References
- Price, N. D., J. L. Reed, and B. O. Palsson (2004) Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat. Rev. Microbiol. 2: 886-897 https://doi.org/10.1038/nrmicro1023
- Edwards, J. S. and B. O. Palsson (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97: 5528-5533 https://doi.org/10.1073/pnas.97.10.5528
- Reed, J. L., T. D. Vo, C. H. Schilling, and B. Palsson (2003) Escherichia coli iJR904: An expanded genomescale model of E. coli K-12. Genome Biol. 4: R54.1-R54.12.
- Famili, I., J. Forster, J. Nielsen, and B. O. Palsson (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 100: 13134-13139 https://doi.org/10.1073/pnas.2235812100
- Dauner, M. and U. Sauer (2001) Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol. Bioeng. 76: 132-143 https://doi.org/10.1002/bit.1153
- Hong, S. H., J. S. Kim, S. Y. Lee, Y. H. In, S. S. Choi, J. K. Rih, C. H. Kim, H. Jeong, C. G. Hur, and J. J. Kim (2004) The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat. Biotechnol. 22: 1275-1281 https://doi.org/10.1038/nbt1010
- Covert, M. W., E. M. Knight, J. L. Reed, M. J. Herrgard, and B. O. Palsson (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96 https://doi.org/10.1038/nature02456
- Ciaramella, M., A. Napoli, and M. Rossi (2005) Another extreme genome: How to live at pH 0. Trends Microbiol. 13: 49-51 https://doi.org/10.1016/j.tim.2004.12.001
- Forster, J., I. Famili, P. Fu, B. O. Palsson, and J. Nielsen (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13: 244-253 https://doi.org/10.1101/gr.234503
- Schilling, C. H., M. W. Covert, I. Famili, G. M. Church, J. S. Edwards, and B. O. Palsson (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593 https://doi.org/10.1128/JB.184.16.4582-4593.2002
- Varma, A., B. W. Boesch, and B. O. Palsson (1993) Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59: 2465-2473
- Varma, A. and B. O. Palsson (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60: 3724-3731
- Edwards, J. S., R. U. Ibarra, and B. O. Palsson (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130 https://doi.org/10.1038/84379
- Ibarra, R. U., J. S. Edwards, and B. O. Palsson (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189 https://doi.org/10.1038/nature01149
- Varma, A., B. W. Boesch, and B. O. Palsson (1993) Biochemical production capabilities of Escherichia coli. Biotechnol. Bioeng. 42: 59-73 https://doi.org/10.1002/bit.260420109
- Edwards, J. S. and B. O. Palsson (2000) Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1:1
- Segre, D., D. Vitkup, and G. M. Church (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99: 15112-15117 https://doi.org/10.1073/pnas.232349399
- Shlomi, T., O. Berkman, and E. Ruppin (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 102: 7695-7700 https://doi.org/10.1073/pnas.0406346102
- Papp, B., C. Pal, and L. D. Hurst (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664 https://doi.org/10.1038/nature02636
- Segre, D., A. Deluna, G. M. Church, and R. Kishony (2005) Modular epistasis in yeast metabolism. Nat. Genet. 37: 77-83 https://doi.org/10.1038/ng1489
- Mahadevan, R. and B. O. Palsson (2005) Properties of metabolic networks: Structure versus function. Biophys. J. 88: L07-L09 https://doi.org/10.1529/biophysj.104.055723
- DeRisi, J. L., V. R. Iyer, and P. O. Brown (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686 https://doi.org/10.1126/science.278.5338.680
- Patterson, S. D. and R. H. Aebersold (2003) Proteomics: The first decade and beyond. Nat. Genet. 33 Suppl: 311-323 https://doi.org/10.1038/ng1106
- Kell, D. B (2004) Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7: 296-307 https://doi.org/10.1016/j.mib.2004.04.012
- Churchill, G. A. (2004) Using ANOVA to analyze microarray data. Biotechniques 37: 173-177
- Sharan, R., R. Elkon, and R. Shamir (2002) Cluster analysis and its applications to gene expression data. Ernst. Schering. Res Found. Workshop 83-108
- Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934 https://doi.org/10.1126/science.292.5518.929
- Burgard, A. P., E. V. Nikolaev, C. H. Schilling, and C. D. Maranas (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14: 301-312 https://doi.org/10.1101/gr.1926504
- Oh, M. K. and J. C. Liao (2000) Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16: 278-286 https://doi.org/10.1021/bp000002n
- Tao, H., R. Gonzalez, A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam (2001) Engineering a homo-ethanol pathway in Escherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J. Bacteriol. 183: 2979-2988 https://doi.org/10.1128/JB.183.10.2979-2988.2001
- Akesson, M., J. Forster, and J. Nielsen (2004) Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6: 285-293 https://doi.org/10.1016/j.ymben.2003.12.002
- Patil, K. R. and J. Nielsen (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. USA 102: 2685-2689 https://doi.org/10.1073/pnas.0406811102
- Covert, M. W., C. H. Schilling, and B. Palsson (2001) Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213: 73-88 https://doi.org/10.1006/jtbi.2001.2405
- van der Heijden, R. T. J. M., J. J. Heijnen, C. Hellinga, B. Romein, and K. C. A. M. Luyben (1994) Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross measurement errors. Biotechnol. Bioeng. 43: 11-20 https://doi.org/10.1002/bit.260430104
- Raghunathan, A. U., J. R. Perez-Correa, and L. T. Biegler (2003) Data reconciliation and parameter estimation in flux-balance analysis. Biotechnol. Bioeng. 84: 700-708 https://doi.org/10.1002/bit.10823
- Mahadevan, R. and C. H. Schilling (2003) The effects of alternate optimal solutions in constraint-based genomescale metabolic models. Metab. Eng. 5: 264-276 https://doi.org/10.1016/j.ymben.2003.09.002
- Vallino, J. J. and G. Stephanopoulos (1993) Metabolic fluc distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 41: 633-646 https://doi.org/10.1002/bit.260410606
- van Gulik, W. M., W. T. de Laat, J. L. Vinke, and J. J. Heijnen (2000) Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G. Biotechnol. Bioeng. 68: 602-618 https://doi.org/10.1002/(SICI)1097-0290(20000620)68:6<602::AID-BIT3>3.0.CO;2-2
- Schilling, C. H., J. S. Edwards, and B. O. Palsson (1999) Toward metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol. Prog. 15: 288-295 https://doi.org/10.1021/bp9900357
- Shimizu, H., N. Takiguchi, H. Tanaka, and S. Shioya (1999) A maximum production strategy of lysine based on a simplified model derived from a metabolic reaction network. Metab. Eng. 1: 299-308 https://doi.org/10.1006/mben.1999.0127
-
Wiechert, W (2001)
$^{13}C$ metabolic flux analysis. Metab. Eng. 195-206 - Marx, A., A. A. de Graaf, W. Wiechert, L. Eggeling, and H. Sahm (1996) Determination of the fluxes in central metabolism of Corynebacterium glutamicum by NMR spectroscopy combined with metabolite balancing. Biotechnol. Bioeng. 49: 111-129 https://doi.org/10.1002/(SICI)1097-0290(19960120)49:2<111::AID-BIT1>3.0.CO;2-T
- Dauner, M. and U. Sauer (2000) GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol. Prog. 16: 642-649 https://doi.org/10.1021/bp000058h
- Schmidt, K., M. Carlsen, J. Nielsen, and J. Villadsen (1997) Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840 https://doi.org/10.1002/(SICI)1097-0290(19970920)55:6<831::AID-BIT2>3.0.CO;2-H
-
van Dien, S. J., T. Strovas, and M. E. Lidstrom (2003) Quantification of central metabolic fluxes in the facultative methylotroph methylobacterium extorquens AM1 using
$^{13}C$ -label tracing and mass spectrometry. Biotechnol. Bioeng. 84: 45-55 https://doi.org/10.1002/bit.10745 - Wiechert, W., C. Siefke, A. A. de Graaf, and A. Marx (1997) Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol. Bioeng. 55: 118-135 https://doi.org/10.1002/(SICI)1097-0290(19970705)55:1<118::AID-BIT13>3.0.CO;2-I
