Abell LM, Villafranca JJ. Investigation of the mechanism of phosphinothricin inactivation of Escherichia coli glutamine synthetase using rapid quench kinetic technique. Biochemistry 30: 6135-6141 (1991).

Affourtit C, Krab K, Moore AL. Control of plant mitochondrial respiration. Biochim. Biophys. Acta 1504: 58-69 (2001).

Ahrens K, Menzel K, Zeng A, Deckwer W. Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: III. Enzymes and fluxes of glycerol dissimilation and 1,3-propanediol formation. Biotechnol. Bioeng. 59: 544-552 (1998).

Akagawa H, Ishii A, Mizuno S. Suppression of thermotolerance development through cycloheximide-induced negative control of stress protein gene expression. J. Biochem. (Tokyo) 123: 226-232 (1998).

Alagappan G, Cowan R. Substrate inhibition kinetics for toluene and benzene degrading pure cultures and a method for collection and analysis of respirometric data for strongly inhibited cultures. Biotechnol. Bioeng. 83: 798-809 (2003).

Alagappan G, Cowan RM. Biokinetic models for representing the complete inhibition of microbial activity at high substrate concentrations. Biotechnol. Bioeng. 75: 393-405 (2001).

Albert R, Othmer HG. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 223: 1-18 (2003).

Alper H, Jin YS, Moxley JF, Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164 (2005).

Alshafie M, Ghoshal S. Naphthalene biodegradation from non-aqueous-phase liquids in batch and column systems: comparison of biokinetic rate coefficients. Biotechnol. Prog. 19: 844-852 (2003).

Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS. Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol. Bioeng. 94: 273-295 (2006).

Altmann T, Kossmann J. Photosynthesis and primary metabolism. Trends Plant Sci. 6: 93-94 (2001).

Alvarez-Vasquez F, Gonzalez-Alcon C, Torres NV. Metabolism of citric acid production by Aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate. Biotechnol. Bioeng. 70: 82-108 (2000).

Alvarez-Vasquez F, Sims KJ, Cowart LA, Okamoto Y, Voit EO, Hannun YA. Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 433: 425-430 (2005).

Alves R, Antunes F, Salvador A. Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. 24: 667-672 (2006).

Anderson KJ, Allen AP, Gillooly JF, Brown JH. Temperature-dependence of biomass accumulation rates during secondary succession. Ecol. Lett. 9: 673-682 (2006).

Andreou AZ, Vanko M, Bezakova L, Feussner I. Properties of a mini 9R-lipoxygenase from Nostoc sp. PCC 7120 and its mutant forms. Phytochemistry 69: 1832-1837 (2008).

Andrieu B, Hillier J, Birch C. Onset of sheath extension and duration of lamina extension are major determinants of the response of maize lamina length to plant density. Ann. Bot. (Lond.) 98: 1005-1016 (2006).

Ao P, Lee LW, Lidstrom ME, Yin L, Zhu X. Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation. Sheng Wu Gong Cheng Xue Bao 24: 980-994 (2008).

Aranda-Barradas JS, Delia ML, Riba JP. Kinetic study and modelling of the xylitol production using Candida parapsilosis in oxygen-limited culture conditions. Bioprocess Engineering 22: 219-225 (2000).

Armstrong W, Webb T, Darwent M, Beckett PM. Measuring and interpreting respiratory critical oxygen pressures in roots. Ann. Bot. (Lond.) 103: 281-293 (2009).

Arnold S, Siemann M, Scharnweber K, Werner M, Baumann S, Reuss M. Kinetic modeling and simulation of in vitro transcription by phage T7 RNA polymerase. Biotechnol. Bioeng. 72: 548-561 (2001).

Atkins WM, Cader BM, Hemmingsen J, Villafranca JJ. Time-resolved fluorescence and computational studies of adenylylated glutamine synthetase: analysis of intersubunit interactions. Protein Sci. 2: 800-813 (1993).

Atkins WM, Villafranca JJ. Time-resolved fluorescence studies of tryptophan mutants of Escherichia coli glutamine synthetase: conformational analysis of intermediates and transition-state complexes. Protein Sci. 1: 342-355 (1992).

Bacchi CJ, Barker RH Jr, Rodriguez A, Hirth B, Rattendi D, Yarlett N, Hendrick CL, Sybertz E. Trypanocidal activity of 8-methyl-5'-{[(Z)-4-aminobut-2-enyl]-(methylamino)}adenosine (Genz-644131), an adenosylmethionine decarboxylase inhibitor. Antimicrob. Agents Chemother. 53: 3269-3272 (2009).

Bakker BM, Michels PAM, Opperdoes FR, Westerhoff HV. Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272: 3207-3215 (1997).

Balaban RS. Modeling mitochondrial function. Am. J. Physiol. Cell Physiol. 291: C1107-C1113 (2006).

Balaji B, O'Connor K, Lucas JR, Anderson JM, Csonka LN. Timing of induction of osmotically controlled genes in Salmonella enterica serovar typhimurium, determined with quantitative real-time reverse transcription-PCR. Appl. Environ. Microbiol. 71: 8273-8283 (2005).

Bali M, Thomas SR. A modelling study of feedforward activation in human erythrocyte glycolysis. C. R. Acad. Sci. III 324: 185-199 (2001).

Banks EC, Doughty SW, Toms SM, Wheelhouse RT, Nicolaou A. Inhibition of cobalamin-dependent methionine synthase by substituted benzo-fused heterocycles. FEBS J. 274: 287-299 (2007).

Banta S, Boston M, Jarnagin A, Anderson S. Mathematical modeling of in vitro enzymatic production of 2-keto-L-gulonic acid using NAD(H) or NADP(H) as cofactors. Metab. Eng. 4: 273-284 (2002).

Barlowe CK, Appling DR. Isolation and characterization of a novel eukaryotic monofunctional NAD(+)-dependent 5,10-methylenetetrahydrofolate dehydrogenase. Biochemistry 29: 7089-7094 (1990).

Barrett PH, Bell BM, Cobelli C, Golde H, Schumitzky A, Vicini P, Foster DM. SAAM II: Simulation, Analysis, and Modeling Software for tracer and pharmacokinetic studies. Metabolism 47: 484-492 (1998).

Barrett PH, Chan DC, Watts GF. Thematic review series: patient-oriented research. Design and analysis of lipoprotein tracer kinetics studies in humans. J. Lipid Res. 47: 1607-1619 (2006).

Barrett PHR, Foster DM. Design and analysis of lipid tracer kinetic studies. Curr. Opin. Lipidol. 7: 143-148 (1996).

Bassingthwaighte JB. Strategies for the physiome project. Ann. Biomed. Eng. 28: 1043-1058 (2000).

Bastianelli D, Sauvant D, Rerat A. Mathematical modeling of digestion and nutrient absorption in pigs. J. Anim. Sci. 74: 1873-1887 (1996).

Bejar CM, Jin X, Ballicora MA, Preiss J. Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases. J. Biol. Chem. 281: 40473-40484 (2006).

Belic A, Grabnar I, Karba R, Mrhar A, Irman-Florjanc T, Primozic S. Interdependence of histamine and methylhistamine kinetics: modelling and simulation approach. Comput. Biol. Med. 29: 361-375 (1999).

Bell CI, Cram WJ, Clarkson DT. Compartmental analysis of (SO(4)2-)-S-35 exchange kinetics in roots and leaves of a tropical legume Macroptilium atropurpureum cv Siratro. J. Exp. Bot. 45: 879-886 (1994).

Bellazzi R, Guglielmann R, Ironi L, Patrini C. A hybrid input-output approach to model metabolic systems: an application to intracellular thiamine kinetics. J. Biomed. Inform. 34: 221-248 (2001).

Berg OG, Paulsson J, Ehrenberg M. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79: 1228-1236 (2000).

Bernacchi CJ, Singsaas EL, Pimentel C, Portis AR Jr, Long SP. Improved temperature response functions for models of Rubisco-limited photosynthesis. Plant Cell Environ. 24: 253-259 (2001).

Bernard O, Bastin G, Stentelaire C, Lesage-Meessen L, Asther M. Mass balance modeling of vanillin production from vanillic acid by cultures of the fungus Pycnoporus cinnabarinus in bioreactors. Biotechnol. Bioeng. 65: 558-571 (1999).

Berry S, Rumberg B. Kinetic modeling of the photosynthetic electron transport chain. Bioelectrochemistry 53: 35-53 (2001).

Bertail P, Clemencon S, Tressou J. A storage model with random release rate for modeling exposure to food contaminants. Math. Biosci. Eng. 5: 35-60 (2008).

Bertilsson M, Andersson J, Liden G. Modeling simultaneous glucose and xylose uptake in Saccharomyces cerevisiae from kinetics and gene expression of sugar transporters. Bioprocess. Biosyst. Eng. 31: 369-377 (2008).

Bertoldi M, Cellini B, Maras B, Voltattorni CB. A quinonoid is an intermediate of oxidative deamination reaction catalyzed by Dopa decarboxylase. FEBS Lett. 579: 5175-5180 (2005).

Bertoldi M, Voltattorni CB. Dopa decarboxylase exhibits low pH half-transaminase and high pH oxidative deaminase activities toward serotonin (5-hydroxytryptamine). Protein Sci. 10: 1178-1186 (2001).

Bertoldo A, Peltoniemi P, Oikonen V, Knuuti J, Nuutila P, Cobelli C. Kinetic modeling of [(18)F]FDG in skeletal muscle by PET: a four-compartment five-rate-constant model. Am. J. Physiol. Endocrinol. Metab. 281: E524-E536 (2001).

Beun JJ, Dircks K, Van Loosdrecht MC, Heijnen JJ. Poly-beta-hydroxybutyrate metabolism in dynamically fed mixed microbial cultures. Water Res. 36: 1167-1180 (2002).

Beun JJ, Paletta F, Van Loosdrecht MC, Heijnen JJ. Stoichiometry and kinetics of poly-beta-hydroxybutyrate metabolism in aerobic, slow growing, activated sludge cultures. Biotechnol. Bioeng. 67: 379-389 (2000).

Beun JJ, Verhoef EV, Van Loosdrecht MC, Heijnen JJ. Stoichiometry and kinetics of poly-beta-hydroxybutyrate metabolism under denitrifying conditions in activated sludge cultures. Biotechnol. Bioeng. 68: 496-507 (2000).

Beyl S, Timin EN, Hohaus A, Stary A, Kudrnac M, Guy RH, Hering S. Probing the architecture of an L-type calcium channel with a charged phenylalkylamine: evidence for a widely open pore and drug trapping. J. Biol. Chem. 282: 3864-3870 (2007).

Bier DM. Stable isotopes in biosciences, their measurement and models for amino acid metabolism. Eur. J. Pediatr. 156: S2-S8 (1997).

Bilsel O, Yang L, Zitzewitz JA, Beechem JM, Matthews CR. Time-resolved fluorescence anisotropy study of the refolding reaction of the alpha-subunit of tryptophan synthase reveals nonmonotonic behavior of the rotational correlation time. Biochemistry 38: 4177-4187 (1999).

Bilsel O, Zitzewitz JA, Bowers KE, Matthews CR. Folding mechanism of the alpha-subunit of tryptophan synthase, an alpha/beta barrel protein: global analysis highlights the interconversion of multiple native, intermediate, and unfolded forms through parallel channels. Biochemistry 38: 1018-1029 (1999).

Binder BM, Mortimore LA, Stepanova AN, Ecker JR, Bleecker AB. Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent. Plant Physiol. 136: 2921-2927 (2004).

Binder BM, O'malley RC, Wang W, Moore JM, Parks BM, Spalding EP, Bleecker AB. Arabidopsis seedling growth response and recovery to ethylene. A kinetic analysis. Plant Physiol. 136: 2913-2920 (2004).

Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N. Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 135: 1993-2011 (2004).

Bogaards JJ, Hissink EM, Briggs M, Weaver R, Jochemsen R, Jackson P, Bertrand M, van Bladeren PJ. Prediction of interindividual variation in drug plasma levels in vivo from individual enzyme kinetic data and physiologically based pharmacokinetic modeling. Eur. J. Pharm. Sci. 12: 117-124 (2000).

Bohme CC, Arscott LD, Becker K, Schirmer RH, Williams CH Jr. Kinetic characterization of glutathione reductase from the malarial parasite Plasmodium falciparum. Comparison with the human enzyme. J. Biol. Chem. 275: 37317-37323 (2000).

Bomati EK, Noel JP. Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase. Plant Cell 17: 1598-1611 (2005).

Boon MA, Janssen AE, van der Padt A. Modelling and parameter estimation of the enzymatic synthesis of oligosaccharides by beta-galactosidase from Bacillus circulans. Biotechnol. Bioeng. 64: 558-567 (1999).

Borger S, Liebermeister W, Klipp E. Prediction of enzyme kinetic parameters based on statistical learning. Genome Inform. 17: 80-87 (2006).

Bramley H, Turner NC, Turner DW, Tyerman SD. Comparison between gradient-dependent hydraulic conductivities of roots using the root pressure probe: the role of pressure propagations and implications for the relative roles of parallel radial pathways. Plant Cell Environ. 30: 861-874 (2007).

Brandt S, Fisahn J. Identification of a K+ channel from potato leaves by functional expression in Xenopus oocytes. Plant Cell Physiol. 39: 600-606 (1998).

