Aalto T, Juurola E. A three-dimensional model of CO2 transport in airspaces and mesophyll cells of a silver birch leaf. Plant Cell Environ. 25: 1399-1409 (2002).

Aalto T, Vesala T, Mattila T, Simbierowicz P, Hari P. A three-dimensional stomatal CO2 exchange model including gaseous phase and leaf mesophyll separated by irregular interface. J. Theor. Biol. 196: 115-128 (1998).

Adamatzky A. ModelMaker. Kybernetes 30: 120-125 (2001).

Ainscow EK, Brand MD. Errors associated with metabolic control analysis. Application of Monte-Carlo simulation of experimental data. J. Theor. Biol. 194: 223-233 (1998).

Aita T, Ota M, Husimi Y. An in silico exploration of the neutral network in protein sequence space. J. Theor. Biol. 221: 599-613 (2003).

Aksenov SV, Church B, Dhiman A, Georgieva A, Sarangapani R, Helmlinger G, Khalil IG. An integrated approach for inference and mechanistic modeling for advancing drug development. FEBS Lett. 579: 1878-1883 (2005).

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

Albe KR, Wright BE. Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. II. Control analysis. J. Biol. Chem. 267: 3106-3114 (1992).

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).

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).

Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Toma's-Oliveira I, Serrano L. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst. Biol. 1: 129-138 (2004).

Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M. GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics 7: 168 (2006).

Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 13: 2455-2466 (2003).

Arkin IT, Xu H, Jensen MO, Arbely E, Bennett ER, Bowers KJ, Chow E, Dror RO, Eastwood MP, Flitman-Tene R, Gregersen BA, Klepeis JL, Kolossváry I, Shan Y, Shaw DE. Mechanism of Na+/H+ antiporting. Science 317: 799-803 (2007).

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).

Athawale MV, Dordick JS, Garde S. Osmolyte trimethylamine-N-oxide does not affect the strength of hydrophobic interactions: origin of osmolyte compatibility. Biophys. J. 89: 858-866 (2005).

Baart GJ, Willemsen M, Khatami E, de Haan A, Zomer B, Beuvery EC, Tramper J, Martens DE. Modeling Neisseria meningitidis B metabolism at different specific growth rates. Biotechnol. Bioeng. 101: 1022-1035 (2008).

Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA. Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol. Biochem. Parasitol. 106: 1-10 (2000).

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

Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C. Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst. Biol. 2: 26 (2008).

Bancal P, Soltani F. Source-sink partitioning. Do we need Munch? J. Exp. Bot. 53: 1919-1928 (2002).

Baptist F, Choler P. A simulation of the importance of length of growing season and canopy functional properties on the seasonal gross primary production of temperate alpine meadows. Ann. Bot. (Lond.) 101: 549-559 (2008).

Baptista T, Costa E. Evolution of a multi-agent system in a cyclical environment. Theory Biosci. 127: 141-148 (2008).

Barabe D, Lacroix C, Jeune B. Following the initiation and development of individual leaf primordia at the level of the shoot apical meristem: the case of distichous phyllotaxis in Begonia. Ann. Bot. (Lond.) 99: 555-560 (2007).

Barbano PE, Spivak M, Flajolet M, Nairn AC, Greengard P, Greengard L. A mathematical tool for exploring the dynamics of biological networks. Proc. Natl. Acad. Sci. U.S.A. 104: 19169-19174 (2007).

Barjaktarovic Z, Nordheim A, Lamkemeyer T, Fladerer C, Madlung J, Hampp R. Time-course of changes in amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation, and 3-D random positioning of Arabidopsis cell cultures. J. Exp. Bot. 58: 4357-4363 (2007).

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).

Barshop BA, Wrenn RF, Frieden C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system. Anal. Biochem. 130: 134-145 (1983).

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).

Batz O, Logemann E, Reinold S, Hahlbrock K. Extensive reprogramming of primary and secondary metabolism by fungal elicitor or infection in parsley cells. Biol. Chem. 379: 1127-1135 (1998).

Beard DA, Liang SD, Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 83: 79-86 (2002).

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).

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).

Berleth T, Scarpella E, Prusinkiewicz P. Towards the systems biology of auxin-transport-mediated patterning. Trends Plant Sci. 12: 151-159 (2007).

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).

Berthon HA, Bubb WA, Kuchel PW. 13C NMR isotopomer and computer-simulation studies of the nonoxidative pentose-phosphate pathway of human erythrocytes. Biochem. J. 296: 379-387 (1993).