- Wiechert, W. and A. A. de Graaf (1997) Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55: 101-117 https://doi.org/10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P
- Wittmann, C. and E. Heinzle (1999) Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62: 739-750 https://doi.org/10.1002/(SICI)1097-0290(19990320)62:6<739::AID-BIT13>3.0.CO;2-E
- Walsh, K. and D. E. Jr. Koshland (1984) Determination of flux through the branch point of two metabolic cycles. The tricarboxylic acid cycle and the glyoxylate shunt. J. Biol. Chem. 259: 9646-9654
- Park, S. M., M. I. Klapa, A. J. Sinskey, and G. N. Stephanopoulos (1999) Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. Biotechnol. Bioeng. 62: 392-401 https://doi.org/10.1002/(SICI)1097-0290(19990220)62:4<392::AID-BIT2>3.0.CO;2-S
- Wendisch, V. F., A. A. de Graaf, H. Sahm, and B. J. Eikmanns (2000) Quantitative determination of metabolic fluxes during coutilization of two carbon sources: Comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J. Bacteriol. 182: 3088-3096 https://doi.org/10.1128/JB.182.11.3088-3096.2000
- Petersen, S., A. A. de Graaf, L. Eggeling, M. Mollney, W. Wiechert, and H. Sahm (2000) In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. Metab. Eng. 3: 195-206 https://doi.org/10.1006/mben.2001.0187
- Wittmann, C., H. M. Kim, and E. Heinzle (2004) Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale. Biotechnol. Bioeng. 87: 1-6 https://doi.org/10.1002/bit.20103
- Sauer, U., D. R. Lasko, J. Fiaux, M. Hochuli, R. Glaser, T. Szyperski, K. Wuthrich, and J. E. Bailey (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181: 6679-6688
-
Wahl, A., M. El Massaoudi, D. Schipper, W. Wiechert, and R. Takors (2004) Serial
$^{13}C$ -based flux analysis of an L-phenylalanine-producing E. coli strain using a sensor reactor. Biotechnol. Prog. 20: 706-714 https://doi.org/10.1021/bp0342755 - Sauer, U., V. Hatzimanikatis, J. E. Bailey, M. Hochuli, T. Szyperski, and K. Wuthrich (1997) Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat. Biotechnol. 15: 448-452 https://doi.org/10.1038/nbt0597-448
- Gombert, A. K., S. M. Moreira dos, B. Christensen, and J. Nielsen (2001) Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183: 1441-1451 https://doi.org/10.1128/JB.183.4.1441-1451.2001
-
Christensen, B. and J. Nielsen (2000) Metabolic network analysis of Penicillium chrysogenum using
$^{13}C$ -labeled glucose. Biotechnol. Bioeng. 68: 652-659 https://doi.org/10.1002/(SICI)1097-0290(20000620)68:6<652::AID-BIT8>3.0.CO;2-J -
Jensen, N. B. S., B. Christensen, J. Nielsen, and J. Villadsen (2002) The simultaneous biosynthesis and uptake of amino acids by Lactococcus lactis studied by
$^{13}C$ -labeling experiments. Biotechnol. Bioeng. 78: 11-16 https://doi.org/10.1002/bit.10211 - Burgard, A. P. and C. D. Maranas (2001) Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375 https://doi.org/10.1002/bit.1127
- Carlson, R., D. Fell, and F. Srienc (2002) Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79: 121-34 https://doi.org/10.1002/bit.10305
- Fong, S. S. and B. O. Palsson (2004) Metabolic genedeletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36: 1056-1058 https://doi.org/10.1038/ng1432
- Burgard, A. P., P. Pharkya, and C. D. Maranas (2003) OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84: 647-657 https://doi.org/10.1002/bit.10803
- Pharkya, P., A. P. Burgard, and C. D. Maranas (2003) Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol. Bioeng. 84: 887-899 https://doi.org/10.1002/bit.10857
- Alper, H., Y. S. Jin, J. F. Moxley, and G. Stephanopoulos (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164 https://doi.org/10.1016/j.ymben.2004.12.003
- Wilson, E. K. (2005) Engineering cell-based factories. Chem. Eng. News 83: 41-44
