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Volumn 14, Issue 9, 2004, Pages 1797-1805

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states

Author keywords

[No Author keywords available]

Indexed keywords

FORMATE DEHYDROGENASE; FUMARATE REDUCTASE; HYDROGENASE; ISOENZYME;

EID: 4644220226     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2546004     Document Type: Article
Times cited : (175)

References (36)
  • 1
    • 10744232769 scopus 로고    scopus 로고
    • Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets
    • Allen, T.E., Herrgard, M.J., Liu, M., Qiu, Y, Glasner, J.D., Blattner, F.R., and Palsson, B.Ø. 2003. Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets. J. Bacteriol. 185: 6392-6399.
    • (2003) J. Bacteriol. , vol.185 , pp. 6392-6399
    • Allen, T.E.1    Herrgard, M.J.2    Liu, M.3    Qiu, Y.4    Glasner, J.D.5    Blattner, F.R.6    Palsson, B.Ø.7
  • 2
    • 1542288938 scopus 로고    scopus 로고
    • Global organization of metabolic fluxes in the bacterium Escherichia coli
    • Almaas, E., Kovacs, B., Vicsek, T., Oltvai, Z.N., and Barabasi, A.L. 2004. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843.
    • (2004) Nature , vol.427 , pp. 839-843
    • Almaas, E.1    Kovacs, B.2    Vicsek, T.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 3
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • Beard, D.A., Liang, S.D., and Qian, H. 2002. Energy balance for analysis of complex metabolic networks. Biophys. J. 83: 79-86.
    • (2002) Biophys. J. , vol.83 , pp. 79-86
    • Beard, D.A.1    Liang, S.D.2    Qian, H.3
  • 4
    • 0035812464 scopus 로고    scopus 로고
    • Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
    • Burgard, A.P. and Maranas, C.D. 2001. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375.
    • (2001) Biotechnol. Bioeng. , vol.74 , pp. 364-375
    • Burgard, A.P.1    Maranas, C.D.2
  • 5
    • 0034798879 scopus 로고    scopus 로고
    • Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments
    • Burgard, A.P., Vaidyaraman, S., and Maranas, C.D. 2001. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog. 17: 791-797.
    • (2001) Biotechnol. Prog. , vol.17 , pp. 791-797
    • Burgard, A.P.1    Vaidyaraman, S.2    Maranas, C.D.3
  • 6
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard, A.P., Pharkya, P., and Maranas, C.D. 2003. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84: 647-657.
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 7
    • 1242274402 scopus 로고    scopus 로고
    • Flux coupling analysis of genome-scale metabolic network reconstructions
    • Burgard, A.P., Nikolaev, E.V., Schilling, C.H., and Maranas, C.D. 2004. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14: 301-312.
    • (2004) Genome Res. , vol.14 , pp. 301-312
    • Burgard, A.P.1    Nikolaev, E.V.2    Schilling, C.H.3    Maranas, C.D.4
  • 8
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • Covert, M.W., Schilling, C.H., and Palsson, B. 2001. Regulation of gene expression in flux balance models of metabolism. J. Theoret. Biol. 213: 73-88.
    • (2001) J. Theoret. Biol. , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.3
  • 9
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.Ø. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.Ø.5
  • 10
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards, J.S. and Palsson, B.Ø. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. 97: 5528-5533.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.Ø.2
  • 11
    • 0142152457 scopus 로고    scopus 로고
    • Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 using a genome-scale in silico metabolic model
    • Fong, S.S., Marciniak, J.Y., and Palsson, B.Ø. 2003. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 using a genome-scale in silico metabolic model. J. Bacteriol. 185: 6400-6408.
    • (2003) J. Bacteriol. , vol.185 , pp. 6400-6408
    • Fong, S.S.1    Marciniak, J.Y.2    Palsson, B.Ø.3
  • 12
    • 0042816453 scopus 로고    scopus 로고
    • Large-scale evaluation of in silico gene knockouts in Saccharomyces cerevisiae
    • Forster, J., Famili, I., Palsson, B.Ø., and Nielsen, J. 2003. Large-scale evaluation of in silico gene knockouts in Saccharomyces cerevisiae. OMICS 7: 193-202.
    • (2003) OMICS , vol.7 , pp. 193-202
    • Forster, J.1    Famili, I.2    Palsson, B.Ø.3    Nielsen, J.4
  • 13
    • 0000598585 scopus 로고    scopus 로고
    • Respiration
    • (ed. F.C. Neidhardt), ASM Press, Washington, DC
    • Gennis, R.B. and Stewart, V. 1996. Respiration. In Escherichia coli and salmonella (ed. F.C. Neidhardt), pp. 217-261. ASM Press, Washington, DC.
    • (1996) Escherichia Coli and Salmonella , pp. 217-261
