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  • Alper H, Jin YS, Moxley JF, Stephanopoulos G. 2005. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 7(3): 155164.
  • Aristidou AA, San KY, Bennett GN. 1999. Metabolic flux analysis of Escherichia coli expressing the Bacillus subtilis acetolactate synthase in batch and continuous cultures. Biotechnol Bioeng 63(6): 737749.
  • Barabasi AL, Oltvai ZN. 2004. Network biology: Understanding the cell's functional organization. Nat Rev Genet 5(2): 101113.
  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2005. GenBank. Nucleic Acids Res 33 (Database issue): D34D38.
  • Borodina I, Krabben P, Nielsen J. 2005. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15(6): 820829.
  • Burgard AP, Pharkya P, Maranas CD. 2003. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6): 647657.
  • Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY , et al. 2006. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34 (Database issue): D511D5116.
  • Davis CP, Cleven D, Brown J, Balish E. 1976. Anaerobiospirillum, a new genus of spiral-shaped bacteria. Int J Syst Bacteriol 26: 498504.
  • Edwards JS, Ramakrishna R, Schilling CH, Palsson BO. 1999. Metabolic flux balance analysis. In: LeeSY, PapoutsakisET, editors. Metabolic engineering. New York: Marcel Dekker Inc., p 1357.
  • Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. 2006. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2: 2006.0004.
  • Forster J, Famili I, Fu P, Palsson BO, Nielsen J. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13(2): 244253.
  • Gombert AK, Nielsen J. 2000. Mathematical modeling of metabolism. Curr Opin Biotechnol 11: 180186.
  • Guettler MV, Rumler D, Jain MK. 1999. Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen. Int J Syst Bacteriol 49 (Pt 1): 207216.
  • Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ. 2004. The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 22(10): 12751281.
  • Jeanmougin F, Thompson JD, Higgins DG, Gibson TJ. 1998. Multiple sequence alignment with ClustalX. Trends Biochem Sci 23: 403405.
  • Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. 2000. The large-scale organization of metabolic networks. Nature 407(6804): 651654.
  • Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34 (Database issue): D354D357.
  • Kim P, Laivenieks M, McKinlay J, Vieille C, Gregory Zeikus J. 2004. Construction of a shuttle vector for the overexpression of recombinant proteins in Actinobacillus succinogenes. Plasmid 51(2): 108115.
  • Lee J, Blaschek HP. 2001. Glucose uptake in Clostridium beijerinckii NCIMB 8052 and the solvent-hyperproducing mutant BA101. Appl Environ Microbiol 67(11): 50255031.
  • Lee PC, Lee SY, Hong SH, Chang HN. 2002. Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducensMBEL55E, from bovine rumen. Appl Microbiol Biotechnol 58(5): 663668.
  • Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY. 2005a. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol 71(12): 78807887.
  • Lee SY, Lee DY, Kim TY. 2005b. Systems biotechnology for strain improvement. Trends Biotechnol 23(7): 349358.
  • Lee SJ, Song H, Lee SY. 2006. Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol 72(3): 19391948.
  • Ma HW, Zeng AP. 2003. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19(11): 14231430.
  • Peltroche-Llacsahuanga H, Schmidt S, Lutticken R, Haase G. 2000. Discriminative power of fatty acid methyl ester (FAME) analysis using the microbial identification system (MIS) for Candida (Torulopsis) glabrata and Saccharomyces cerevisiae. Diagn Microbiol Infect Dis 38(4): 213221.
  • Peng L, Shimizu K. 2003. Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Appl Microbiol Biotechnol 61(2): 163178.
  • Price ND, Reed JL, Palsson BO. 2004. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2(11): 886897.
  • Reed JL, Vo TD, Schilling CH, Palsson BO. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4(9): R54.
  • Ren Q, Paulsen IT. 2005. Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol 1(3): e27.
  • Song H, Lee SY. 2006. Production of succinic acid by bacterial fermentation. Enzyme Microb Technol 39: 352361.
  • Stephanopoulos GN, Aristidou AA, Nielsen J. 1998. Metabolic engineering—Principles and methodologies. San Diego: Academic Press.
  • Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29(1): 2228.
  • Terada K, Murata T, Izui K. 1991. Site-directed mutagenesis of phosphoenolpyruvate carboxylase from E. coli: The role of His579 in the catalytic and regulatory functions. J Biochem (Tokyo) 109(1): 4954.
  • Van der Werf MJ, Guettler MV, Jain MK, Zeikus JG. 1997. Environmental and physiological factors affecting the succinate product ratio during carbohydrate fermentation by Actinobacillus sp. 130Z. Arch Microbiol 167(6): 332342.
  • Varma A, Palsson BO. 1994a. Metabolic flux balancing: Basic concepts, scientific and practical use. Bio-Technology 12: 994998.
  • Varma A, Palsson BO. 1994b. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60(10): 37243731.
  • Varma A, Boesch BW, Palsson BO. 1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 59(8): 24652473.