnol. 2008 Oct;80(5):849-62. Epub 2008 Aug 29.PMID: 18758767 [PubMed - indexed for MEDLINE]Related articles

Estimating the size of the solution space of metabolic networks.

Braunstein A, Mulet R, Pagnani A.

BMC Bioinformatics. 2008 May 19;9:240.PMID: 18489757 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale analysis of Mannheimia succiniciproducens metabolism.

Kim TY, Kim HU, Park JM, Song H, Kim JS, Lee SY.

Biotechnol Bioeng. 2007 Jul 1;97(4):657-71.PMID: 17405177 [PubMed - indexed for MEDLINE]Related articles

Evolutionary programming as a platform for in silico metabolic engineering.

Patil KR, Rocha I, Förster J, Nielsen J.

BMC Bioinformatics. 2005 Dec 23;6:308.PMID: 16375763 [PubMed - indexed for MEDLINE]Related articlesFree article

Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.

Edwards JS, Palsson BO.

BMC Bioinformatics. 2000;1:1. Epub 2000 Jul 27.PMID: 11001586 [PubMed - indexed for MEDLINE]Related articlesFree article

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

Barrett CL, Herring CD, Reed JL, Palsson BO.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19103-8. Epub 2005 Dec 15.PMID: 16357206 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis on relationship between extreme pathways and correlated reaction sets.

Xi Y, Chen YP, Cao M, Wang W, Wang F.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S58.PMID: 19208161 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural robustness of metabolic networks with respect to multiple knockouts.

Behre J, Wilhelm T, von Kamp A, Ruppin E, Schuster S.

J Theor Biol. 2008 Jun 7;252(3):433-41. Epub 2007 Oct 9.PMID: 18023456 [PubMed - indexed for MEDLINE]Related articles

Metabolic network structure determines key aspects of functionality and regulation.

Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED.

Nature. 2002 Nov 14;420(6912):190-3.PMID: 12432396 [PubMed - indexed for MEDLINE]Related articles

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41.PMID: 18462493 [PubMed - indexed for MEDLINE]Related articlesFree article

Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media.

Imielinski M, Belta C, Rubin H, Halász A.

Biophys J. 2006 Apr 15;90(8):2659-72. Epub 2006 Feb 3. Erratum in: Biophys J. 2007 Jul 15;93(2):704. PMID: 16461408 [PubMed - indexed for MEDLINE]Related articlesFree article