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).

Bhartiya S, Rawool S, Venkatesh KV. Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design. Eur. J. Biochem. 270: 2644-2651 (2003).

Blank LM, Ebert BE, Buhler B, Schmid A. Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: constraint-based modeling and experimental verification. Biotechnol. Bioeng. 100: 1050-1065 (2008).

Blasius B, Beck F, Luttge U. Oscillatory model of Crassulacean acid metabolism: structural analysis and stability boundaries with a discrete hysteresis switch. Plant Cell Environ. 21: 775-784 (1998).

Bochenek EA, Klinck JM, Powell EN, Hofmann EE. A biochemically based model of the growth and development of Crassostrea gigas larvae. J. Shellfish Res. 20: 243-265 (2001).

Bond-Lamberty B, Gower ST, Ahl DE. Improved simulation of poorly drained forests using Biome-BGC. Tree Physiol. 27: 703-715 (2007).

Booth G. Gecko: a continuous 2D world for ecological modeling. Artif Life 3: 147-163 (1997).

Borodina I, Siebring J, Zhang J, Smith CP, van Keulen G, Dijkhuizen L, Nielsen J. Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. J. Biol. Chem. 283: 25186-25199 (2008).

Bost B, Dillmann C, de Vienne D. Fluxes and metabolic pools as model traits for quantitative genetics. I. The L-shaped distribution of gene effects. Genetics 153: 2001-2012 (1999).

Brandman O, Ferrell JE Jr, Li R, Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310: 496-498 (2005).

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).

Bray D, Bourret RB, Simon MI. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Mol. Biol. Cell 4: 469-482 (1993).

Broadley MR, Seginer I, Burns A, Escobar-Gutierrez AJ, Burns IG, White PJ. The nitrogen and nitrate economy of butterhead lettuce (Lactuca sativa var. capitata L.). J. Exp. Bot. 54: 2081-2090 (2003).

Bruggeman FJ, Libbenga KR, Van Duijn B. The diffusive transport of gibberellins and abscisic acid through the aleurone layer of germinating barley grain: a mathematical model. Planta 214: 89-96 (2001).

Bruggeman FJ, van Heeswijk WC, Boogerd FC, Westerhoff HV. Macromolecular intelligence in microorganisms. Biol. Chem. 381: 965-972 (2000).

Brunel S, Teulat-Merah B, Wagner MH, Huguet T, Prosperi JM, Dürr C. Using a model-based framework for analysing genetic diversity during germination and heterotrophic growth of Medicago truncatula. Ann. Bot. (Lond.) 103: 1103-1117 (2009).

Buckley TN, Mott KA. Dynamics of stomatal water relations during the humidity response: implications of two hypothetical mechanisms. Plant Cell Environ. 25: 407-419 (2002).

Budiman ME, Knaggs MH, Fetrow JS, Alexander RW. Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins 68: 670-689 (2007).

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).

Butcher EC, Berg EL, Kunkel EJ. Systems biology in drug discovery. Nat. Biotechnol. 22: 1253-1259 (2004).

Cabrera ME, Saidel GM, Kalhan SC. Lactate metabolism during exercise: analysis by an integrative systems model. Am. J. Physiol. 277: R1522-R1536 (1999).

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).

Capps GJ, Samuels DC, Chinnery PF. A model of the nuclear control of mitochondrial DNA replication. J. Theor. Biol. 221: 565-583 (2003).

Cardy DL, Murrell JC. Cloning, sequencing and expression of the glutamine synthetase structural gene (glnA) from the obligate methanotroph Methylococcus capsulatus (Bath). J. Gen. Microbiol. 136: 343-352 (1990).

Carlson R, Srienc F. Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86: 149-162 (2004).

Chaitali M, Kapadi M, Suraishkumar GK, Gudi RD. Productivity improvement in xanthan gum fermentation using multiple substrate optimization. Biotechnol. Prog. 19: 1190-1198 (2003).

Challinor AJ, Ewert F, Arnold S, Simelton E, Fraser E. Crops and climate change: progress, trends, and challenges in simulating impacts and informing adaptation. J. Exp. Bot. 60: 2775-2789 (2009).

Chang DM. The snowball effect in fed-batch bioreactions. Biotechnol. Prog. 19: 1064-1070 (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).

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 WD, Tong XD, Dong XY, Sun Y. Expanded bed adsorption of protein with DEAE Spherodex M. Biotechnol. Prog. 19: 880-886 (2003).

