TY - JOUR AU - Blattner, F. R. AU - Plunkett, G. I. I. I. AU - Bloch, C. A. AU - Perna, N. T. AU - Burland, V. AU - Riley, M. AU - Collado-Vides, J. AU - Glasner, J. D. AU - Rode, C. K. AU - Mayhew, G. F. AU - Gregor, J. AU - Davis, N. W. AU - Kirkpatrick, H. A. AU - Goeden, M. A. AU - Rose, D. J. AU - Mau, B. AU - Shao, Y. PY - 1997 DA - 1997// TI - The complete genome sequence of Escherichia coli K-12 JO - Science VL - 277 UR - https://doi.org/10.1126/science.277.5331.1453 DO - 10.1126/science.277.5331.1453 ID - Blattner1997 ER - TY - JOUR AU - Fiehn, O. AU - Kopka, J. AU - Dormann, P. AU - Altmann, T. AU - Trethewey, R. N. AU - Willmitzer, L. PY - 2000 DA - 2000// TI - Metabolite profiling for plant functional genomics JO - Nature Biotechnology VL - 18 UR - https://doi.org/10.1038/81137 DO - 10.1038/81137 ID - Fiehn2000 ER - TY - JOUR AU - Wang, Y. AU - Liu, C. L. AU - Storey, J. D. AU - Tibshirani, R. J. AU - Herschlag, D. AU - Brown, P. O. PY - 2002 DA - 2002// TI - Precision and functional specificity in mRNA decay JO - Proceedings of the National Academy of Sciences of the United States of America VL - 99 UR - https://doi.org/10.1073/pnas.092538799 DO - 10.1073/pnas.092538799 ID - Wang2002 ER - TY - JOUR AU - Edwards, J. S. AU - Palsson, B. O. PY - 2000 DA - 2000// TI - The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities JO - Proceedings of the National Academy of Sciences of the United States of America VL - 97 UR - https://doi.org/10.1073/pnas.97.10.5528 DO - 10.1073/pnas.97.10.5528 ID - Edwards2000 ER - TY - JOUR AU - Shen-Orr, S. S. AU - Milo, R. AU - Mangan, S. AU - Alon, U. PY - 2002 DA - 2002// TI - Network motifs in the transcriptional regulation network of Escherichia coli JO - Nature Genetics VL - 31 UR - https://doi.org/10.1038/ng881 DO - 10.1038/ng881 ID - Shen-Orr2002 ER - TY - JOUR AU - Bakker, B. M. AU - Michels, P. A. AU - Opperdoes, F. R. AU - Westerhoff, H. V. PY - 1999 DA - 1999// TI - What controls glycolysis in bloodstream form Trypanosoma brucei? JO - Journal of Biological Chemistry VL - 274 UR - https://doi.org/10.1074/jbc.274.21.14551 DO - 10.1074/jbc.274.21.14551 ID - Bakker1999 ER - TY - JOUR AU - Barkai, N. AU - Leibler, S. PY - 1997 DA - 1997// TI - Robustness in simple biochemical networks JO - Nature VL - 387 UR - https://doi.org/10.1038/43199 DO - 10.1038/43199 ID - Barkai1997 ER - TY - JOUR AU - Bhalla, U. S. AU - Iyengar, R. PY - 1999 DA - 1999// TI - Emergent properties of networks of biological signaling pathways. JO - Science VL - 283 UR - https://doi.org/10.1126/science.283.5400.381 DO - 10.1126/science.283.5400.381 ID - Bhalla1999 ER - TY - JOUR AU - Cornish-Bowden, A. AU - Cardenas, M. L. PY - 2001 DA - 2001// TI - Information transfer in metabolic pathways: effects of irreversible steps in computer models. JO - European Journal of Biochemistry VL - 268 UR - https://doi.org/10.1046/j.0014-2956.2001.02616.x DO - 10.1046/j.0014-2956.2001.02616.x ID - Cornish-Bowden2001 ER - TY - JOUR AU - Chance, B. AU - Garfinkel, D. AU - Higgins, J. AU - Hess, B. PY - 1960 DA - 1960// TI - Metabolic control mechanisms V: a solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells JO - Journal of Biological Chemistry VL - 235 ID - Chance1960 ER - TY - JOUR AU - Monod, J. AU - Wyman, J. AU - Changeux, J. P. PY - 1965 DA - 1965// TI - On the nature of allosteric transitions: a plausible model JO - Journal of Molecular Biology VL - 12 UR - https://doi.org/10.1016/S0022-2836(65)80285-6 DO - 10.1016/S0022-2836(65)80285-6 ID - Monod1965 ER - TY - JOUR AU - King, E. L. AU - Altman, C. PY - 1956 DA - 1956// TI - A schematic method of deriving the rate laws for enzyme catalyzed reactions JO - Journal of Physical Chemistry VL - 60 UR - https://doi.org/10.1021/j150544a010 DO - 10.1021/j150544a010 ID - King1956 ER - TY - JOUR AU - Joshi, A. AU - Palsson, B. O. PY - 1989 DA - 1989// TI - Metabolic dynamics in the human red cell: part I. a comprehensive kinetic model. JO - Journal of Theoretical Biology VL - 141 UR - https://doi.org/10.1016/S0022-5193(89)80233-4 DO - 10.1016/S0022-5193(89)80233-4 ID - Joshi1989 ER - TY - JOUR AU - Ni, T. C. AU - Savageau, M. A. PY - 1996 DA - 1996// TI - Model assessment and refinement using strategies from biochemical systems theory: application to metabolism in human red blood cells. JO - Journal of Theoretical Biology VL - 179 UR - https://doi.org/10.1006/jtbi.1996.0072 DO - 10.1006/jtbi.1996.0072 ID - Ni1996 ER - TY - JOUR AU - Henriksen, C. M. AU - Christensen, L. H. AU - Nielsen, J. AU - Villadsen, J. PY - 1996 DA - 1996// TI - Growth energetics and metabolic fluxes in continuous cultures of Penicillium chrysogenum JO - Journal of Biotechnology VL - 45 UR - https://doi.org/10.1016/0168-1656(95)00164-6 DO - 10.1016/0168-1656(95)00164-6 ID - Henriksen1996 ER - TY - JOUR AU - Ibarra, R. U. AU - Edwards, J. S. AU - Palsson, B. O. PY - 2002 DA - 2002// TI - Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01149 DO - 10.1038/nature01149 ID - Ibarra2002 ER - TY - JOUR AU - Aiba, S. AU - Matsuoka, M. PY - 1979 DA - 1979// TI - Identification of metabolic model: citrate production from glucose by Candida lipolytica JO - Biotechnology and Bioengineering VL - 21 UR - https://doi.org/10.1002/bit.260210806 DO - 10.1002/bit.260210806 ID - Aiba1979 ER - TY - JOUR AU - Varner, J. AU - Ramkrishna, D. PY - 1999 DA - 1999// TI - Mathematical models of metabolic pathways JO - Current Opinion in Biotechnology VL - 10 UR - https://doi.org/10.1016/S0958-1669(99)80025-1 DO - 10.1016/S0958-1669(99)80025-1 ID - Varner1999 ER - TY - JOUR AU - Mahadevan, R. AU - Edwards, J. S. AU - Doyle, F. J. PY - 2002 DA - 2002// TI - Dynamic flux balance analysis of diauxic growth in Escherichia coli. JO - Biophysical Journal VL - 83 UR - https://doi.org/10.1016/S0006-3495(02)73903-9 DO - 10.1016/S0006-3495(02)73903-9 ID - Mahadevan2002 ER - TY - JOUR AU - Mulquiney, P. J. AU - Kuchel, P. W. PY - 1999 DA - 1999// TI - Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. JO - Biochemical Journal VL - 342 UR - https://doi.org/10.1042/bj3420581 DO - 10.1042/bj3420581 ID - Mulquiney1999 ER - TY - JOUR AU - Fell, D. A. PY - 1992 DA - 1992// TI - Metabolic control analysis: a survey of its theoretical and experimental development JO - Biochemical Journal VL - 286 UR - https://doi.org/10.1042/bj2860313 DO - 10.1042/bj2860313 ID - Fell1992 ER - TY - JOUR AU - Wittmann, C. AU - Heinzle, E. PY - 2002 DA - 2002// TI - Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria. JO - Applied and Environmental Microbiology VL - 68 UR - https://doi.org/10.1128/AEM.68.12.5843-5859.2002 DO - 10.1128/AEM.68.12.5843-5859.2002 ID - Wittmann2002 ER - TY - JOUR AU - Ghaemmaghami, S. AU - Huh, W. K. AU - Bower, K. AU - Howson, R. W. AU - Belle, A. AU - Dephoure, N. AU - O'Shea, E. K. AU - Weissman, J. S. PY - 2003 DA - 2003// TI - Global analysis of protein expression in yeast JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02046 DO - 10.1038/nature02046 ID - Ghaemmaghami2003 ER - TY - JOUR AU - Soga, T. AU - Kakazu, Y. AU - Robert, M. AU - Tomita, M. AU - Nishioka, T. PY - 2004 DA - 2004// TI - Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry JO - Electrophoresis VL - 25 UR - https://doi.org/10.1002/elps.200305791 DO - 10.1002/elps.200305791 ID - Soga2004 ER - TY - JOUR AU - Soga, T. AU - Ohashi, Y. AU - Ueno, Y. AU - Naraoka, H. AU - Tomita, M. AU - Nishioka, T. PY - 2003 DA - 2003// TI - Quantitative metabolome analysis using capillary electrophoresis mass spectrometry JO - J Proteome Res VL - 2 UR - https://doi.org/10.1021/pr034020m DO - 10.1021/pr034020m ID - Soga2003 ER - TY - JOUR AU - Soga, T. AU - Ueno, Y. AU - Naraoka, H. AU - Ohashi, O. AU - Tomita, M. AU - Nishioka, T. PY - 2002 DA - 2002// TI - Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray Ionization mass spectrometry JO - Analytical Chemistry VL - 74 UR - https://doi.org/10.1021/ac020064n DO - 10.1021/ac020064n ID - Soga2002 ER - TY - JOUR AU - Ishii, N. AU - Robert, M. AU - Nakayama, Y. AU - Kanai, A. AU - Tomita, M. PY - 2004 DA - 2004// TI - Toward large-scale modeling of the microbial cell for computer simulation JO - J Biotechnol VL - 113 UR - https://doi.org/10.1016/j.jbiotec.2004.04.038 DO - 10.1016/j.jbiotec.2004.04.038 ID - Ishii2004 ER - TY - JOUR AU - Delgado, J. AU - Liao, J. C. PY - 1992 DA - 1992// TI - Determination of flux control coefficients from transient metabolite concentrations. JO - Biochemical Journal VL - 282 UR - https://doi.org/10.1042/bj2820919 DO - 10.1042/bj2820919 ID - Delgado1992 ER - TY - JOUR AU - Acerenza, L. AU - Cornish-Bowden, A. PY - 1997 DA - 1997// TI - Generalization of the double-modulation method for in situ determination of elasticities JO - Biochemical Journal VL - 327 UR - https://doi.org/10.1042/bj3270217 DO - 10.1042/bj3270217 ID - Acerenza1997 ER - TY - JOUR AU - de la Fuente, A. AU - Snoep, J. L. AU - Westerhoff, H. V. AU - Mendes, P. PY - 2002 DA - 2002// TI - Metabolic control in integrated biochemical systems. JO - European Journal of Biochemistry VL - 269 UR - https://doi.org/10.1046/j.1432-1033.2002.03088.x DO - 10.1046/j.1432-1033.2002.03088.x ID - de la Fuente2002 ER - TY - JOUR AU - Wu, L. AU - Wang, W. AU - van Winden, W. A. AU - van Gulik, W. M. AU - Heijnen, J. J. PY - 2004 DA - 2004// TI - A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics. JO - European Journal of Biochemistry VL - 271 UR - https://doi.org/10.1111/j.0014-2956.2004.04269.x DO - 10.1111/j.0014-2956.2004.04269.x ID - Wu2004 ER - TY - BOOK AU - Stephanopoulos, G. N. AU - Aristidou, A. A. AU - Nielsen, J. PY - 1998 DA - 1998// TI - Metabolic Engineering: Principles and Methodologies PB - San Diego CY - Academic Press ID - Stephanopoulos1998 ER -