TY - BOOK AU - Stephanopoulos, G. AU - Aristidou, A. AU - Nielsen, J. PY - 1998 DA - 1998// TI - Metabolic Engineering: Principles and Methodologies PB - Academic Press CY - USA ID - Stephanopoulos1998 ER - TY - BOOK AU - Torres, N. AU - Voit, E. PY - 2002 DA - 2002// TI - Pathway Analysis and Optimization in Metabolic Engineering PB - Cambridge University Press CY - England UR - https://doi.org/10.1017/CBO9780511546334 DO - 10.1017/CBO9780511546334 ID - Torres2002 ER - TY - JOUR AU - Mendes, P. AU - Kell, D. PY - 1998 DA - 1998// TI - Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.10.869 DO - 10.1093/bioinformatics/14.10.869 ID - Mendes1998 ER - TY - STD TI - Varma A, Boesch BW, Palsson BO: Metabolic flux balancing: Basic concepts, scientific and practical use. Bio-Technology. 1994, 994-998. 12 ID - ref4 ER - TY - JOUR AU - Savageau, M. PY - 1969 DA - 1969// TI - Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions JO - J Theor Biol VL - 25 UR - https://doi.org/10.1016/S0022-5193(69)80026-3 DO - 10.1016/S0022-5193(69)80026-3 ID - Savageau1969 ER - TY - JOUR AU - Savageau, M. PY - 1969 DA - 1969// TI - Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation JO - J Theor Biol VL - 25 UR - https://doi.org/10.1016/S0022-5193(69)80027-5 DO - 10.1016/S0022-5193(69)80027-5 ID - Savageau1969 ER - TY - BOOK AU - Voit, E. PY - 2000 DA - 2000// TI - Computational Analysis of Biochemical Systems. A Practical Guide for Biochemists and Molecular Biologists PB - Cambridge University Press CY - England ID - Voit2000 ER - TY - STD TI - Voit E: Optimization in integrated biochemical systems. Biotechnol Bioeng. 1992, 572-582. 10.1002/bit.260400504. 40 ID - ref8 ER - TY - STD TI - Hatzimanikatis V, Bailey JE: MCA has more to say. J Theor Biol. 1996, 233-242. 10.1006/jtbi.1996.0160. 182 ID - ref9 ER - TY - JOUR AU - Torres, N. AU - Voit, E. AU - Glez-Alcon, C. AU - Rodriguez, F. PY - 1997 DA - 1997// TI - An indirect optimization method for biochemical systems. Description of method and application to ethanol, glycerol and carbohydrate production in Saccharomyces cerevisiae JO - Biotech Bioeng VL - 5 UR - https://doi.org/3.0.CO;2-A DO - 3.0.CO;2-A ID - Torres1997 ER - TY - JOUR AU - Shiraishi, F. AU - Savageau, M. A. PY - 1992 DA - 1992// TI - The tricarboxylic acid cycle in Dictyostelium discoideum. III. Analysis of steady state and dynamic behavior JO - J Biol Chem VL - 267 ID - Shiraishi1992 ER - TY - BOOK AU - Savageau, M. PY - 1976 DA - 1976// TI - Biochemical Systems Analysis. A Study of Function and Design in Molecular Biology PB - Addison-Wesley, Reading, Massachusetts CY - California ID - Savageau1976 ER - TY - STD TI - De Atauri P, Curto R, Puigjaner J, Cornish-Bowden A, Cascante M: Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modelling metabolic pathways. Eur J Biochem. 265 (2): 671-679. 10.1046/j.1432-1327.1999.00760.x. ID - ref13 ER - TY - STD TI - Savageau M, Voit E: Recasting nonlinear differential equations as S-systems: A canonical nonlinear form. Math Biosci. 1987, 83-115. 10.1016/0025-5564(87)90035-6. 87 ID - ref14 ER - TY - BOOK AU - Dantzig, G. PY - 1963 DA - 1963// TI - Linear Programming and Extensions PB - Princeton University Press CY - Princeton, New Jersey ID - Dantzig1963 ER - TY - CHAP AU - Xu, G. AU - Shao, C. AU - Xiu, Z. PY - 2005 DA - 2005// TI - A Modified Iterative IOM Approach for Optimization of Biochemical Systems BT - eprint arXiv:q-bio/0508038 ID - Xu2005 ER - TY - JOUR AU - Vera, J. AU - de Atauri, P. AU - Cascante, M. AU - Torres, N. PY - 2003 DA - 2003// TI - Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by Saccharomyces cerevisiae JO - Biotechnol Bioeng VL - 83 UR - https://doi.org/10.1002/bit.10676 