Chenu K, Chapman SC, Hammer GL, McLean G, Salah HB, Tardieu F. Short-term responses of leaf growth rate to water deficit scale up to whole-plant and crop levels: an integrated modelling approach in maize. Plant Cell Environ. 31: 378-391 (2008).

Chiku T, Padovani D, Zhu W, Singh S, Vitvitsky V, Banerjee R. H2S biogenesis by human cystathionine gamma-lyase leads to the novel sulfur metabolites lanthionine and homolanthionine and is responsive to the grade of hyperhomocysteinemia. J. Biol. Chem. 284: 11601-11612 (2009).

Chuine I. A unified model for budburst of trees. J. Theor. Biol. 207: 337-347 (2000).

Clark AG. Mutation-selection balance and metabolic control theory. Genetics 129: 909-923 (1991).

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

Cochard H, Nardini A, Coll L. Hydraulic architecture of leaf blades: where is the main resistance?. Plant Cell Environ. 27: 1257-1267 (2004).

Cochard H, Venisse JS, Barigah TS, Brunel N, Herbette S, Guilliot A, Tyree MT, Sakr S. Putative role of aquaporins in variable hydraulic conductance of leaves in response to light. Plant Physiol. 143: 122-133 (2007).

Cohen DM, Bergman RN. SYNTAX: A rule-based stochastic simulation of the time-varying concentrations of positional isotopomers of metabolic intermediates. Computers and Biomedical Research 27: 130-147 (1994).

Coiro VM, Di Nola A, Vanoni MA, Aschi M, Coda A, Curti B, Roccatano D. Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Protein Sci. 13: 2979-2991 (2004).

Collado-Vides J, Hofestadt R, Mavrovouniotis M, Michal G. Modeling and simulation of gene regulation and metabolic pathways. Biosystems 49: 79-82 (1999).

Condon AG, Richards RA, Rebetzke GJ, Farquhar GD. Breeding for high water-use efficiency. J. Exp. Bot. 55: 2447-2460 (2004).

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).

Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgower F, Gilles ED. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Syst. Biol. 1: 159-169 (2004).

Coops NC, Coggins SB, Kurz WA. Mapping the environmental limitations to growth of coastal Douglas-fir stands on Vancouver Island, British Columbia. Tree Physiol. 27: 805-815 (2007).

Cornish-Bowden A, Cardenas ML. Information transfer in metabolic pathways. Effects of irreversible steps in computer models. Eur. J. Biochem. 268: 6616-6624 (2001).

Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26: 179-186 (2001).

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

Cowling SA, Betts RA, Cox PM, Ettwein VJ, Jones CD, Maslin MA, Spall SA. Contrasting simulated past and future responses of the Amazonian forest to atmospheric change. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 359: 539-547 (2004).

Cramer W, Bondeau A, Schaphoff S, Lucht W, Smith B, Sitch S. Tropical forests and the global carbon cycle: impacts of atmospheric carbon dioxide, climate change and rate of deforestation. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 359: 331-343 (2004).

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, Dunnill P, Mitsky TA, Padgette SR, Taylor NB, Valentin HE, Gruys KJ. Metabolic modeling as a tool for evaluating polyhydroxyalkanoate copolymer production in plants. Metab. Eng. 1: 243-254 (1999).

Dampier W, Tozeren A. Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach. J. Theor. Biol. 248: 130-144 (2007).

Dang Q, Frieden C. New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM. Trends Biochem. Sci. 22: 317 (1997).

Dassau E, Palerm CC, Zisser H, Buckingham BA, Jovanovic L, Doyle FJ. In silico evaluation platform for artificial pancreatic beta-cell development - a dynamic simulator for closed-loop control with hardware-in-the-loop. Diabetes Technol. Ther. 11: 187-194 (2009).

Dauzat J, Clouvel P, Luquet D, Martin P. Using virtual plants to analyse the light-foraging efficiency of a low-density cotton crop. Ann. Bot. (Lond.) 101: 1153-1166 (2008).

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

de la Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems. Eur. J. Biochem. 269: 4399-4408 (2002).

De Maria C, Grassini D, Vozzi F, Vinci B, Landi A, Ahluwalia A, Vozzi G. HEMET: mathematical model of biochemical pathways for simulation and prediction of HEpatocyte METabolism. Comput. Methods Programs Biomed. 92: 121-134 (2008).

de Reuille PB, Bohn-Courseau I, Ljung K, Morin H, Carraro N, Godin C, Traas J. Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 103: 1627-1632 (2006).