- Broadbelt, L. J., S. M. Stark, and M. T. Klein (1994) Computer-generated pyrolysis modeling-on-the-fly generation of species, reactions, and rates. Ind. Eng. Chem. Res. 33: 790-799 https://doi.org/10.1021/ie00028a003
- Broadbelt, L. J., S. M. Stark, and M. T. Klein (1995) Termination of computer-generated reaction-mechanismsspecies rank-based convergence criterion. Ind. Eng. Chem. Res. 34: 2566-2573 https://doi.org/10.1021/ie00047a003
- Broadbelt, L. J., S. M. Stark, and M. T. Klein (1996) Computer generated reaction modelling: Decomposition and encoding algorithms for determining species uniqueness. Comput. Chem. Eng. 20: 113-129 https://doi.org/10.1016/0098-1354(94)00009-D
- Hatzimanikatis, V., C. Li, J. A. Ionita, and L. J. Broadbelt (2004) Metabolic networks: Enzyme function and metabolite structure. Curr. Opin. Struct. Biol. 14: 300-306 https://doi.org/10.1016/j.sbi.2004.04.004
- Kanehisa, M., S. Goto, S. Kawashima, Y. Okuno, and M. Hattori (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 Database issue: D277-D280 https://doi.org/10.1093/nar/gkh063
- Karp, P. D., M. Riley, M. Saier, I. T. Paulsen, S. M. Paley, and A. Pellegrini-Toole (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res. 28: 56-59 https://doi.org/10.1093/nar/28.1.56
- Krieger, C. J., P. Zhang, L. A. Mueller, A. Wang, S. Paley, M. Arnaud, J. Pick, S. Y. Rhee, and P. D. Karp (2004) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32 Database issue: D438-D442 https://doi.org/10.1093/nar/gkh100
- Li, C., C. S. Henry, M. D. Jankowski, J. A. Ionita, V. Hatzimanikatis, and L. J. Broadbelt (2004) Computational discovery of biochemical routes to specialty chemicals. Chem. Eng. Sci. 59: 5051-5060 https://doi.org/10.1016/j.ces.2004.09.021
- Hatzimanikatis, V., C. Li, J. A. Ionita, C. S. Henry, M. D. Jankowski, and L. J. Broadbelt (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21: 1603-1609 https://doi.org/10.1093/bioinformatics/bti213
- Pharkya, P., A. P. Burgard, and C. D. Maranas (2004) OptStrain: A computational framework for redesign of microbial production systems. Genome Res. 14: 2367-2376 https://doi.org/10.1101/gr.2872004
- Komives, C. and R. S. Parker (2003) Bioreactor state estimation and control. Curr. Opin. Biotechnol. 14: 468-474 https://doi.org/10.1016/j.copbio.2003.09.001
- Covert, M. W. and B. O. Palsson (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277: 28058-28064 https://doi.org/10.1074/jbc.M201691200
- Mahadevan, R., J. S. Edwards, and F. J. Doyle (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophysical J. 83: 1331-1340 https://doi.org/10.1016/S0006-3495(02)73903-9
- Gadkar, K. G., F. J. Doyle, III, T. J. Crowley, and J. D. Varner (2003) Cybernetic model predictive control of a continuous bioreactor with cell recycle. Biotechnol Prog. 19: 1487-1497 https://doi.org/10.1021/bp025776d
- Mahadevan, R. and F. J. Doyle (2003) On-line optimization of recombinant product in a fed-batch bioreactor. Biotechnol. Prog. 19: 639-646 https://doi.org/10.1021/bp025546z
- Parekh, S., V. A. Vinci, and R. J. Strobel (2000) Improvement of microbial strains and fermentation processes. Appl. Microbiol. Biotechnol. 54: 287-301 https://doi.org/10.1007/s002530000403
- Zhang, S., J. Chu, and Y. Zhuang (2004) A multi-scale study of industrial fermentation processes and their optimization. Adv. Biochem. Eng. Biotechnol. 87: 97-150
- Gadkar, K. G., F. J. Doyle, J. S. Edwards, and R. Mahadevan (2005) Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnol. Bioeng. 89: 243-251 https://doi.org/10.1002/bit.20349
- Lovley, D. R. (2003) Cleaning up with genomics: Applying molecular biology to bioremediation. Nat. Rev. Microbiol. 1: 35-44 https://doi.org/10.1038/nrmicro731
- Beard, D. A. and H. Qian (2005) Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. Am. J. Physiol. Endocrinol. Metab. 288: E633-E644 https://doi.org/10.1152/ajpendo.00239.2004