DO - 10.1002/bit.10676 ID - Vera2003 ER - TY - JOUR AU - Alvarez-Vasquez, F. AU - Gonzalez-Alcon, C. AU - Torres, N. PY - 2000 DA - 2000// TI - Metabolism of citric acid production by aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate JO - Biotechnol Bioeng VL - 70 UR - https://doi.org/3.0.CO;2-V DO - 3.0.CO;2-V ID - Alvarez-Vasquez2000 ER - TY - CHAP AU - Polisetty, P. AU - Voit, E. AU - Gatzke, E. P. PY - 2005 DA - 2005// TI - Yield Optimization of Saccharomyces cerevisiae using a GMA Model and a MILP-based piecewise linear relaxation method BT - Proceedings of: Foundations of Systems Biology in Engineering ID - Polisetty2005 ER - TY - BOOK AU - Zener, C. PY - 1971 DA - 1971// TI - Engineering Design by Geometric Programming PB - John Wiley and Sons CY - Inc ID - Zener1971 ER - TY - BOOK AU - Boyd, S. AU - Vandenberghe, L. PY - 2004 DA - 2004// TI - Convex Optmization PB - Cambridge University Press CY - England UR - https://doi.org/10.1017/CBO9780511804441 DO - 10.1017/CBO9780511804441 ID - Boyd2004 ER - TY - BOOK AU - Grant, M. AU - Boyd, S. AU - Ye, Y. PY - 2005 DA - 2005// TI - CVX: Matlab Software for Disciplined Convex Programming ID - Grant2005 ER - TY - BOOK AU - Koh, K. AU - Kim, S. AU - Mutapic, A. AU - Boyd, S. PY - 2006 DA - 2006// TI - GGPLAB: A simple Matlab toolbox for Geometric Programming ID - Koh2006 ER - TY - BOOK AU - Floudas, C. A. PY - 2000 DA - 2000// TI - Deterministic Global Optimization PB - Kluwer Academic Publishers CY - Berlin UR - https://doi.org/10.1007/978-1-4757-4949-6 DO - 10.1007/978-1-4757-4949-6 ID - Floudas2000 ER - TY - STD TI - Boyd S, Kim S, Vandenberghe L, Hassibi : A tutorial on geometric programming. [To be published in Optimization and Engineering] ID - ref25 ER - TY - JOUR AU - Roundtree, D. AU - Rigler, A. PY - 1982 DA - 1982// TI - A penalty treatment of equality constraints in generalized geometric programming JO - Journal of Optimization Theory and Applications VL - 38 UR - https://doi.org/10.1007/BF00934080 DO - 10.1007/BF00934080 ID - Roundtree1982 ER - TY - JOUR AU - Goldfarb, D. PY - 1970 DA - 1970// TI - A Family of Variable Metric Updates Derived by Variational Mean JO - Mathematics of Computing VL - 24 UR - https://doi.org/10.1090/S0025-5718-1970-0258249-6 DO - 10.1090/S0025-5718-1970-0258249-6 ID - Goldfarb1970 ER - TY - JOUR AU - Fletcher, D. AU - Powell, M. PY - 1963 DA - 1963// TI - A rapidly convergent Descent Method for minimization JO - Computer Journal VL - 6 UR - https://doi.org/10.1093/comjnl/6.2.163 DO - 10.1093/comjnl/6.2.163 ID - Fletcher1963 ER - TY - JOUR AU - Curto, R. AU - Sorribas, A. AU - Cascante, M. PY - 1995 DA - 1995// TI - Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature JO - Math Biosci VL - 130 UR - https://doi.org/10.1016/0025-5564(94)00092-E DO - 10.1016/0025-5564(94)00092-E ID - Curto1995 ER - TY - STD TI - Galazzo J, Bailey J: Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae. Enzyme Microb Technol. 1990, 162-172. 10.1016/0141-0229(90)90033-M. 12 ID - ref30 ER - TY - JOUR AU - Marin-Sanguino, A. AU - Torres, N. V. PY - 2000 DA - 2000// TI - Optimization of tryptophan production in bacteria. Design of a strategy for genetic manipulation of the tryptophan operon for tryptophan flux maximization JO - Biotechnol Prog VL - 16 UR - https://doi.org/10.1021/bp990144l DO - 10.1021/bp990144l ID - Marin-Sanguino2000 ER - TY - JOUR AU - Xiu, Z. AU - Chang, Z. AU - Zeng, A. PY - 2002 DA - 2002// TI - Nonlinear dynamics of regulation of bacterial trp operon: model analysis of integrated effects of repression, feedback inhibition, and attenuation JO - Biotechnol Prog VL - 18 UR - https://doi.org/10.1021/bp020052n DO - 10.1021/bp020052n ID - Xiu2002 ER -