Brosch G, Ransom R, Lechner T, Walton JD, Loidl P. Inhibition of maize histone deacetylases by HC toxin, the host-selective toxin of Cochliobolus carbonum. Plant Cell 7: 1941-1950 (1995).

Browning ST, Shuler ML. Towards the development of a minimal cell model by generalization of a model of Escherichia coli: Use of dimensionless rate parameters. Biotechnol. Bioeng. 76: 187-92 (2001).

Bruggeman FJ, Boogerd FC, Westerhoff HV. The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. FEBS J. 272: 1965-1985 (2005).

Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhutter HG. Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws- a promising method for speeding up the kinetic modelling of complex metabolic networks. FEBS J. 276: 410-424 (2009).

Bulock KG, Beardsley GP, Anderson KS. The kinetic mechanism of the human bifunctional enzyme ATIC (5-amino-4-imidazolecarboxamide ribonucleotide transformylase/inosine 5'-monophosphate cyclohydrolase). A surprising lack of substrate channeling. J. Biol. Chem. 277: 22168-22174 (2002).

Burger C, Buck A. Tracer kinetic modelling of receptor data with mathematical metabolite correction. Eur. J. Nucl. Med. 23: 539-545 (1996).

Burnett JR, Barrett PH. Apolipoprotein B metabolism: tracer kinetics, models, and metabolic studies. Crit. Rev. Clin. Lab. Sci. 39: 89-137. (2002).

Busch K, Piehler J, Fromm H. Plant succinic semialdehyde dehydrogenase: dissection of nucleotide binding by surface plasmon resonance and fluorescence spectroscopy. Biochemistry 39: 10110-10117 (2000).

Buswell AM, Middelberg AP. A new kinetic scheme for lysozyme refolding and aggregation. Biotechnol. Bioeng. 83: 567-577 (2003).

Butler CS, Charnock JM, Bennett B, Sears HJ, Reilly AJ, Ferguson SJ, Garner CD, Lowe DJ, Thomson AJ, Berks BC, Richardson DJ. Models for molybdenum coordination during the catalytic cycle of periplasmic nitrate reductase from Paracoccus denitrificans derived from EPR and EXAFS spectroscopy. Biochemistry 38: 9000-9012 (1999).

Bywater RP, Sorensen A, Rogen P, Hjorth PG. Construction of the simplest model to explain complex receptor activation kinetics. J. Theor. Biol. 218: 139-147 (2002).

Cabrera ME, Saidel GM, Kalhan SC. Role of O2 in regulation of lactate dynamics during hypoxia: mathematical model and analysis. Ann. Biomed. Eng. 26: 1-27 (1998).

Caldara M, Dupont G, Leroy F, Goldbeter A, De Vuyst L, Cunin R. Arginine biosynthesis in Escherichia coli: experimental perturbation and mathematical modeling. J. Biol. Chem. 283: 6347-6358 (2008).

Canaud B, Bosc JY, Cabrol L, Leray-Moragues H, Navino C, Verzetti G, Thomaseth K. Urea as a marker of adequacy in hemodialysis: lesson from in vivo urea dynamics monitoring. Kidney Int. 58 Suppl. 76: S28-S40 (2000).

Cao Y, Colegate SM, Edgar JA. Safety assessment of food and herbal products containing hepatotoxic pyrrolizidine alkaloids: interlaboratory consistency and the importance of N-oxide determination. Phytochem. Anal. 19: 526-533 (2008).

Cape JL, Bowman MK, Kramer DM. Understanding the cytochrome bc complexes by what they don't do. The Q-cycle at 30. Trends Plant Sci. 11: 46-55 (2006).

Carvalho AP, Malcata FX. Kinetic modeling of the autotrophic growth of Pavlova lutheri: study of the combined influence of light and temperature. Biotechnol. Prog. 19: 1128-1135 (2003).

Cascao-Pereira LG, Hickel A, Radke CJ, Blanch HW. Interfacial versus homogeneous enzymatic cleavage of mandelonitrile by hydroxynitrile lyase in a biphasic system. Biotechnol. Bioeng. 83: 498-501 (2003).

Cedersund G, Stralfors P. Putting the pieces together in diabetes research: towards a hierarchical model of whole-body glucose homeostasis. Eur. J. Pharm. Sci. 36: 91-104 (2009).

Centritto M, Loreto F, Chartzoulakis K. The use of low [CO2] to estimate diffusional and non-diffusional limitations of photosynthetic capacity of salt-stressed olive saplings. Plant Cell Environ. 26: 585-594 (2003).

Chandler RJ, Aswani V, Tsai MS, Falk M, Wehrli N, Stabler S, Allen R, Sedensky M, Kazazian HH, Venditti CP. Propionyl-CoA and adenosylcobalamin metabolism in Caenorhabditis elegans: evidence for a role of methylmalonyl-CoA epimerase in intermediary metabolism. Mol. Genet. Metab. 89: 64-73 (2006).

Chandraprabha MN, Modak JM, Natarajan KA, Raichur AM. Modeling and analysis of biooxidation of gold bearing pyrite-arsenopyrite concentrates by Thiobacillus ferrooxidans. Biotechnol. Prog. 19: 1244-1254 (2003).

Chang AK, Duggleby RG. Expression, purification and characterization of Arabidopsis thaliana acetohydroxyacid synthase. Biochem. J. 327: 161-169 (1997).

Chassagnole C, Diano A, Letisse F, Lindley ND. Metabolic network analysis during fed-batch cultivation of Corynebacterium glutamicum for pantothenic acid production: first quantitative data and analysis of by-product formation. J. Biotechnol. 104: 261-272 (2003).

Chassagnole C, Fell DA, Rais B, Kudla B, Mazat JP. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach. Biochem. J. 356: 433-444 (2001).

Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79: 53-73 (2002).

Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem. J. 356: 415-423 (2001).

Chatham JC, Forder JR, Glickson JD, Chance EM. Calculation of absolute metabolic flux and the elucidation of the pathways of glutamate labeling in perfused rat heart by 13C NMR spectroscopy and nonlinear least squares analysis. J. Biol. Chem. 270: 7999-8008 (1995).

Chattopadhyay S, Bisaria VS, Srivastava AK. Enhanced production of podophyllotoxin by Podophyllum hexandrum using in situ cell retention bioreactor. Biotechnol. Prog. 19: 1026-1028 (2003).

Chen DX, Coughenour MB, Knapp AK, Owensby CE. Mathematical simulation of C4 grass photosynthesis in ambient and elevated CO2. Ecological Modelling 73: 63-80 (1994).

Chen KC, Wu JY, Yang WB, Hwang SC. Evaluation of effective diffusion coefficient and intrinsic kinetic parameters on azo dye biodegradation using PVA-immobilized cell beads. Biotechnol. Bioeng. 83: 821-832 (2003).

Chen QG, Bleecker AB. Analysis of ethylene signal-transduction kinetics associated with seedling-growth response and chitinase induction in wild-type and mutant Arabidopsis. Plant Physiol. 108: 597-607 (1995).

Chen S, Ho C, Feng D, Chi Z. Tracer kinetic modeling of 11C-acetate applied in the liver with positron emission tomography. IEEE Trans. Med. Imaging 23: 426-432 (2004).

Chen T, He HL, Church GM. Modeling gene expression with differential equations. Pac. Symp. Biocomput. 1999: 29-40 (1999).

Chinchilla D, Schwarz FP, Eisenstein E. Amino acid substitutions in the C-terminal regulatory domain disrupt allosteric effector binding to biosynthetic threonine deaminase from Escherichia coli. J. Biol. Chem. 273: 23219-23224 (1998).

Clough RC, Casal JJ, Jordan ET, Christou P, Vierstra RD. Expression of functional oat phytochrome A in transgenic rice. Plant Physiol. 109: 1039-1045 (1995).

Cloutier M, Bouchard-Marchand E, Perrier M, Jolicoeur M. A predictive nutritional model for plant cells and hairy roots. Biotechnol. Bioeng. 99: 189-200 (2008).

Cloutier M, Chen J, Tatge F, McMurray-Beaulieu V, Perrier M, Jolicoeur M. Kinetic metabolic modelling for the control of plant cells cytoplasmic phosphate. J. Theor. Biol. 259: 118-131 (2009).

Cloutier M, Perrier M, Jolicoeur M. Dynamic flux cartography of hairy roots primary metabolism. Phytochemistry 68: 2393-2404 (2007).

Cobelli C, Toffolo G, Foster DM. Tracer-to-tracee ratio for analysis of stable isotope tracer data: link with radioactive kinetic formalism. Am. J. Physiol. 262: E968-E975 (1992).

Cohen I, Sapir Y, Shapira M. A conserved mechanism controls translation of Rubisco large subunit in different photosynthetic organisms. Plant Physiol. 141: 1089-1097 (2006).

Collatz GJ, Ribascarbo M, Berry JA. Coupled photosynthesis-stomatal conductance model for leaves of C4 plants. Aust. J. Plant Physiol. 19: 519-538 (1992).

Conrado RJ, Mansell TJ, Varner JD, Delisa MP. Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway. Metab. Eng. 9: 355-363 (2007).

Contador CA, Rizk ML, Asenjo JA, Liao JC. Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab. Eng. 11: 221-233 (2009).

Converti A, Arni S, Sato S, De Carvalho JC, Aquarone E. Simplified modeling of fed-batch alcoholic fermentation of sugarcane blackstrap molasses. Biotechnol. Bioeng. 84: 88-95 (2003).

Cornet JF, Favier L, Dussap CG. Modeling stability of photoheterotrophic continuous cultures in photobioreactors. Biotechnol. Prog. 19: 1216-1227 (2003).

Coutand C, Fournier M, Moulia B. The gravitropic response of poplar trunks: key roles of prestressed wood regulation and the relative kinetics of cambial growth versus wood maturation. Plant Physiol. 144: 1166-1180 (2007).

Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050 (2008).

Cronwright GR, Rohwer JM, Prior BA. Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 68: 4448-4456 (2002).

Crowther GJ, Kosaly G, Lidstrom ME. Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J. Bacteriol. 190: 5057-5062 (2008).

Cruz F, Cerdan S. Quantitative 13C NMR studies of metabolic compartmentation in the adult mammalian brain. NMR Biomed. 12: 451-462 (1999).

Curien G, Job D, Douce R, Dumas R. Allosteric activation of Arabidopsis threonine synthase by S-adenosylmethionine. Biochemistry 37: 13212-13221 (1998).

Curien G, Ravanel S, Dumas R. A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana. Eur. J. Biochem. 270: 4615-4627 (2003).

Curto R, Voit EO, Sorribas A, Cascante M. Mathematical models of purine metabolism in man. Math. Biosci. 151: 1-49 (1998).

d'Anjou MC, Daugulis AJ. A rational approach to improving productivity in recombinant Pichia pastoris fermentation. Biotechnol. Bioeng. 72: 1-11 (2001).

D'Argenio DZ, Schumitzky A, Wolf W. Simulation of linear compartment models with application to nuclear medicine kinetic modeling. Comput. Methods Programs Biomed. 27: 47-54 (1988).

Daae EB, Ison AP. A simple structured model describing the growth of Streptomyces lividans. Biotechnol. Bioeng. 58: 263-296 (1998).

Daniel RM, Danson MJ, Eisenthal R. The temperature optima of enzymes: a new perspective on an old phenomenon. Trends Biochem. Sci. 26: 223-225 (2001).

Davis EA, Cuesta-Munoz A, Raoul M, Buettger C, Sweet I, Moates M, Magnuson MA, Matschinsky FM. Mutants of glucokinase cause hypoglycaemia- and hyperglycaemia syndromes and their analysis illuminates fundamental quantitative concepts of glucose homeostasis. Diabetologia 42: 1175-1186 (1999).

De Anda R, Lara AR, Hernandez V, Hernandez-Montalvo V, Gosset G, Bolivar F, Ramirez OT. Replacement of the glucose phosphotransferase transport system by galactose permease reduces acetate accumulation and improves process performance of Escherichia coli for recombinant protein production without impairment of growth rate. Metab. Eng. 8: 281-290 (2006).

de Atauri P, Orrell D, Ramsey S, Bolouri H. Evolution of ‘design’ principles in biochemical networks. Syst. Biol. 1: 28-40 (2004).

de Groot MJ, Prathumpai W, Visser J, Ruijter GJ. Metabolic control analysis of Aspergillus niger l-arabinose catabolism. Biotechnol. Prog. 21: 1610-1616 (2005).

de la Torre F, Moya-Garcia AA, Suarez MF, Rodriguez-Caso C, Canas RA, Sanchez-Jimenez F, Canovas FM. Molecular modeling and site-directed mutagenesis reveal essential residues for catalysis in a prokaryote-type aspartate aminotransferase. Plant Physiol. 149: 1648-1660 (2009).

de Meer K, Roef MJ, Kulik W, Jakobs C. In vivo research with stable isotopes in biochemistry, nutrition and clinical medicine: an overview. Isotopes in Environ. & Health Studies 35: 19-37 (1999).

De Wild HP, Otma EC, Peppelenbos HW. Carbon dioxide action on ethylene biosynthesis of preclimacteric and climacteric pear fruit. J. Exp. Bot. 54: 1537-1544 (2003).