    • Gennis, R.B.1    Stewart, V.2
  • 15
    • 0242574985 scopus 로고    scopus 로고
    • Reconciling gene expression data with known genome-scale regulatory network structures
    • Herrgard, M.J., Covert, M.W., and Palsson, B.Ø. 2003. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res. 13: 2423-2434.
    • (2003) Genome Res. , vol.13 , pp. 2423-2434
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.Ø.3
  • 16
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra, R.U., Edwards, J.S., and Palsson, B.Ø. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.Ø.3
  • 19
    • 0034661295 scopus 로고    scopus 로고
    • Recursive MILP model for finding all the alternate optima in LP models for metabolic networks
    • Lee, S., Phalakornkule, C., Domach, M.M., and Grossmann, I.E. 2000. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comp. Chem. Eng. 24: 711-716.
    • (2000) Comp. Chem. Eng. , vol.24 , pp. 711-716
    • Lee, S.1    Phalakornkule, C.2    Domach, M.M.3    Grossmann, I.E.4
  • 20
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan, R. and Schilling, C.H. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5: 264-276.
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 21
    • 0036916269 scopus 로고    scopus 로고
    • Extreme pathway lengths and reaction participation in genome-scale metabolic networks
    • Papin, J.A., Price, N.D., and Palsson, B.Ø. 2002. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12: 1889-1900.
    • (2002) Genome Res. , vol.12 , pp. 1889-1900
    • Papin, J.A.1    Price, N.D.2    Palsson, B.Ø.3
  • 23
    • 0034805665 scopus 로고    scopus 로고
    • A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering
    • Phalakornkule, C., Lee, S., Zhu, T., Koepsel, R., Ataai, M.M., Grossmann, I.E., and Domach, M.M. 2001. A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering. Metab. Eng. 3: 124-137.
    • (2001) Metab. Eng. , vol.3 , pp. 124-137
    • Phalakornkule, C.1    Lee, S.2    Zhu, T.3    Koepsel, R.4    Ataai, M.M.5    Grossmann, I.E.6    Domach, M.M.7
  • 25
    • 0037385718 scopus 로고    scopus 로고
    • Genome-scale microbial in silico models: The constraints-based approach
    • Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B. 2003. Genome-scale microbial in silico models: The constraints-based approach. Trends Biotechnol. 21: 162-169.
    • (2003) Trends Biotechnol. , vol.21 , pp. 162-169
    • Price, N.D.1    Papin, J.A.2    Schilling, C.H.3    Palsson, B.4
  • 26
    • 4644225683 scopus 로고    scopus 로고
    • Uniform sampling of steady state flux spaces: Means to design experiments and to interpret enzymopathies
    • (in press)
    • Price, N.D., Schellenberger, J., and Palsson, B.Ø. 2004. Uniform sampling of steady state flux spaces: Means to design experiments and to interpret enzymopathies. J. Biol. Chem. (in press).
    • (2004) J. Biol. Chem.
    • Price, N.D.1    Schellenberger, J.2    Palsson, B.Ø.3
  • 28
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • Reed, J.L., and Palsson, B.Ø. 2003. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185: 2692-2699.
    • (2003) J. Bacteriol. , vol.185 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.Ø.2
  • 29
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed, J.L., Vo, T.D., Schilling, C.H., and Palsson, B.Ø. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4: R54.51-R54.12.
    • (2003) Genome Biol. , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.Ø.4
  • 33
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segre, D., Vitkup, D., and Church, G.M. 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. 99: 15112-15117.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 34
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E.D. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 35
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific and practical use
    • Varma, A. and Palsson, B.Ø. 1994. Metabolic flux balancing: Basic concepts, scientific and practical use. Bio/Technology 12: 994-998.
    • (1994) Bio/Technology , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.Ø.2
  • 36
    • 2642513030 scopus 로고    scopus 로고
    • Monte Carlo sampling can be used to determine the size and shape of the steady state flux space
    • Wiback, S.J., Famili, I., Greenberg, H.J., and Palsson, B.Ø. 2004. Monte Carlo sampling can be used to determine the size and shape of the steady state flux space. J. Theor. Biol. 228: 437-447.
    • (2004) J. Theor. Biol. , vol.228 , pp. 437-447
    • Wiback, S.J.1    Famili, I.2    Greenberg, H.J.3    Palsson, B.Ø.4


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