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Predicting biological system objectives de novo from internal state measurements.

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA.

BMC Bioinformatics. 2008 Jan 24;9:43.PMID: 18218092 [PubMed - indexed for MEDLINE]Related articlesFree article

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks.

Hoppe A, Hoffmann S, Holzhütter HG.

BMC Syst Biol. 2007 Jun 1;1:23.PMID: 17543097 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Is maximization of molar yield in metabolic networks favoured by evolution?

Schuster S, Pfeiffer T, Fell DA.

J Theor Biol. 2008 Jun 7;252(3):497-504. Epub 2007 Dec 23.PMID: 18249414 [PubMed - indexed for MEDLINE]Related articles

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006.PMID: 19194908 [PubMed - indexed for MEDLINE]Related articles

Flux balance analysis: interrogating genome-scale metabolic networks.

Oberhardt MA, Chavali AK, Papin JA.

Methods Mol Biol. 2009;500:61-80.PMID: 19399432 [PubMed - indexed for MEDLINE]Related articles

Flux balance analysis of biological systems: applications and challenges.

Raman K, Chandra N.

Brief Bioinform. 2009 Jul;10(4):435-49. Epub 2009 Mar 15.PMID: 19287049 [PubMed - indexed for MEDLINE]Related articles

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

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

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

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. Review.PMID: 19381531 [PubMed - indexed for MEDLINE]Related articles

Multiobjective flux balancing using the NISE method for metabolic network analysis.

Oh YG, Lee DY, Lee SY, Park S.

Biotechnol Prog. 2009 Jul-Aug;25(4):999-1008.PMID: 19572405 [PubMed - in process]Related articles

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae.

Alves R, Sorribas A.

BMC Syst Biol. 2007 Jan 31;1:10.PMID: 17408500 [PubMed - indexed for MEDLINE]Related articlesFree article

From bit to it: how a complex metabolic network transforms information into living matter.

Wagner A.

BMC Syst Biol. 2007 Jul 30;1:33.PMID: 17663759 [PubMed - indexed for MEDLINE]Related articlesFree article

Combining flux and energy balance analysis to model large-scale biochemical networks.

Heuett WJ, Qian H.

J Bioinform Comput Biol. 2006 Dec;4(6):1227-43.PMID: 17245812 [PubMed - indexed for MEDLINE]Related articles

Connecting extracellular metabolomic measurements to intracellular flux states in yeast.

Mo ML, Palsson BO, Herrgård MJ.

BMC Syst Biol. 2009 Mar 25;3:37.PMID: 19321003 [PubMed - indexed for MEDLINE]Related articlesFree article

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.

Schilling CH, Edwards JS, Letscher D, Palsson BØ.

Biotechnol Bioeng. 2000-2001;71(4):286-306.PMID: 11291038 [PubMed - indexed for MEDLINE]Related articles

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.

Schuetz R, Kuepfer L, Sauer U.

Mol Syst Biol. 2007;3:119. Epub 2007 Jul 10.PMID: 17625511 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks.

Nookaew I, Meechai A, Thammarongtham C, Laoteng K, Ruanglek V, Cheevadhanarak S, Nielsen J, Bhumiratana S.

Biotechnol Bioeng. 2007 Aug 15;97(6):1535-49.PMID: 17238207 [PubMed - indexed for MEDLINE]Related articles

Identification of functional modules using network topology and high-throughput data.

Ulitsky I, Shamir R.

BMC Syst Biol. 2007 Jan 26;1:8.PMID: 17408515 [PubMed - indexed for MEDLINE]Related articlesFree article