Deep P, Kuwabara H, Gjedde A, Cumming P. The kinetic behaviour of [3H]DOPA in living rat brain investigated by compartmental modelling of static autoradiograms. J. Neurosci. Methods 78: 157-168 (1997).

Dekker RJ, Pannekoek H, Horrevoets AJ. A steady-state competition model describes the modulating effects of thrombomodulin on thrombin inhibition by plasminogen activator inhibitor-1 in the absence and presence of vitronectin. Eur. J. Biochem. 270: 1942-1951 (2003).

Demant T, Seeberg K, Bedynek A, Seidel D. The metabolism of lipoprotein(a) and other apolipoprotein B-containing lipoproteins: a kinetic study in humans. Atherosclerosis 157: 325-339 (2001).

Di Paolo ML, Vianello F, Stevanato R, Rigo A. Kinetic characterization of soybean seedling amine oxidase. Arch. Biochem. Biophys. 323: 329-334 (1995).

Downer J, Sevinsky JR, Ahn NG, Resing KA, Betterton MD. Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase. J. Theor. Biol. 240: 464-474 (2006).

Drager A, Hassis N, Supper J, Schroder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst. Biol. 2: 39 (2008).

Drager A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst. Biol. 3: 5 (2009).

Draye X. Consequences of root growth kinetics and vascular structure on the distribution of lateral roots. Plant Cell Environ. 25: 1463-1474 (2002).

Durkee JW, Aantich PP, Lewis MA, Parkey RW. A fully coupled binary biochemical reactive-diffusion model with analytic solution. J. Theor. Biol. 221: 163-191 (2003).

Edelstein-Keshet L. A mathematical approach to cytoskeletal assembly. Eur. Biophys. J. 27: 521-531 (1998).

Edwards JS, Palsson BO. Multiple steady states in kinetic models of red cell metabolism. J. Theor. Biol. 207: 125-127 (2000).

Elzenga JT, Van volkenburgh E. Kinetics of Ca(2+)- and ATP-dependent, voltage-controlled anion conductance in the plasma membrane of mesophyll cells of Pisum sativum. Planta 201: 415-423 (1997).

Ethier GJ, Livingston NJ. On the need to incorporate sensitivity to CO2 transfer conductance into the Farquhar-von Caemmerer-Berry leaf photosynthesis model. Plant Cell Environ. 27: 137-153 (2004).

Fajmut A, Brumen M, Schuster S. Theoretical model of the interactions between Ca2+, calmodulin and myosin light chain kinase. FEBS Lett. 579: 4361-4366 (2005).

Famili I, Mahadevan R, Palsson BO. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys. J. 88: 1616-1625 (2005).

Fan YX, McPhie P, Miles EW. Regulation of tryptophan synthase by temperature, monovalent cations, and an allosteric ligand. Evidence from Arrhenius plots, absorption spectra, and primary kinetic isotope effects. Biochemistry 39: 4692-4703 (2000).

Fan YX, McPhie P, Miles EW. Thermal repair of tryptophan synthase mutations in a regulatory intersubunit salt bridge. Evidence from arrhenius plots, absorption spectra, and primary kinetic isotope effects. J. Biol. Chem. 275: 20302-20307 (2000).

Farquhar GD, von Caemmerer S, Berry JA. Models of photosynthesis. Plant Physiol. 125: 42-45 (2001).

Farrington GK, Kumar A, Shames SL, Ewaskiewicz JI, Ash DE, Wedler FC. Threonine synthase of Escherichia coli: inhibition by classical and slow-binding analogues of homoserine phosphate. Arch. Biochem. Biophys. 307: 165-174 (1993).

Faulkner C, Akman OE, Bell K, Jeffree C, Oparka K. Peeking into pit fields: a multiple twinning model of secondary plasmodesmata formation in tobacco. Plant Cell 20: 1504-1518 (2008).

Feelisch M, Fernandez BO, Bryan NS, Garcia-Saura MF, Bauer S, Whitlock DR, Ford PC, Janero DR, Rodriguez J, Ashrafian H. Tissue processing of nitrite in hypoxia: an intricate interplay of nitric oxide-generating and -scavenging systems. J. Biol. Chem. 283: 33927-33934 (2008).

Fell DA. Systems properties of metabolic networks. Proceedings of the International Conference on Complex Systems, Nashua, NH, 21-26 Sept, 1997 (1997).

Fell DA, Wagner A. The small world of metabolism. Nat. Biotechnol. 18: 1121-1122 (2000).

Feng L, Kirsch JF. L-Vinylglycine is an alternative substrate as well as a mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 39: 2436-2444 (2000).

Filipe CD, Daigger GT, Grady CP Jr. A metabolic model for acetate uptake under anaerobic conditions by glycogen accumulating organisms: Stoichiometry, kinetics, and the effect of pH. Biotechnol. Bioeng. 76: 17-31 (2001).

Filipe CD, Daigger GT, Grady CP Jr. Stoichiometry and kinetics of acetate uptake under anaerobic conditions by an enriched culture of phosphorus-accumulating organisms at different pHs. Biotechnol. Bioeng. 76: 32-43 (2001).

Findrik Z, Vasic-Racki D. Biotransformation of D-methionine into L-methionine in the cascade of four enzymes. Biotechnol. Bioeng. 98: 956-967 (2007).

Finke JM, Onuchic JN. Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Biophys. J. 89: 488-505 (2005).

Fouchard S, Pruvost J, Degrenne B, Titica M, Legrand J. Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production with Chlamydomonas reinhardtii: Part I. Model development and parameter identification. Biotechnol. Bioeng. 102: 232-245 (2009).

Fowler S, Zhang H. In vitro evaluation of reversible and irreversible cytochrome P450 inhibition: current status on methodologies and their utility for predicting drug-drug interactions. AAPS J. 10: 410-424 (2008).

Fridlyand LE, Backhausen JE, Holtgrefe S, Kitzmann C, Scheibe R. Quantitative evaluation of the rate of 3-phosphoglycerate reduction in chloroplasts. Plant Cell Physiol. 38: 1177-1186 (1997).

Fridlyand LE, Backhausen JE, Scheibe R. Flux control of the malate valve in leaf cells. Arch. Biochem. Biophys. 349: 290-298 (1998).

Fridlyand LE, Scheibe R. Controlled distribution of electrons between acceptors in chloroplasts: a theoretical consideration Biochim. Biophys. Acta 1413: 31-42 (1999).

Fuentes JD, Lerdau M, Atkinson R, Baldocchi D, Bottenheim JW, Ciccioli P, Lamb B, Geron C, Gu L, Guenther A, Sharkey TD, Stockwell W. Biogenic hydrocarbons in the atmospheric boundary layer: A review. Bull. Amer. Meteorol. Soc. 81: 1537-1575 (2000).

Fussenegger M, Bailey JE, Varner J. A mathematical model of caspase function in apoptosis. Nat. Biotechnol. 18: 768-774 (2000).

Gagneur J, Casari G. From molecular networks to qualitative cell behavior. FEBS Lett. 579: 1867-1871 (2005).

Galban CJ, Locke BR. Analysis of cell growth in a polymer scaffold using a moving boundary approach. Biotechnol. Bioeng. 56: 422-432 (1997).

Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD, Burstin J. Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol. 133: 664-682 (2003).

Gerdtzen ZP, Daoutidis P, Hu WS. Non-linear reduction for kinetic models of metabolic reaction networks. Metab. Eng. 6: 140-154 (2004).

Gille C, Hoffmann S, Holzhutter HG. Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks. Genome Inform. Ser. Workshop Genome Inform. 16: 223-232 (2005).

Giordani R, Buc J. Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli. Eur. J. Biochem. 271: 2400-2407 (2004).

Giuseppin ML, van Riel NA. Metabolic modeling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition. Metab. Eng. 2: 14-33 (2000).

Gloge A, Zon J, Kovari A, Poppe L, Retey J. Phenylalanine ammonia-lyase: the use of its broad substrate specificity for mechanistic investigations and biocatalysis--synthesis of L-arylalanines. Chemistry 6: 3386-3390 (2000).

Goda S, Kojima M, Nishikawa Y, Kujo C, Kawakami R, Kuramitsu S, Sakuraba H, Hiragi Y, Ohshima T. Intersubunit interaction induced by subunit rearrangement is essential for the catalytic activity of the hyperthermophilic glutamate dehydrogenase from Pyrobaculum islandicum. Biochemistry 44: 15304-15313 (2005).

Gombert AK, Nielsen J. Mathematical modelling of metabolism. Curr. Opin. Biotechnol. 11: 180-186 (2000).

Gonzalez-Saiz JM, Pizarro C, Garrido-Vidal D. Evaluation of kinetic models for industrial acetic fermentation: proposal of a new model optimized by genetic algorithms. Biotechnol. Prog. 19: 599-611 (2003).

Goutsias J, Kim S. A nonlinear discrete dynamical model for transcriptional regulation: construction and properties. Biophys. J. 86: 1922-1945 (2004).

Green MH. Introduction to modeling. J. Nutr. 122: 690-694 (1992).

Gronwald JW, Plaisance KL. Isolation and characterization of glutathione S-transferase isozymes from sorghum. Plant Physiol. 117: 877-892 (1998).

Guebel DV. Canonical sensitivities: a useful tool to deal with large perturbations in metabolic network modeling. In Silico Biol. 4: 0015 (2004).

Guiducci L, Jarvisalo M, Kiss J, Nagren K, Viljanen A, Naum AG, Gastaldelli A, Savunen T, Knuuti J, Salvadori PA, Ferrannini E, Nuutila P, Iozzo P. [11C]Palmitate kinetics across the splanchnic bed in arterial, portal and hepatic venous plasma during fasting and euglycemic hyperinsulinemia. Nucl. Med. Biol. 33: 521-528 (2006).

Guo Y, Ma Y, Zhan Z, Li B, Dingkuhn M, Luquet D, DE Reffye P. Parameter optimization and field validation of the functional-structural model GREENLAB for maize. Ann. Bot. (Lond.) 97: 217-230 (2006).

Haddad S, Charest-Tardif G, Krishnan K. Physiologically based modeling of the maximal effect of metabolic interactions on the kinetics of components of complex chemical mixtures. J. Toxicol. Environ. Health A. 61: 209-223 (2000).

Hadlich F, Noack S, Wiechert W. Translating biochemical network models between different kinetic formats. Metab. Eng. 11: 87-100 (2009).

Hagedorn A, Legge RL, Budman H. Evaluation of spectrofluorometry as a tool for estimation in fed-batch fermentations. Biotechnol. Bioeng. 83: 104-111 (2003).

Hagedorn PH, Flyvbjerg H, Moller IM. Modelling NADH turnover in plant mitochondria. Physiol. Plant. 120: 370-385 (2004).

Halling PJ, Wilson SK, Jacobs R, McKee S, Coles CW. Modeling the kinetics of enzymic reactions in mainly solid reaction mixtures. Biotechnol. Prog. 19: 1228-1237 (2003).

Hamby DM, Palmer TS. Analysis of an internal kinetic model for free and bound tritium. Health Phys. 81: 426-437 (2001).

Hammond ET, Andrews TJ, Woodrow IE. Regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase by carbamylation and 2-carboxyarabinitol 1-phosphate in tobacco: insights from studies of antisense plants containing reduced amounts of Rubisco activase. Plant Physiol. 118: 1463-1471 (1998).

Hannaert V, Albert MA, Rigden DJ, da Silva Giotto MT, Thiemann O, Garratt RC, Van Roy J, Opperdoes FR, Michels PA. Kinetic characterization, structure modelling studies and crystallization of Trypanosoma brucei enolase. Eur. J. Biochem. 270: 3205-3213 (2003).

Hardin SC, Tang GQ, Scholz A, Holtgraewe D, Winter H, Huber SC. Phosphorylation of sucrose synthase at serine 170: occurrence and possible role as a signal for proteolysis. Plant J. 35: 588-603 (2003).

Harding MM, Anderberg PI, Haymet AD. 'Antifreeze' glycoproteins from polar fish. Eur. J. Biochem. 270: 1381-1392 (2003).

Harel Y, Ohad I, Kaplan A. Activation of photosynthesis and resistance to photoinhibition in cyanobacteria within biological desert crust. Plant Physiol. 136: 3070-3079 (2004).

Hatzimanikatis V, Bailey JE. MCA has more to say. J. Theor. Biol. 182: 233-242 (1996).

Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE. Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol. Bioeng. 58: 154-161 (1998).

Hayes DE, Smith FA, Walker NA. High-affinity potassium transport into wheat roots involves sodium - a role for HKT1?. Aust. J. Plant Physiol. 28: 643-652 (2001).

Heijnen JJ. New experimental and theoretical tools for metabolic engineering of micro-organisms. Meded. Rijksuniv. Gent. Fak. Landbouwkd.Toegep. Biol. Wet. 66: 11-30 (2001).

Heinrich R, Brumen M, Jaeger A, Muller P, Herrmann A. Modelling of phospholipid translocation in the erythrocyte membrane: a combined kinetic and thermodynamic approach. J. Theor. Biol. 185: 295-312 (1997).

Heinzle E, Matsuda F, Miyagawa H, Wakasa K, Nishioka T. Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation. Plant J. 50: 176-187 (2007).

