Advances in flux balance analysis

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Iliopoulos, 2003, Evaluation of annotation strategies using an entire genome sequence, Bioinformatics, 19, 717, 10.1093/bioinformatics/btg077

Stephanopoulos, 1994, Metabolic engineering, Curr. Opin. Biotechnol, 5, 196, 10.1016/S0958-1669(05)80036-9

Edwards, 2000, The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities, Proc. Natl. Acad Sci. USA, 97, 5528, 10.1073/pnas.97.10.5528

Edwards, 1999, Systems properties of the Haemophilus influenzae Rd metabolic genotype, J. Biol. Chem, 274, 17410, 10.1074/jbc.274.25.17410

Forster, 2003, Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network, Genome Res, 13, 244, 10.1101/gr.234503

Ramakrishna, 2001, Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints, Am. J. Physiol. Regul. Integr. Comp. Physiol, 280, R695, 10.1152/ajpregu.2001.280.3.R695

Varma, 1993, Biochemical production capabilities of Escherichia coli, Biotechnol. Bioeng, 42, 59, 10.1002/bit.260420109

Varma, 1993, Metabolic capabilities of Escherichia coli: I. Synthesis of biosynthetic precursors and cofactors, J. Theor. Biol, 165, 477, 10.1006/jtbi.1993.1202

Varma, 1993, Metabolic capabilities of Escherichia coli: II. Optimal growth patterns, J. Theor. Biol, 165, 503, 10.1006/jtbi.1993.1203

Varma, 1994, Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110, Appl. Environ. Microbiol, 60, 3724, 10.1128/aem.60.10.3724-3731.1994

Varma, 1993, Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates, Appl. Environ. Microbiol, 59, 2465, 10.1128/aem.59.8.2465-2473.1993

Segre, 2002, Analysis of optimality in natural and perturbed metabolic networks, Proc. Natl. Acad Sci. USA, 99, 15112, 10.1073/pnas.232349399

Schilling, 2000, Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems, Biotechnol. Bioeng, 71, 286, 10.1002/1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R

Schilling, 2002, Genome-scale metabolic model of Helicobacter pylori 26695, J. Bacteriol, 184, 4582, 10.1128/JB.184.16.4582-4593.2002

Schilling, 1999, Toward metabolic phenomics: analysis of genomic data using flux balances, Biotechnol. Prog, 15, 288, 10.1021/bp9900357

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Edwards, 2001, In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data, Nat. Biotechnol, 19, 125, 10.1038/84379

Ibarra, 2002, Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth, Nature, 420, 186, 10.1038/nature01149

Lee, 2000, Recursive MILP model for finding all alternate optima in LP models for metabolic networks, Comp. Chem. Eng, 24, 711, 10.1016/S0098-1354(00)00323-9

Phalakornkule, 2001, A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering, Metab. Eng, 3, 124, 10.1006/mben.2000.0165

Papin, 2002, The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy, J. Theor. Biol, 215, 67, 10.1006/jtbi.2001.2499

Covert, 2001, Regulation of gene expression in flux balance models of metabolism, J. Theor. Biol, 213, 73, 10.1006/jtbi.2001.2405

Covert, 2003, Constraints-based models: regulation of gene expression reduces the steady-state solution space, J. Theor. Biol, 221, 309, 10.1006/jtbi.2003.3071

Mahadevan, 2002, Dynamic flux balance analysis of diauxic growth in Escherichia coli, Biophys. J, 83, 1331, 10.1016/S0006-3495(02)73903-9

Beard, 2002, Energy balance for analysis of complex metabolic networks, Biophys. J, 83, 79, 10.1016/S0006-3495(02)75150-3

Burgard, 2001, Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions, Biotechnol. Bioeng, 74, 364, 10.1002/bit.1127

Edwards, 2002, Characterizing the metabolic phenotype: a phenotype phase plane analysis, Biotechnol. Bioeng, 77, 27, 10.1002/bit.10047

Van Dien, 2002, Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C-3 and C-4 metabolism, Biotechnol. Bioeng, 78, 296, 10.1002/bit.10200

Covert, 2002, Transcriptional regulation in constraints-based metabolic models of Escherichia coli, J. Biol. Chem, 277, 28058, 10.1074/jbc.M201691200

Edwards, 2000, Robustness analysis of the Escherichia coli metabolic network, Biotechnol. Prog, 16, 927, 10.1021/bp0000712

Burgard, 2003, Optimization-based framework for inferring and testing hypothesized metabolic objective functions, Biotechnol. Bioeng, 82, 670, 10.1002/bit.10617

Klamt, 2002, Calculating as many fluxes as possible in underdetermined metabolic networks, Mol. Biol. Rep, 29, 243, 10.1023/A:1020394300385

Klamt, 2002, Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria, Biotechnol. Bioeng, 77, 734, 10.1002/bit.10153

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Savinell, 1992, Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism, J. Theor. Biol, 155, 215, 10.1016/S0022-5193(05)80596-X

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Pramanik, 1998, Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model, Biotechnol. Bioeng, 60, 230, 10.1002/(SICI)1097-0290(19981020)60:2<230::AID-BIT10>3.0.CO;2-Q