Hennig L, Buche C, Eichenberg K, Schafer E. Dynamic properties of endogenous phytochrome A in Arabidopsis seedlings. Plant Physiol. 121: 571-578 (1999).

Hernandez-Bermejo B, Fairen V, Sorribas A. Power-law modeling based on least-squares criteria: consequences for system analysis and simulation. Math. Biosci. 167: 87-107 (2000).

Herrero P, Kisrieva-Ware Z, Dence CS, Patterson B, Coggan AR, Han DH, Ishii Y, Eisenbeis P, Gropler RJ. PET measurements of myocardial glucose metabolism with 1-11C-glucose and kinetic modeling. J. Nucl. Med. 48: 955-964 (2007).

Herwig C, Doerries C, Marison I, von Stockar U. Quantitative analysis of the regulation scheme of invertase expression in Saccharomyces cerevisiae. Biotechnol. Bioeng. 76: 247-258 (2001).

Hill CM, Duggleby RG. Mutagenesis of Escherichia coli acetohydroxyacid synthase isoenzyme II and characterization of three herbicide-insensitive forms. Biochem. J. 335: 653-661 (1998).

Ho QT, Verboven P, Verlinden BE, Lammertyn J, Vandewalle S, Nicolai BM. A continuum model for metabolic gas exchange in pear fruit. PLoS Comput. Biol. 4: e1000023 (2008).

Hodgson RJ, Jia Z, Plaxton WC. A fluorescence study of ligand-induced conformational changes in cytosolic fructose-1,6-bisphosphatase from germinating castor oil seeds. Biochim. Biophys. Acta 1388: 285-294 (1998).

Hoefnagel MH, Starrenburg MJ, Martens DE, Hugenholtz J, Kleerebezem M, Van Swam II, Bongers R, Westerhoff HV, Snoep JL. Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology 148: 1003-1013 (2002).

Hofer T, Heinrich R. A second-order approach to metabolic control analysis. J. Theor. Biol. 164: 85-102 (1993).

Holzhutter HG. The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies. Biosystems 83: 98-107 (2006).

Holzhutter HG. Compartmental analysis: theoretical aspects and application. Biomed. Biochim. Acta 44: 863-873 (1985).

Holzhutter HG, Schuster R, Buckwitz D, Jacobasch G. Mathematical modelling of metabolic pathways affected by an enzyme deficiency. Biomed. Biochim. Acta 49: 791-800 (1990).

Holzhutter HG, Schwendel A, Grune T, Quedenau J, Siems W. Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments. Comput. Appl. Biosci. 9: 573-580 (1993).

Hope AB. Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms. Biochim. Biophys. Acta 1456: 5-26 (2000).

Hua Q, Yang C, Shimizu K. Metabolic control analysis for lysine synthesis using Corynebacterium glutamicum and experimental verification. J. Biosci. Bioeng. 90: 184-192 (2000).

Hunter GJ, Hamberg LM, Alpert NM, Choi NC, Fischman AJ. Simplified measurement of deoxyglucose utilization rate. J. Nucl. Med. 37: 950-955 (1996).

Hwang I, Harper JF, Liang F, Sze H. Calmodulin activation of an endoplasmic reticulum-located calcium pump involves an interaction with the N-terminal autoinhibitory domain. Plant Physiol. 122: 157-168 (2000).

Ihekwaba AEC, Broomhead DS, Grimley RL, Benson N, Kell DB. Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kB pathway: the roles of IKK and IkBa. Syst. Biol. 1: 93-103 (2004).

Jackson RC. Toxicity prediction from metabolic pathway modelling. Toxicology 102: 197-205 (1995).

Jackson RH, Cole JA, Cornish-Bowden A. The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction. Biochem. J. 199: 171-178 (1981).

Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286-287 (2001).

Jamshidi N, Palsson BO. Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Comput. Biol. 4: e1000177 (2008).

Jayaraman A, Yarmush ML, Roth CM. Dynamics of gene expression in rat hepatocytes under stress. Metab. Eng. 2: 239-251 (2000).

Johnson TN, Kerbusch T, Jones B, Tucker GT, Rostami-Hodjegan A, Milligan PA. Assessing the efficiency of mixed effects modelling in quantifying metabolism based drug-drug interactions: using in vitro data as an aid to assess study power. Pharm. Stat. 8: 186-202 (2009).

Joshi M, Seidel-Morgenstern A, Kremling A. Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems. Metab. Eng. 8: 447-455 (2006).

Kamgang E, Peyret T, Krishnan K. An integrated QSPR-PBPK modelling approach for in vitro-in vivo extrapolation of pharmacokinetics in rats. SAR QSAR Environ. Res. 19: 669-680 (2008).

Karpen JW, Ruiz M. Ion channels: does each subunit do something on its own? Trends Biochem. Sci. 27: 402-409 (2002).

Kaszycki P, Gabrys H, Appenroth KJ, Jaglarz A, Sedziwy S, Walczak T, Koloczek H. Exogenously applied sulphate as a tool to investigate transport and reduction of chromate in the duckweed Spirodela polyrhiza. Plant Cell Environ. 28: 260-268 (2005).

Keating MJ, Holmes R, Lerner S, Ho DH. L-asparaginase and PEG asparaginase--past, present, and future. Leuk. Lymphoma 10: 153-157 (1993).

Kelley DE, Price JC, Cobelli C. Assessing skeletal muscle glucose metabolism with positron emission tomography. IUBMB Life 52: 279-284 (2001).

Kelly CJ, Hsiung CJ, Lajoie CA. Kinetic analysis of bacterial bioluminescence. Biotechnol. Bioeng. 81: 370-378 (2003).

Kemp GJ, Manners DN, Clark JF, Bastin ME, Radda GK. Theoretical modelling of some spatial and temporal aspects of the mitochondrion/creatine kinase/myofibril system in muscle. Mol. Cell Biochem. 184: 249-289 (1998).

Kersemans V, Cornelissen B, Kersemans K, Dierckx RA, De Spiegeleer B, Mertens J, Slegers G. Comparative biodistribution study of the new tumor tracer [123I]-2-iodo-L-phenylalanine with [123I]-2-iodo-L-tyrosine. Nucl. Med. Biol. 33: 111-117 (2006).

Ketterman AJ, Prommeenate P, Boonchauy C, Chanama U, Leetachewa S, Promtet N, Prapanthadara L. Single amino acid changes outside the active site significantly affect activity of glutathione S-transferases. Insect Biochem. Mol. Biol. 31: 65-74 (2001).

Keusch GT. What do -omics mean for the science and policy of the nutritional sciences? Am. J. Clin. Nutr. 83: 520S-522S (2006).

Khan AI, Chowdhry BZ, Yon RJ. Wheat-germ aspartate transcarbamoylase: revised purification, stability and re-evaluation of regulatory kinetics in terms of the Monod-Wyman-Changeux model. Eur. J. Biochem. 259: 71-78 (1999).

Kiirats O, Lea PJ, Franceschi VR, Edwards GE. Bundle sheath diffusive resistance to CO2 and effectiveness of C(4) photosynthesis and refixation of photorespired CO(2) in a C(4) cycle mutant and wild-type Amaranthus edulis. Plant Physiol. 130: 964-976 (2002).

Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363 (2007).

Kim SJ, Lee JS, Im KC, Kim SY, Park SA, Lee SJ, Oh SJ, Lee DS, Moon DH. Kinetic modeling of 3'-deoxy-3'-18F-fluorothymidine for quantitative cell proliferation imaging in subcutaneous tumor models in mice. J. Nucl. Med. 49: 2057-2066 (2008).

Kinnersley AM, Turano FJ. Gamma aminobutyric acid (GABA) and plant responses to stress. Crit. Rev. Plant Sci. 19: 479-509 (2000).

Kinoshita A, Nakayama Y, Tomita M. Towards simulation of whole metabolic pathways in human erythrocyte. Genome Informatics 12: 312-313 (2001).

Kiss L, Immke D, LoTurco J, Korn SJ. The interaction of Na+ and K+ in voltage-gated potassium channels. Evidence for cation binding sites of different affinity. J. Gen. Physiol. 111: 195-206 (1998).

Kitano H. International alliances for quantitative modeling in systems biology. Mol. Syst. Biol. 1: 2005.0007 (2005).

Kleerebezem R, Stams AJ. Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation. Biotechnol. Bioeng. 67: 529-543 (2000).

Kleijn RJ, van Winden WA, van Gulik WM, Heijnen JJ. Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence. FEBS J. 272: 4970-4982 (2005).

Klein CT, Mayer B. Sources for structure formation and switches in metabolic pathways. Biosystems 51: 41-52 (1999).

Knapp MJ, Klinman JP. Environmentally coupled hydrogen tunneling. Linking catalysis to dynamics. Eur. J. Biochem. 269: 3113-3121 (2002).

Kocheva KV, Georgiev GI, Kochev VK. A diffusion approach to the electrolyte leakage from plant tissues. Physiol. Plant. 125: 1-9 (2005).

Kolch W, Calder M, Gilbert D. When kinases meet mathematics: the systems biology of MAPK signalling. FEBS Lett. 579: 1891-1895 (2005).

Koller M, Horvat P, Hesse P, Bona R, Kutschera C, Atlic A, Braunegg G. Assessment of formal and low structured kinetic modeling of polyhydroxyalkanoate synthesis from complex substrates. Bioprocess. Biosyst. Eng. 29: 367-377 (2006).

Koo CW, Blanchard JS. Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase. Biochemistry 38: 4416-4422 (1999).

Korzeniewski B. Is it possible to predict any properties of oxidative phosphorylation in a theoretical way? Mol. Cell Biochem. 184: 345-358 (1998).

Kotb M, Kredich NM. Regulation of human lymphocyte S-adenosylmethionine synthetase by product inhibition. Biochim. Biophys. Acta 1039: 253-260 (1990).

Krab K. Kinetic and regulatory aspects of the function of the alternative oxidase in plant respiration. J. Bioenerg. Biomembr. 27: 387-396 (1995).

Krappmann S, Helmstaedt K, Gerstberger T, Eckert S, Hoffmann B, Hoppert M, Schnappauf G, Braus GH. The aroC gene of Aspergillus nidulans codes for a monofunctional, allosterically regulated chorismate mutase. J. Biol. Chem. 274: 22275-22282 (1999).

Kreim M, Giersch C. Measuring in vivo elasticities of Calvin cycle enzymes: network structure and patterns of modulations. Phytochemistry 68: 2152-2162 (2007).

Kresnowati MT, van Winden WA, Heijnen JJ. Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics. Metab. Eng. 7: 142-153 (2005).

Krishnaswamy S, Bryan JK. Ligand-induced interconversions of maize homoserine dehydrogenase among different states. Arch. Biochem. Biophys. 222: 449-463 (1983).

Kucera I. Inhibition by phenylglyoxal of nitrate transport in Paracoccus denitrificans: a comparison with the effect of a protonophorous uncoupler. Arch. Biochem. Biophys. 409: 327-334 (2003).

Kummel A, Panke S, Heinemann M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2: 2006.0034 (2006).

Kusnan MB, Klug K, Fock HP. Ammonia assimilation by Aspergillus nidulans: [15N]ammonia study. J. Gen. Microbiol. 135: 729-738 (1989).

Laisk A, Eichelmann H, Oja V. C3 photosynthesis in silico. Photosynth. Res. 90: 45-66 (2006).

Langdon G, Wilkins J, McFadyen L, McIlleron H, Smith P, Simonsson US. Population pharmacokinetics of rifapentine and its primary desacetyl metabolite in South African tuberculosis patients. Antimicrob. Agents Chemother. 49: 4429-4436 (2005).

Larsson JA, Pardue HL. Linearized model for error-compensated kinetic determinations without prior knowledge of reaction order or rate constant. Anal. Chem. 61: 1949-1954 (1989).

Latowski D, Burda K, Strzalka K. A mathematical model describing kinetics of conversion of violaxanthin to zeaxanthin via intermediate antheraxanthin by the xanthophyll cycle enzyme violaxanthin de-epoxidase. J. Theor. Biol. 206: 507-514 (2000).

Latowski D, Kruk J, Burda K, Skrzynecka-Jaskier M, Kostecka-Gugala A, Strzalka K. Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophyll cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Eur. J. Biochem. 269: 4656-4665 (2002).

Leaf TA, Srienc F. Metabolic modeling of polyhydroxybutyrate biosynthesis. Biotechnol. Bioeng. 57: 557-570 (1998).

Lee B, Yen J, Yang L, Liao JC. Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic. Biotechnol. Bioeng. 62: 722-729 (1999).

Lee DC, Park JH, Kim GJ, Kim HS. Modeling, simulation, and kinetic analysis of a heterogeneous reaction system for the enzymatic conversion of poorly soluble substrate. Biotechnol. Bioeng. 64: 272-283 (1999).

Lee DY, Saha R, Yusufi FN, Park W, Karimi IA. Web-based applications for building, managing and analysing kinetic models of biological systems. Brief. Bioinform. 10: 65-74 (2009).

Lee DY, Yun C, Cho A, Hou BK, Park S, Lee SY. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 22: 1150-1151 (2006).

Lee DY, Zimmer R, Lee SY, Park S. Colored Petri net modeling and simulation of signal transduction pathways. Metab. Eng. 8: 112-122 (2006).

Lee YS, Cho YD. Identification of essential active-site residues in ornithine decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and L-lysine. Biochem. J. 360: 657-665 (2001).

Legendre L, Rueter S, Heinstein PF, Low PS. Characterization of the oligogalacturonide-induced oxidative burst in cultured soybean (Glycine max) cells. Plant Physiol. 102: 233-240 (1993).

Lemerle C, Di Ventura B, Serrano L. Space as the final frontier in stochastic simulations of biological systems. FEBS Lett. 579: 1789-1794 (2005).

Lemoff AS, Williams ER. Binding energies of water to lithiated valine: formation of solution-phase structure in vacuo. J. Am. Soc. Mass Spectrom. 15: 1014-1024 (2004).

Letisse F, Lindley ND, Roux G. Development of a phenomenological modeling approach for prediction of growth and xanthan gum production using Xanthomonas campestris. Biotechnol. Prog. 19: 822-827 (2003).

Leubner-Metzger G. Seed after-ripening and over-expression of class I beta-1,3-glucanase confer maternal effects on tobacco testa rupture and dormancy release. Planta 215: 959-968 (2002).

Lexa M, Genkov T, Malbeck J, Machackova I, Brzobohaty B. Dynamics of endogenous cytokinin pools in tobacco seedlings: a modelling approach. Ann. Bot. (Lond.) 91: 585-597 (2003).

Li J, Wang S, VanDusen WJ, Schultz LD, George HA, Herber WK, Chae HJ, Bentley WE, Rao G. Green fluorescent protein in Saccharomyces cerevisiae: real-time studies of the GAL1 promoter. Biotechnol. Bioeng. 70: 187-196 (2000).

Li JF, Qu LH, Li N. Tyr152 plays a central role in the catalysis of 1-aminocyclopropane-1-carboxylate synthase. J. Exp. Bot. 56: 2203-2210 (2005).

Li Y, Feng L, Kirsch JF. Kinetic and spectroscopic investigations of wild-type and mutant forms of apple 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 36: 15477-15488 (1997).

Li Y, Goldbeter A. Oscillatory isozymes as the simplest model for coupled biochemical oscillators. J. Theor. Biol. 138: 149-174 (1989).

Liebermeister W. Predicting physiological concentrations of metabolites from their molecular structure. J. Comput. Biol. 12: 1307-1315 (2005).

Liebermeister W. Response to temporal parameter fluctuations in biochemical networks. J. Theor. Biol. 234: 423-438 (2005).

Liebermeister W, Baur U, Klipp E. Biochemical network models simplified by balanced truncation. FEBS J. 272: 4034-4043 (2005).

Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor. Biol. Med. Model. 3: 41 (2006).

Liebermeister W, Klipp E. Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med. Model. 3: 42 (2006).

Lillo C, Ruoff P. Hysteretic behavior of nitrate reductase. Evidence of an allosteric binding site for reduced pyridine nucleotides. J. Biol. Chem. 267: 13456-13459 (1992).

Lin BF, Kim JS, Hsu JC, Osborne C, Lowe K, Garrow T, Shane B. Molecular biology in nutrition research: modeling of folate metabolism. Adv. Food Nutr. Res. 40: 95-106 (1996).

Lin YP, Hsu FL, Chen CS, Chern JW, Lee MH. Constituents from the Formosan apple reduce tyrosinase activity in human epidermal melanocytes. Phytochemistry 68: 1189-1199 (2007).

Lipscomb JC, Poet TS. In vitro measurements of metabolism for application in pharmacokinetic modeling. Pharmacol. Ther. 118: 82-103 (2008).

Liu PK, Wang FS. Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics 24: 1085-1092 (2008).

Llaneras F, Pico J. Stoichiometric modelling of cell metabolism. J. Biosci. Bioeng. 105: 1-11 (2008).

Locatelli F, Di Filippo S, Manzoni C. Relevance of the conductivity kinetic model in the control of sodium pool. Kidney Int. 58 Suppl. 76: S89-S95 (2000).

Lohr M, Wilhelm C. Xanthophyll synthesis in diatoms: quantification of putative intermediates and comparison of pigment conversion kinetics with rate constants derived from a model. Planta 212: 382-391 (2001).

Lopez C, Chevalier N, Hannaert V, Rigden DJ, Michels PA, Ramirez JL. Leishmania donovani phosphofructokinase. Gene characterization, biochemical properties and structure-modeling studies. Eur. J. Biochem. 269: 3978-3989 (2002).

Maathuis FJ, Sanders D, Gradmann D. Kinetics of high-affinity K+ uptake in plants, derived from K(+)-induced changes in current-voltage relationships. A modelling approach to the analysis of carrier-mediated transport. Planta 203: 229-236 (1997).

MacCleery SA, Kiss JZ. Plastid sedimentation kinetics in roots of wild-type and starch-deficient mutants of Arabidopsis. Plant Physiol. 120: 183-192 (1999).

MacRae I, Segel IH. ATP sulfurylase from filamentous fungi: which sulfonucleotide is the true allosteric effector? Arch. Biochem. Biophys. 337: 17-26 (1997).

Majumder K, Selvapandiyan A, Fattah FA, Arora N, Ahmad S, Bhatnagar RK. 5-Enolpyruvylshikimate-3-phosphate synthase of Bacillus subtilis is an allosteric enzyme. Analysis of Arg24-->Asp, Pro105-->Ser and His385-->Lys mutations suggests a hidden phosphoenolpyruvate-binding site. Eur. J. Biochem. 229: 99-106 (1995).

Malagoli P, Britto DT, Schulze LM, Kronzucker HJ. Futile Na+ cycling at the root plasma membrane in rice (Oryza sativa L.): kinetics, energetics, and relationship to salinity tolerance. J. Exp. Bot. 59: 4109-4117 (2008).

Malagoli P, Laine P, Le Deunff E, Rossato L, Ney B, Ourry A. Modeling nitrogen uptake in oilseed rape cv Capitol during a growth cycle using influx kinetics of root nitrate transport systems and field experimental data. Plant Physiol. 134: 388-400 (2004).

Malphettes L, Fussenegger M. Impact of RNA interference on gene networks. Metab. Eng. 8: 672-683 (2006).

Maniscalco SJ, Saha SK, Fisher HF. Identification and characterization of kinetically competent carbinolamine and alpha-iminoglutarate complexes in the glutamate dehydrogenase-catalyzed oxidation of L-glutamate using a multiwavelength transient state approach. Biochemistry 37: 14585-14590 (1998).

Markham GD, Reczkowski RS. Structural studies of inhibition of S-adenosylmethionine synthetase by slow, tight-binding intermediate and product analogues. Biochemistry 43: 3415-3425 (2004).

Markova M, Peneff C, Hewlins MJ, Schirmer T, John RA. Determinants of substrate specificity in omega-aminotransferases. J. Biol. Chem. 280: 36409-36416 (2005).

Martelli C, De Martino A, Marinari E, Marsili M, Castillo IP. Identifying essential genes in Escherichia coli from a metabolic optimization principle. Proc. Natl. Acad. Sci. U.S.A. 106: 2607-2611 (2009).

Martinez MB, Flickinger MC, Nelsestuen GL. Steady-state enzyme kinetics in the Escherichia coli periplasm: a model of whole cell biocatalyst. J. Biotechnol. 71: 59-66 (1999).

Martinov MV, Vitvitsky VM, Mosharov EV, Banerjee R, Ataullakhanov FI. A substrate switch: a new mode of regulation in the methionine metabolic pathway. J. Theor. Biol. 204: 521-532 (2000).

Marzabadi MR, Gruys KJ, Pansegrau PD, Walker MC, Yuen HK, Sikorski JA. An EPSP synthase inhibitor joining shikimate 3-phosphate with glyphosate: synthesis and ligand binding studies. Biochemistry 35: 4199-4210 (1996).

Massiah A. Physiology and metabolism - web alert. Curr. Opin. Plant Biol. 3: 177-178 (2000).

Matheson LA, Hanton SL, Rossi M, Latijnhouwers M, Stefano G, Renna L, Brandizzi F. Multiple roles of ADP-ribosylation factor 1 in plant cells include spatially regulated recruitment of coatomer and elements of the Golgi matrix. Plant Physiol. 143: 1615-1627 (2007).

Mayer SM, Gawlita E, Avissar YJ, Anderson VE, Beale SI. Intermolecular nitrogen transfer in the enzymic conversion of glutamate to d-aminolevulinic acid by extracts of Chlorella vulgaris. Plant Physiol. 101: 1029-1038 (1993).

McAdams HH, Shapiro L. Circuit simulation of genetic networks. Science 269: 650-656 (1995).

McMahon M, Mulcahy P. Bioaffinity purification of NADP(+)-dependent dehydrogenases: Studies with alcohol dehydrogenase from Thermoanaerobacter brockii. Biotechnol. Bioeng. 77: 517-527 (2002).

McMahon M, Tynan J, Mulcahy P. Kinetic locking-on and auxiliary tactics for bioaffinity purification of NADP+-dependent dehydrogenases using N6-linked immobilized NADP+ derivatives: Studies with mammalian and microbial glutamate dehydrogenases. Biotechnol. Bioeng. 81: 356-369 (2003).

McNeil SD, Nuccio ML, Rhodes D, Shachar-Hill Y, Hanson AD. Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco. Plant Physiol. 123: 371-380 (2000).

McNeil SD, Rhodes D, Russell BL, Nuccio ML, Shachar-Hill Y, Hanson AD. Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco. Plant Physiol. 124: 153-162 (2000).

McNevin D, von Caemmerer S, Farquhar G. Determining RuBisCO activation kinetics and other rate and equilibrium constants by simultaneous multiple non-linear regression of a kinetic model. J. Exp. Bot. 57: 3883-3900 (2006).

McQueney MS, Anderson KS, Markham GD. Energetics of S-adenosylmethionine synthetase catalysis. Biochemistry 39: 4443-4454 (2000).

Meijer SC, Van Loosdrecht MC, Heijnen JJ. Metabolic modelling of full-scale biological nitrogen and phosphorus removing wwtp's. Water Res. 35: 2711-2723. (2001).

Melin JA, Vanoverschelde JL, Bol A, Heyndrickx G, Wijns W. The use of carbon 11-labeled acetate for assessment of aerobic metabolism. J. Nucl. Cardiol. 1: S48-S57 (1994).

Mendes P, Kell D. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883 (1998).

Mendes P, Kell DB. On the analysis of the inverse problem of metabolic pathways using artificial neural networks. Biosystems 38: 15-28 (1996).

Mendes P, Kell DB, Westerhoff HV. Channelling can decrease pool size. Eur. J. Biochem. 204: 257-266 (1992).

Mendes P, Sha W, Ye K. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19 Suppl. 2: II122-II129 (2003).

Mendoza-Cozatl DG, Moreno-Sanchez R. Control of glutathione and phytochelatin synthesis under cadmium stress. Pathway modeling for plants. J. Theor. Biol. 238: 919-936 (2006).

Miller GP. Advances in the interpretation and prediction of CYP2E1 metabolism from a biochemical perspective. Expert Opin. Drug Metab. Toxicol. 4: 1053-1064 (2008).

Min Lee J, Gianchandani EP, Eddy JA, Papin JA. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4: e1000086 (2008).

Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A. Dynamic simulations on the mitochondrial fatty acid beta-oxidation network. BMC Syst. Biol. 3: 2 (2009).

Moehren G, Markevich N, Demin O, Kiyatkin A, Goryanin I, Hoek JB, Kholodenko BN. Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry 41: 306-320 (2002).

Monero A, Lanza L, Zilli M, Sene L, Converti A. Batch kinetics of Pseudomonas sp. growth on benzene. modeling of product and substrate inhibitions. Biotechnol. Prog. 19: 676-679 (2003).

Morbiducci U, Andrea Tura, Grigioni M. Genetic algorithms for parameter estimation in mathematical modeling of glucose metabolism. Comput. Biol. Med. 35: 862-874 (2005).

Moreno-Sanchez R, Encalada R, Marin-Hernandez A, Saavedra E. Experimental validation of metabolic pathway modeling. An illustration with glycotic segments from Entamoeba histolytica. FEBS J. 275: 3454-3469 (2008).

Morgan JA, Rhodes D. Mathematical modeling of plant metabolic pathways. Metab. Eng. 4: 80-89 (2002).

Moroni A, Bardella L, Thiel G. The impermeant ion methylammonium blocks K+ and NH4+ currents through KAT1 channel differently: evidence for ion interaction in channel permeation. J. Membr. Biol. 163: 25-35 (1998).

Mulquiney PJ, Bubb WA, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations in vivo kinetic characterization of 2,3-bisphosphoglycerate synthase/phosphatase using C-13 and P-31 NMR. Biochem. J. 342: 567-580 (1999).

Mulquiney PJ, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. Biochem. J. 342: 581-596 (1999).

Mulquiney PJ, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and Metabolic Control Analysis. Biochem. J. 342: 597-604 (1999).

Murase K, Mochizuki T, Kikuchi T, Ikezoe J. Kinetic parameter estimation from compartment models using a genetic algorithm. Nucl. Med. Commun. 20: 925-932 (1999).

Murphy EF, Gilmour SG, Crabbe MJ. Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics. FEBS Lett. 556: 193-198 (2004).

Myers JK, Oas TG. Mechanism of fast protein folding. Annu. Rev. Biochem. 71: 783-815 (2002).

Nagpal S, Chuichulcherm S, Livingston A, Peeva L. Ethanol utilization by sulfate-reducing bacteria: an experimental and modeling study. Biotechnol. Bioeng. 70: 533-543 (2000).

Nakayama Y, Matsushima R, Tomita M. Computer simulation of human erythrocyte using the E-cell system. Genome Informatics 10: 364-365 (1999).

Natarajan A, Srienc F. Dynamics of glucose uptake by single Escherichia coli cells. Metab. Eng. 1: 320-333 (1999).

Nath S, Jain S. Kinetic modeling of ATP synthesis by ATP synthase and its mechanistic implications. Biochem. Biophys. Res. Commun. 272: 629-633 (2000).

Neubauer P, Lin HY, Mathiszik B. Metabolic load of recombinant protein production: Inhibition of cellular capacities for glucose uptake and respiration after induction of a heterologous gene in Escherichia coli. Biotechnol. Bioeng. 83: 53-64 (2003).

Neves AR, Ramos A, Nunes MC, Kleerebezem M, Hugenholtz J, de Vos WM, Almeida J, Santos H. In vivo nuclear magnetic resonance studies of glycolytic kinetics in Lactococcus lactis. Biotechnol. Bioeng. 64: 200-212 (1999).

Ni TC, Savageau MA. Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J. Biol. Chem. 271: 7927-7941 (1996).

Nielsen J. Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58: 125-132 (1998).

Nikerel IE, van Winden WA, Verheijen PJ, Heijnen JJ. Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics. Metab. Eng. 11: 20-30 (2009).

Nunes C, Han J, Monkhouse DC, Suryanarayanan R. Preformulation studies to meet the challenges in the manufacture of betaine solid dosage form. J. Pharm. Sci. 93: 38-47 (2004).

Nuno JC, Sanchez-Valdenebro I, Perez-Iratxeta C, Melendez-Hevia E, Montero F. Network organization of cell metabolism: monosaccharide interconversion. Biochem. J. 324: 103-111 (1997).

O'Flaherty M, O'Carra P, McMahon M, Mulcahy P. A "stripping" ligand tactic for use with the kinetic locking-on strategy: its use in the resolution and bioaffinity chromatographic purification of NAD(+)-dependent dehydrogenases. Protein Expr. Purif. 16: 424-431 (1999).

Ohno H, Naito Y, Nakajima H, Tomita M. Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule. Artif. Life 14: 3-28 (2008).

Olah J, Orosz F, Puskas LG, Hackler L Jr, Horanyi M, Polgar L, Hollan S, Ovadi J. Triosephosphate isomerase deficiency: consequences of an inherited mutation at mRNA, protein and metabolic levels. Biochem J. 392: 675-683 (2005).

Olsen KM, Slimestad R, Lea US, Brede C, Lovdal T, Ruoff P, Verheul M, Lillo C. Temperature and nitrogen effects on regulators and products of the flavonoid pathway: experimental and kinetic model studies. Plant Cell Environ. 32: 286-299 (2009).

Owen MR, Sherratt JA. Mathematical modelling of juxtacrine cell signalling. Math Biosci. 153: 125-150 (1998).

Palmieri M, Kiss JZ. Disruption of the F-actin cytoskeleton limits statolith movement in Arabidopsis hypocotyls. J. Exp. Bot. 56: 2539-2550 (2005).

Palsson BO, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. V. Static bifurcations in single biochemical control loops. J. Theor. Biol. 113: 279-298 (1985).

Palsson BO, Palsson H, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. III. Linear reaction sequences. J. Theor. Biol. 113: 231-259 (1985).

Pan Y, Durfee T, Bockhorst J, Craven M. Connecting quantitative regulatory-network models to the genome. Bioinformatics 23: i367-i376 (2007).

Park LJ, Park CH, Park C, Lee T. Application of genetic algorithms to parameter estimation of bioprocesses. Med. Biol. Eng. Comput. 35: 47-49 (1997).

Pavan A, Thomaseth K, Valerio A. Modeling population kinetics of free fatty acids in isolated rat hepatocytes using Markov Chain Monte Carlo. Ann. Biomed. Eng. 31: 854-866 (2003).

Personeni E, Nguyen C, Marchal P, Pages L. Experimental evaluation of an efflux-influx model of C exudation by individual apical root segments. J. Exp. Bot. 58: 2091-2099 (2007).

Peters WS, Knoblauch M, Warmann SA, Schnetter R, Shen AQ, Pickard WF. Tailed forisomes of Canavalia gladiata: a new model to study Ca2+-driven protein contractility. Ann. Bot. (Lond.) 100: 101-109 (2007).

Petkov SB, Maranas CD. Quantitative assessment of uncertainty in the optimization of metabolic pathways. Biotechnol. Bioeng. 56: 145-161 (1997).

Pettersson G. Control properties of the Calvin photosynthesis cycle at physiological carbon dioxide concentrations. Biochim. Biophys. Acta 1322: 173-182 (1997).

Pettersson G, Ryde-Pettersson U. A rapid-equilibrium model for the control of the Calvin photosynthesis cycle by cytosolic orthophosphate. Eur. J. Biochem. 169: 423-429 (1987).

Pettersson G, Ryde-Pettersson U. Model studies of the regulation of the Calvin photosynthesis cycle by cytosolic metabolites. Biomed. Biochim. Acta 49: 723-732 (1990).

Phair RD. Development of kinetic models in the nonlinear world of molecular cell biology. Metabolism 46: 1489-1495 (1997).

Pham HT, Larsson G, Enfors SO. Growth and energy metabolism in aerobic fed-batch cultures of Saccharomyces cerevisiae: simulation and model verification. Biotechnol. Bioeng. 60: 474-482 (1998).

Piert M, Zittel TT, Becker GA, Jahn M, Stahlschmidt A, Maier G, Machulla HJ, Bares R. Assessment of porcine bone metabolism by dynamic. J. Nucl. Med. 42: 1091-1100 (2001).

Pineda T, Churchich JE. Unfolding of 4-aminobutyrate aminotransferase equilibrium and kinetic studies. Biochim. Biophys. Acta 1207: 173-178 (1994).

Pitt RE, Chandrasekaran M, Parks JE. Performance of a kinetic model for intracellular ice formation based on the extent of supercooling. Cryobiology 29: 359-373 (1992).

Polle A. Dissecting the superoxide dismutase-ascorbate-glutathione-pathway in chloroplasts by metabolic modeling. Computer simulations as a step towards flux analysis. Plant Physiol. 126: 445-462 (2001).

Pont F, Duvillard L, Verges B, Gambert P. Development of compartmental models in stable-isotope experiments: application to lipid metabolism. Arterioscler. Thromb. Vasc. Biol. 18: 853-860 (1998).

Poolman MG, Fell DA. Modelling and experimental evidence for two separate steady states in the photosynthetic Calvin cycle. In: "Animating the cellular map" (Hofmeyr J-HS, Rohwer JM, Snoep JL eds) Stellenbosch Press, Stellenbosch, pp. 249-254 (2000).

Poolman MG, Assmus HE, Fell DA. Applications of metabolic modelling to plant metabolism. J. Exp. Bot. 55: 1177-1186 (2004).

Pottosin II, Martinez-Estevez M, Dobrovinskaya OR, Muniz J, Schonknecht G. Mechanism of luminal Ca2+ and Mg2+ action on the vacuolar slowly activating channels. Planta 219: 1057-1070 (2004).

Powles JE, Buckley TN, Nicotra AB, Farquhar GD. Dynamics of stomatal water relations following leaf excision. Plant Cell Environ. 29: 981-992 (2006).

Prasannan P, Suliman HS, Robertus JD. Kinetic analysis of site-directed mutants of methionine synthase from Candida albicans. Biochem. Biophys. Res. Commun. 382: 730-734 (2009).

Prathumpai W, Gabelgaard JB, Wanchanthuek P, Van De Vondervoort PJ, De Groot MJ, McIntyre M, Nielsen J. Metabolic control analysis of xylose catabolism in Aspergillus. Biotechnol. Prog. 19: 1136-1141 (2003).

Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. J. Theor. Biol. 225: 185-194 (2003).

Price WD, Jockusch RA, Williams ER. Binding energies of protonated betaine complexes: a probe of zwitterion structure in the gas phase. J. Am. Chem. Soc. 120: 3474-3484 (1998).

Prokudina EI, Valeev RYu, Tchuraev RN. A new method for the analysis of the dynamics of the molecular genetic control systems. II. Application of the method of generalized threshold models in the investigation of concrete genetic systems. J. Theor. Biol. 151: 89-110 (1991).

Pross A. The driving force for life's emergence: kinetic and thermodynamic considerations. J. Theor. Biol. 220: 393-406 (2003).

Prudhomme MP, Moore TS. Phosphatidylcholine synthesis in castor bean endosperm: free bases as intermediates. Plant Physiol. 100: 1527-1535 (1992).

Przybilski R, Graf S, Lescoute A, Nellen W, Westhof E, Steger G, Hammann C. Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell 17: 1877-1885 (2005).

Puigjaner J, Rais B, Burgos M, Comin B, Ovadi J, Cascante M. Comparison of control analysis data using different approaches: modelling and experiments with muscle extract. FEBS Lett. 418: 47-52 (1997).

Rabeh WM, Mather T, Cook PF. A three-dimensional homology model of the O-acetylserine sulfhydrylase-B from Salmonella typhimurium. Protein Pept. Lett. 13: 7-13 (2006).

Radulescu O, Gorban AN, Zinovyev A, Lilienbaum A. Robust simplifications of multiscale biochemical networks. BMC Syst. Biol. 2: 86 (2008).

Rajagopalan K, Watt DS, Haley BE. Orientation of GTP and ADP within their respective binding sites in glutamate dehydrogenase. Eur. J. Biochem. 265: 564-571 (1999).

Raman K, Chandra N. Flux balance analysis of biological systems: applications and challenges. Brief. Bioinform. 10: 435-449 (2009).

Ramirez DM, Bentley WE. Characterization of stress and protein turnover from protein overexpression in fed-batch E. coli cultures. J. Biotechnol. 71: 39-58 (1999).

Ranaldi F, Vanni P, Giachetti E. Multisite inhibition of Pinus pinea isocitrate lyase by phosphate. Plant Physiol. 124: 1131-1138 (2000).

Ranocha P, McNeil SD, Ziemak MJ, Li C, Tarczynski MC, Hanson AD. The S-methylmethionine cycle in angiosperms: ubiquity, antiquity and activity. Plant J. 25: 575-584 (2001).

Reed MC, Nijhout HF, Neuhouser ML, Gregory JF 3rd, Shane B, James SJ, Boynton A, Ulrich CM. A mathematical model gives insights into nutritional and genetic aspects of folate-mediated one-carbon metabolism. J. Nutr. 136: 2653-2661 (2006).

Reed MC, Nijhout HF, Sparks R, Ulrich CM. A mathematical model of the methionine cycle. J. Theor. Biol. 226: 33-43 (2004).

Reo NV, Adinehzadeh M, Foy BD. Kinetic analyses of liver phosphatidylcholine and phosphatidylethanolamine biosynthesis using 13C NMR spectroscopy. Biochim. Biophys. Acta 1580: 171-188 (2002).

Resendis-Antonio O. Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking. PLoS One 4: e4967 (2009).

Reyes-Palomares A, Montanez R, Real-Chicharro A, Chniber O, Kerzazi A, Navas-Delgado I, Medina MA, Aldana-Montes JF, Sanchez-Jimenez F. Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics 25: 834-835 (2009).

Rhodes D, McNeil SD, Nuccio ML, Hanson AD. Metabolic engineering and flux analysis of glycine betaine synthesis in plants: progress and prospects. In (BN Kholodenko, HV Westerhoff, eds.) "Metabolic Engineering in the Post Genomic Era", Horizon Bioscience, Wymondham, Norfolk, U.K., pp. 409-434 (2004).

Riahi E, Ramaswamy HS. High-pressure processing of apple juice: kinetics of pectin methyl esterase inactivation. Biotechnol. Prog. 19: 908-914 (2003).

Rietveld PL, Wilkinson C, Franssen HM, Balk PA, van der Plas LH, Weisbeek PJ, Douwe de Boer A. Low temperature sensing in tulip (Tulipa gesneriana L.) is mediated through an increased response to auxin. J. Exp. Bot. 51: 587-594 (2000).

Rios-Estepa R, Lange BM. Experimental and mathematical approaches to modeling plant metabolic networks. Phytochemistry 68: 2351-2374 (2007).

Rios-Estepa R, Turner GW, Lee JM, Croteau RB, Lange BM. A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint. Proc. Natl. Acad. Sci. U.S.A. 105: 2818-2823 (2008).

Rizzi M, Baltes M, Theobald U, Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 2. Mathematical model. Biotechnol. Bioeng. 55: 592-608 (1997).

Robertson MD, Livesey G, Mathers JC. Quantitative kinetics of glucose appearance and disposal following a 13C-labelled starch-rich meal: comparison of male and female subjects. Br. J. Nutr. 87: 569-577 (2002).

Rodriguez-Caso C, Montanez R, Cascante M, Sanchez-Jimenez F, Medina MA. Mathematical modeling of polyamine metabolism in mammals. J. Biol. Chem. 281: 21799-21812 (2006).

Rogers A, Allen DJ, Davey PA, Morgan PB, Ainsworth EA, Bernacchi CJ, Cornic G, Dermody O, Dohleman FG, Heaton EA, Mahoney J, Zhu XG, Delucia EH, Ort DR, Long SP. Leaf photosynthesis and carbohydrate dynamics of soybeans grown throughout their life-cycle under Free-Air Carbon dioxide Enrichment. Plant Cell Environ. 27: 449-458 (2004).

Rohwer JM, Botha FC. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358: 437-445 (2001).

Rohwer JM, Postma PW, Kholodenko BN, Westerhoff HV. Implications of macromolecular crowding for signal transduction and metabolite channeling. Proc. Natl. Acad. Sci. U.S.A. 95: 10547-10552 (1998).

Rossell S, van der Weijden CC, Kruckeberg A, Bakker BM, Westerhoff HV. Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity. Mol. Biol. Rep. 29: 255-257 (2002).

Rossini L, Bernardi M, Concettoni C, De Florio L, Deslauriers R, Moretti V, Piantelli F, Pigini P, Re L, Rossini P, et al. Some approaches to the pharmacology of multisubstrate enzyme systems. Pharmacol. Res. 29: 313-335 (1994).

Rother D, Poppe L, Morlock G, Viergutz S, Retey J. An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum. Eur. J. Biochem. 269: 3065-3075 (2002).

Rother D, Poppe L, Viergutz S, Langer B, Retey J. Characterization of the active site of histidine ammonia-lyase from Pseudomonas putida. Eur. J. Biochem. 268: 6011-6019 (2001).

Rubio FC, Camacho FG, Sevilla JM, Chisti Y, Grima EM. A mechanistic model of photosynthesis in microalgae. Biotechnol. Bioeng. 81: 459-473 (2003).

Rudy Y. From genome to physiome: integrative models of cardiac excitation. Ann. Biomed. Eng. 28: 945-950 (2000).

Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318: 809-812 (2007).

Ryde-Pettersson U. Identification of possible two-reactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways. Eur. J. Biochem. 198: 613-619 (1991).

Ryde-Pettersson U. Oscillations in coupled enzymatic reactions at high concentration of enzyme. Biochim. Biophys. Acta 1119: 118-122 (1992).

Sainz J, Pizarro F, Perez-Correa JR, Agosin E. Modeling of yeast metabolism and process dynamics in batch fermentation. Biotechnol. Bioeng. 81: 818-828 (2003).

Saks V, Dos Santos P, Gellerich FN, Diolez P. Quantitative studies of enzyme-substrate compartmentation, functional coupling and metabolic channelling in muscle cells. Mol. Cell Biochem. 184: 291-307 (1998).

Salvador A. Synergism analysis of biochemical systems. II. Tensor formulation and treatment of stoichiometric constraints. Math. Biosci. 163: 131-158 (2000).

Sanyal SC, Bhattacharyya D, Das Gupta C. The folding of dimeric cytoplasmic malate dehydrogenase. Equilibrium and kinetic studies. Eur. J. Biochem. 269: 3856-3866 (2002).

Sasaki C, Itoh Y, Takehara H, Kuhara S, Fukamizo T. Family 19 chitinase from rice (Oryza sativa L.): substrate-binding subsites demonstrated by kinetic and molecular modeling studies. Plant Mol. Biol. 52: 43-52 (2003).

Sauro HM. SCAMP: a general-purpose simulator and metabolic control analysis program. Comput. Appl. Biosci. 9: 441-450 (1993).

Schmidt H, Jacobsen EW. Linear systems approach to analysis of complex dynamic behaviours in biochemical networks. Syst. Biol. 1: 149-158 (2004).

Schroen CG, Nierstrasz VA, Moody HM, Hoogschagen MJ, Kroon PJ, Bosma R, Beeftink HH, Janssen AE, Tramper J. Modeling of the enzymatic kinetic synthesis of cephalexin--influence of substrate concentration and temperature. Biotechnol. Bioeng. 73: 171-178 (2001).

Schulz AR, Sudi J. Control analysis of single enzyme sequences with abortive complexes and random substrate binding. J. Theor. Biol. 182: 397-403 (1996).

Schuster S, Marhl M, Hofer T. Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling. Eur. J. Biochem. 269: 1333-1355 (2002).

Schwartz JM, Kanehisa M. Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7: 186 (2006).

Selivanov VA, Meshalkina LE, Solovjeva ON, Kuchel PW, Ramos-Montoya A, Kochetov GA, Lee PW, Cascante M. Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. Bioinformatics 21: 3558-3564 (2005).

Selivanov VA, Sukhomlin T, Centelles JJ, Lee PW, Cascante M. Integration of enzyme kinetic models and isotopomer distribution analysis for studies of in situ cell operation. BMC Neurosci. 7 Suppl. 1: S7 (2006).

Senger RS, Karim MN. Effect of shear stress on intrinsic CHO culture state and glycosylation of recombinant tissue-type plasminogen activator protein. Biotechnol. Prog. 19: 1199-1209 (2003).

Shames SL, Wedler FC. Homoserine kinase of Escherichia coli: kinetic mechanism and inhibition by L-aspartate semialdehyde. Arch. Biochem. Biophys. 235: 359-370 (1984).

Shanks JV, Stephanopoulos G. Biochemical engineering. Bridging the gap between gene and product. Curr. Opin. Biotechnol. 11: 169-170 (2000).

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504 (2003).

Shen P, Larter R. Role of substrate inhibition kinetics in enzymatic chemical oscillations. Biophys. J. 67: 1414-1428 (1994).

Shin HC, Shim HO, Ahn SC, Cho JH, Chung MK, Han SS, Roh JK. Pharmacokinetic analysis for assessing developmental toxicity of a new synthetic acetolactate synthase inhibitor, LGC-40863, in rats. J. Pharmacol. Exp. Ther. 285: 795-799 (1998).

Shin JS, Kim BG. Kinetic modeling of omega-transamination for enzymatic kinetic resolution of alpha-methylbenzylamine. Biotechnol. Bioeng. 60: 534-540 (1998).

Shioya H, Mineura K, Kowada M, Iida H, Murakami M, Ogawa T, Hatazawa J, Uemura K. Hemocirculation and metabolism in intraventricular tumors: kinetic analysis of glucose metabolism. No Shinkei Geka 24: 211-219 (1996).

Shrestha R, Kim SC, Dyer JM, Dixon RA, Chapman KD. Plant fatty acid (ethanol) amide hydrolases. Biochim. Biophys. Acta 1761: 324-334 (2006).

Sicilia F, Fernandez-Recio J, Caprari C, De Lorenzo G, Tsernoglou D, Cervone F, Federici L. The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea. Plant Physiol. 139: 1380-1388 (2005).

Sielewiesiuk J, Gruszecki WI. A simple model describing the kinetics of the xanthophyll cycle. Biophys. Chem. 41: 125-129 (1991).

Sin G, Odman P, Petersen N, Lantz AE, Gernaey KV. Matrix notation for efficient development of first-principles models within PAT applications: integrated modeling of antibiotic production with Streptomyces coelicolor. Biotechnol. Bioeng. 101: 153-171 (2008).

Singh VK, Ghosh I. Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theor. Biol. Med. Model. 3: 27 (2006).

Sivasankar S, Sheldrick B, Rothstein SJ. Expression of allene oxide synthase determines defense gene activation in tomato. Plant Physiol. 122: 1335-1342 (2000).

Smith TJ, Peterson PE, Schmidt T, Fang J, Stanley CA. Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J. Mol. Biol. 307: 707-720 (2001).

Sorribas A, Curto R, Cascante M. Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior. Math. Biosci. 130: 71-84 (1995).

Souren JE, Wiegant FA, Van Wijk R. The role of hsp70 in protection and repair of luciferase activity in vivo; experimental data and mathematical modelling. Cell Mol. Life Sci. 55: 799-811 (1999).

Sparla F, Fermani S, Falini G, Zaffagnini M, Ripamonti A, Sabatino P, Pupillo P, Trost P. Coenzyme site-directed mutants of photosynthetic A4-GAPDH show selectively reduced NADPH-dependent catalysis, similar to regulatory AB-GAPDH inhibited by oxidized thioredoxin. J. Mol. Biol. 340: 1025-1037 (2004).

Spasic I, Simeonidis E, Messiha HL, Paton NW, Kell DB. KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics 25: 1404-1411 (2009).

Srividhya KV, Krishnaswamy S. A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiol. 4: 44 (2004).

Stamatakis K, Nectarios L, Papageorgiou GC. Facilitated water transport in cyanobacterium Synechococcus sp. PCC 7942 studied by phycobilisome-sensitized chlorophyll a fluorescence. Photosynth. Res. 84: 181-185 (2005).

Starkenburg SR, Arp DJ, Bottomley PJ. Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255. Environ. Microbiol. 10: 3036-3042 (2008).

Stephani A, Heinrich R. Kinetic and thermodynamic principles determining the structural design of ATP-producing systems. Bull. Math. Biol. 60: 505-543 (1998).

Steuer R. Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68: 2139-2151 (2007).

Steuer R, Gross T, Selbig J, Blasius B. Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 103: 11868-11873 (2006).

Stirpe A, Guzzi R, Wijma H, Verbeet MP, Canters GW, Sportelli L. Calorimetric and spectroscopic investigations of the thermal denaturation of wild type nitrite reductase. Biochim. Biophys. Acta 1752: 47-55 (2005).

Stojan J, Marcel V, Fournier D. Effect of tetramethylammonium, choline and edrophonium on insect acetylcholinesterase: test of a kinetic model. Chem. Biol. Interact. 119-120: 137-146 (1999).

Streaker ED, Beckett D. The biotin regulatory system: kinetic control of a transcriptional switch. Biochemistry 45: 6417-6425 (2006).

Strong WB, Tendler SJ, Seither RL, Goldman ID, Schirch V. Purification and properties of serine hydroxymethyltransferase and C1-tetrahydrofolate synthase from L1210 cells. J. Biol. Chem. 265: 12149-12155 (1990).

Suarez RK, Darveau CA. Multi-level regulation and metabolic scaling. J. Exp. Biol. 208: 1627-1634 (2005).

Sundstrom JF, Nakayama N, Glimelius K, Irish VF. Direct regulation of the floral homeotic APETALA1 gene by APETALA3 and PISTILLATA in Arabidopsis. Plant J. 46: 593-600 (2006).

Surovtsev IV, Razumov IA, Nekrasov VM, Shvalov AN, Soini JT, Maltsev VP, Petrov AK, Loktev VB, Chernyshev AV. Mathematical modeling the kinetics of cell distribution in the process of ligand-receptor binding. J. Theor. Biol. 206: 407-417 (2000).

Sutter JU, Homann U, Thiel G. Ca(2)+-stimulated exocytosis in maize coleoptile cells. Plant Cell 12: 1127-1136 (2000).

Tabatabaie L, de Koning TJ, Geboers AJ, van den Berg IE, Berger R, Klomp LW. Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. Hum. Mutat. 30: 749-756 (2009).

Tarczynski MC, Outlaw WH Jr. The interactive effects of pH, L-malate, and glucose-6-phosphate on guard-cell phosphoenolpyruvate carboxylase. Plant Physiol. 103: 1189-1194 (1993).

Tartakovsky B, Sheintuch M, Hilmer J-M, Scheper T. Modelling of E. coli fermentations: comparison of multicompartment and variable structure models. Bioprocess Engineering 16: 323-329 (1997).

Taylor DK, Rank DR, Keiser DR, Smith BN, Criddle RS, Hansen LD. Modelling temperature effects on growth-respiration relations of maize. Plant Cell Environ. 21: 1143-1151 (1998).

Theilgaard HA, Nielsen J. Metabolic control analysis of the penicillin biosynthetic pathway: the influence of the LLD-ACV:bisACV ratio on the flux control. Antonie Van Leeuwenhoek 75: 145-154 (1999).

Tholudur A, Ramirez WF, McMillan JD. Mathematical modeling and optimization of cellulase protein production using Trichoderma reesei RL-P37. Biotechnol. Bioeng. 66: 1-16 (1999).

Thomas S, Fell DA. A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation. Eur. J. Biochem. 258: 956-967 (1998).

Thomas S, Mooney PFJ, Burrell MM, Fell DA. Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): Explanation for the low control coefficient of phosphofructokinase over respiratory flux. Biochem. J. 322: 119-127 (1997).

Thomaseth K. A modeling tool for biomedical systems. Simulation Practice & Theory 9: 1-19 (2001).

Thomaseth K. PANSYM: a symbolic equation generator for mathematical modelling, analysis and control of metabolic and pharmacokinetic systems. Comput. Methods Programs Biomed. 42: 99-112 (1994).

Thornley JH. Acclimation of photosynthesis to light and canopy nitrogen distribution: an interpretation. Ann. Bot. (Lond.) 93: 473-475 (2004).

Torres CF, Lessard LP, Hill CG Jr. Lipase-catalyzed esterification of conjugated linoleic acid with sorbitol: a kinetic study. Biotechnol. Prog. 19: 1255-1260 (2003).

Traitel T, Kost J, Lapidot SA. Modeling ionic hydrogels swelling: Characterization of the non-steady state. Biotechnol. Bioeng. 84: 20-28 (2003).

Tran LM, Rizk ML, Liao JC. Ensemble modeling of metabolic networks. Biophys. J. 95: 5606-5617 (2008).

Trinkunas G, Holzwarth AR. Kinetic modeling of exciton migration in photosynthetic systems. 3. Application of genetic algorithms to simulations of excitation dynamics in three-dimensional photosystem I core antenna/reaction center complexes. Biophys. J. 71: 351-364 (1996).

Tripathi P, Lo Leggio L, Mansfeld J, Ulbrich-Hofmann R, Kayastha AM. Alpha-amylase from mung beans (Vigna radiata) - correlation of biochemical properties and tertiary structure by homology modelling. Phytochemistry 68: 1623-1631 (2007).

Trost P, Fermani S, Marri L, Zaffagnini M, Falini G, Scagliarini S, Pupillo P, Sparla F. Thioredoxin-dependent regulation of photosynthetic glyceraldehyde-3-phosphate dehydrogenase: autonomous vs. CP12-dependent mechanisms. Photosynth. Res. 89: 263-275 (2006).

Tsagou V, Aggelis G. Growth dynamics of Azospirillum lipoferum at steady and transitory states in the presence of NH4+. J. Appl. Microbiol. 100: 286-295 (2006).

Tsuji N, Nishikori S, Iwabe O, Matsumoto S, Shiraki K, Miyasaka H, Takagi M, Miyamoto K, Hirata K. Comparative analysis of the two-step reaction catalyzed by prokaryotic and eukaryotic phytochelatin synthase by an ion-pair liquid chromatography assay. Planta 222: 181-191 (2005).

Turnbull J, Cleland WW, Morrison JF. Chorismate mutase-prephenate dehydrogenase from Escherichia coli. 1. Kinetic characterization of the dehydrogenase reaction by use of alternative substrates. Biochemistry 29: 10245-10254 (1990).

Tyree MI, Koh S, Sands P. The determination of membrane transport parameters with the cell pressure probe: theory suggests that unstirred layers have significant impact. Plant Cell Environ. 28: 1475-1486 (2005).

Tyson JJ. Models of cell cycle control in eukaryotes. J. Biotechnol. 71: 239-244 (1999).

Umana P, Bailey JE. A mathematical model of N-linked glycoform biosynthesis. Biotechnol. Bioeng. 55: 890-908 (1997).

Uys L, Botha FC, Hofmeyr JH, Rohwer JM. Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68: 2375-2392 (2007).

Van Praag E. Use of 3-D computer modelling and kinetic studies to analyse grapefruit pyrophosphate-dependent phosphofructokinase. Int. J. Biol. Macromol. 21: 307-317 (1997).

van Riel NA, Giuseppin ML, TerSchure EG, Verrips CT. A structured, minimal parameter model of the central nitrogen metabolism in Saccharomyces cerevisiae: the prediction of the behavior of mutants. J. Theor. Biol. 191: 397-414 (1998).

van Walsum GP, Lynd LR. Allocation of ATP to synthesis of cells and hydrolytic enzymes in cellulolytic fermentative microorganisms: bioenergetics, kinetics, and bioprocessing. Biotechnol. Bioeng. 58: 316-320 (1998).

Van Zijl PC, Davis D, Eleff SM, Moonen CT, Parker RJ, Strong JM. Determination of cerebral glucose transport and metabolic kinetics by dynamic MR spectroscopy. Am. J. Physiol. 273: E1216-E1227 (1997).

Varner J, Ramkrishna D. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 15: 407-425 (1999).

Varner JD. Large-scale prediction of phenotype: concept. Biotechnol. Bioeng. 69: 664-678 (2000).

Vaseghi S, Macherhammer F, Zibek S, Reuss M. Signal transduction dynamics of the protein kinase-A/phosphofructokinase-2 system in Saccharomyces cerevisiae. Metab. Eng. 3: 163-172 (2001).

Vasil'ev S, Shen JR, Kamiya N, Bruce D. The orientations of core antenna chlorophylls in photosystem II are optimized to maximize the quantum yield of photosynthesis. FEBS Lett. 561: 111-116 (2004).

Veng-Pedersen P, Freise KJ, Schmidt RL, Widness JA. Pharmacokinetic differentiation of drug candidates using system analysis and physiological-based modelling. Comparison of C.E.R.A. and erythropoietin. J. Pharm. Pharmacol. 60: 1321-1334 (2008).

Vera J, de Atauri P, Cascante M, Torres NV. Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by Saccharomyces cerevisiae. Biotechnol. Bioeng. 83: 335-343 (2003).

Verkroost AW, Wassen MJ. A simple model for nitrogen-limited plant growth and nitrogen allocation. Ann. Bot. (Lond.) 96: 871-876 (2005).

Veron M, Guillou Y, Fazel A, Cohen GN. Reversible dissociation of aspartokinase I/homoserine dehydrogenase I from Escherichia coli K 12. The active species is the tetramer. Eur. J. Biochem. 151: 521-524 (1985).

Viamajala S, Peyton BM, Petersen JN. Modeling chromate reduction in Shewanella oneidensis MR-1: Development of a novel dual-enzyme kinetic model. Biotechnol. Bioeng. 83: 790-797 (2003).

Vicini P, Kushmerick MJ. Cellular energetics analysis by a mathematical model of energy balance: estimation of parameters in human skeletal muscle. Am. J. Physiol. Cell Physiol. 279: C213-C224 (2000).

Vinnakota K, Kemp ML, Kushmerick MJ. Dynamics of muscle glycogenolysis modeled with pH time course computation and pH-dependent reaction equilibria and enzyme kinetics. Biophys. J. 91: 1264-1287 (2006).

Visser D, Heijnen JJ. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metab. Eng. 5: 164-176 (2003).

Visser D, Schmid JW, Mauch K, Reuss M, Heijnen JJ. Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. Metab. Eng. 6: 378-390 (2004).

Visser D, van der Heijden R, Mauch K, Reuss M, Heijnen S. Tendency modeling: a new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae. Metab. Eng. 2: 252-275 (2000).

Vital-Lopez FG, Armaou A, Nikolaev EV, Maranas CD. A computational procedure for optimal engineering interventions using kinetic models of metabolism. Biotechnol. Prog. 22: 1507-1517 (2006).

Voit EO, Alvarez-Vasquez F, Sims KJ. Analysis of dynamic labeling data. Math. Biosci. 191: 83-99 (2004).

Voit EO, Savageau MA. Accuracy of alternative representations for integrated biochemical systems. Biochemistry 26: 6869-6880 (1987).

Wahl SA, Noh K, Wiechert W. 13C labeling experiments at metabolic nonstationary conditions: an exploratory study. BMC Bioinformatics 9: 152 (2008).

Wan X, Steudle E, Hartung W. Gating of water channels (aquaporins) in cortical cells of young corn roots by mechanical stimuli (pressure pulses): effects of ABA and of HgCl2. J. Exp. Bot. 55: 411-422 (2004).

Wanant S, Quon MJ. Insulin receptor binding kinetics: modeling and simulation studies. J. Theor. Biol. 205: 355-364 (2000).

Wang W, Poland BW, Honzatko RB, Fromm HJ. Identification of arginine residues in the putative L-aspartate binding site of Escherichia coli adenylosuccinate synthetase. J. Biol. Chem. 270: 13160-13163 (1995).

Warrilow AG, Hawkesford MJ. Modulation of cyanoalanine synthase and O-acetylserine (thiol) lyases A and B activity by beta-substituted alanyl and anion inhibitors. J. Exp. Bot. 53: 439-445 (2002).

Wasserman GF, Benkovic PA, Young M, Benkovic SJ. Kinetic relationships between the various activities of the formyl-methenyl-methylenetetrahydrofolate synthetase. Biochemistry 22: 1005-1013 (1983).

Wastney ME, House WA. Development of a compartmental model of zinc kinetics in mice. J. Nutr. 138: 2148-2155 (2008).

Weber WA, Schwaiger M, Avril N. Quantitative assessment of tumor metabolism using FDG-PET imaging. Nucl. Med. Biol. 27: 683-687 (2000).

Wiback SJ, Palsson BO. Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83: 808-818 (2002).

Wilkinson SJ, Benson N, Kell DB. Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Mol. Biosyst. 4: 74-97 (2007).

Williams RE, Lenz EM, Evans JA, Wilson ID, Granger JH, Plumb RS, Stumpf CL. A combined (1)H NMR and HPLC-MS-based metabonomic study of urine from obese (fa/fa) Zucker and normal Wistar-derived rats. J. Pharm. Biomed. Anal. 38: 465-471 (2005).

Wintrode PL, Rojsajjakul T, Vadrevu R, Matthews CR, Smith DL. An obligatory intermediate controls the folding of the alpha-subunit of tryptophan synthase, a TIM barrel protein. J. Mol. Biol. 347: 911-919 (2005).

Wirtz KW. A generic model for changes in microbial kinetic coefficients. J. Biotechnol. 97: 147-162 (2002).

Wirtz M, Droux M, Hell R. O-Acetylserine (thiol) lyase: an enigmatic enzyme of plant cysteine biosynthesis revisited in Arabidopsis thaliana. J. Exp. Bot. 55: 1785-1798 (2004).

Wissing JB, Kornak B, Funke A, Riedel B. Phosphatidate kinase, a novel enzyme in phospholipid metabolism. Characterization of the enzyme from suspension-cultured Catharanthus roseus cells. Plant Physiol. 105: 903-909 (1994).

Wray LV Jr, Fisher SH. A feedback resistant mutant of Bacillus subtilis glutamine synthetase with pleiotropic defects in nitrogen-regulated gene expression. J. Biol. Chem. 280: 33298-33304 (2005).

Wu L, Lange HC, Van Gulik WM, Heijnen JJ. Determination of in vivo oxygen uptake and carbon dioxide evolution rates from off-gas measurements under highly dynamic conditions. Biotechnol. Bioeng. 81: 448-458 (2003).

Yamazaki S, Toth LN, Kimoto E, Bower J, Skaptason J, Romero D, Heath TG. Application of stable isotope methodology in the evaluation of the pharmacokinetics of (S,S)-3-[3-(methylsulfonyl)phenyl]-1-propylpiperidine hydrochloride in rats. Drug Metab. Dispos. 37: 937-945 (2009).

Yan HP, Kang MZ, de Reffye P, Dingkuhn M. A dynamic, architectural plant model simulating resource-dependent growth. Ann. Bot. (Lond.) 93: 591-602 (2004).

Yang C, Hua Q, Shimizu K. Development of a kinetic model for L-lysine biosynthesis in Corynebacterium glutamicum and its application to metabolic control analysis. J. Biosci. Bioeng. 88: 393-403 (1999).

Yennawar NH, Islam MM, Conway M, Wallin R, Hutson SM. Human mitochondrial branched chain aminotransferase isozyme: structural role of the CXXC center in catalysis. J. Biol. Chem. 281: 39660-39671 (2006).

Yugi K, Nakayama Y, Kinoshita A, Tomita M. Hybrid dynamic/static method for large-scale simulation of metabolism. Theor. Biol. Med. Model. 2: 42 (2005).

Yun M, Park CG, Kim JY, Rock CO, Jackowski S, Park HW. Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J. Biol. Chem. 275: 28093-28099 (2000).

Yun YS, Park JM. Kinetic modeling of the light-dependent photosynthetic activity of the green microalga Chlorella vulgaris. Biotechnol. Bioeng. 83: 303-311 (2003).

Yurt N, Sears J, Lewandowski Z. Multiple substrate growth kinetics of Leptothrix discophora SP-6. Biotechnol. Prog. 18: 994-1002 (2002).

Zeng AP, Modak J, Deckwer WD. Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: decarboxylation rate, oscillations, and multiplicity. Biotechnol. Prog. 18: 1265-1276 (2002).

Zeng RJ, Yuan Z, Keller J. Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms. Biotechnol. Bioeng. 83: 293-302 (2003).

Zhang Z, Scharer JM, Moo-Young M. Mathematical model for aerobic culture of a recombinant yeast. Bioprocess Engineering 17: 235-240 (1997).

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M. Extraction of elementary rate constants from global network analysis of E. coli central metabolism. BMC Syst. Biol. 2: 41 (2008).

Zhou M, Xu H, Wei X, Ye Z, Wei L, Gong W, Wang Y, Zhu Z. Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol. 140: 184-195 (2006).

Zhu XG, Govindjee, Baker NR, deSturler E, Ort DO, Long SP. Chlorophyll a fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with Photosystem II. Planta 223: 114-133 (2005).

Zhu XG, Portis AR, Long SP. Would transformation of C-3 crop plants with foreign Rubisco increase productivity? A computational analysis extrapolating from kinetic properties to canopy photosynthesis. Plant Cell Environ. 27: 155-165 (2004).

Zotz G, Mikona C. Photosynthetic induction and leaf carbon gain in the tropical understorey epiphyte, Aspasia principissa. Ann. Bot. (Lond.) 91: 353-359 (2003).

Zouhar J, Vevodova J, Marek J, Damborsky J, Su XD, Brzobohaty B. Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1. Plant Physiol. 127: 973-985 (2001).

Number of references = 548