De Schutter E, Ekeberg O, Kotaleski JH, Achard P, Lansner A. Biophysically detailed modelling of microcircuits and beyond. Trends Neurosci. 28: 562-569 (2005).

Deckmyn G, Op de Beeck M, Low M, Then C, Verbeeck H, Wipfler P, Ceulemans R. Modelling ozone effects on adult beech trees through simulation of defence, damage, and repair costs: implementation of the CASIROZ ozone model in the ANAFORE forest model. Plant Biol. (Stuttg.) 9: 320-330 (2007).

Degenring D, Rohl M, Uhrmacher AM. Discrete event, multi-level simulation of metabolite channeling. Biosystems 75: 29-41 (2004).

Detmers FJ, de Groot BL, Muller EM, Hinton A, Flitsch SL, Grubmuller H, Deen PM. Quaternary ammonium compounds as water channel blockers: specificity, potency and site of action. J. Biol. Chem. 281: 14207-14214 (2006).

Dhar P, Wang E, Nakayama Y, Tomita M. Modeling photorespiration pathway through E-Cell. Genome Informatics 12: 306-307 (2001).

Dietz KJ, Heber U, Mimura T. Modulation of the vacuolar H+-ATPase by adenylates as basis for the transient CO2-dependent acidification of the leaf vacuole upon illumination. Biochim. Biophys. Acta 1373: 87-92 (1998).

Dodd AN, Gardner MJ, Hotta CT, Hubbard KE, Dalchau N, Love J, Assie JM, Robertson FC, Jakobsen MK, Goncalves J, Sanders D, Webb AA. The Arabidopsis circadian clock incorporates a cADPR-based feedback loop. Science 318: 1789-1792 (2007).

Droste P, Weitzel M, Wiechert W. Visual exploration of isotope labeling networks in 3D. Bioprocess. Biosyst. Eng. 31: 227-239 (2008).

Drouet JL, Bonhomme R. Effect of 3D nitrogen, dry mass per area and local irradiance on canopy photosynthesis within leaves of contrasted heterogeneous maize crops. Ann. Bot. (Lond.) 93: 699-710 (2004).

Dunbabin V, Diggle A, Rengel Z. Is there an optimal root architecture for nitrate capture in leaching environments? Plant Cell Environ. 26: 835-844 (2003).

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).

Earl DJ, Deem MW. Evolvability is a selectable trait. Proc. Natl. Acad. Sci. U.S.A. 101: 11531-11536 (2004).

Efremov RG, Volynsky PE, Nolde DE, van Dalen A, de Kruijff B, Arseniev AS. Monte Carlo simulations of voltage-driven translocation of a signal sequence. FEBS Lett. 526: 97-100 (2002).

Ehlde M, Zacchi G. MIST - a user-friendly metabolic simulator. Comp. Appl. Biosci. 11: 201-207 (1995).

Ehlde M, Zacchi G. Influence of experimental errors on the determination of flux control coefficients from transient metabolite concentrations. Biochem. J. 313: 721-727 (1996).

Ekstrom JL, Tolbert WD, Xiong H, Pegg AE, Ealick SE. Structure of a human S-adenosylmethionine decarboxylase self-processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant. Biochemistry 40: 9495-9504 (2001).

Elmore DE. Molecular dynamics simulation of a phosphatidylglycerol membrane. FEBS Lett. 580: 144-148 (2006).

Esterl S, Ozmutlu O, Hartmann C, Delgado A. Three-dimensional numerical approach to investigate the substrate transport and conversion in an immobilized enzyme reactor. Biotechnol. Bioeng. 83: 780-789 (2003).

Etchegoin P, Nollmann M. A model for protein-DNA interaction dynamics. J. Theor. Biol. 220: 233-239 (2003).

Ewert F. Modelling plant responses to elevated CO2: how important is leaf area index? Ann. Bot. (Lond.) 93: 619-627 (2004).

Fan J, Niu Y. Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics 23: 2391-2398 (2007).

Fan Y, Lund L, Yang L, Raushel FM, Gao YQ. Mechanism for the transport of ammonia within carbamoyl phosphate synthetase determined by molecular dynamics simulations. Biochemistry 47: 2935-2944 (2008).

Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol. Syst. Biol. 2: 2006.0004 (2006).

Fell DA, Chassagnole C, Mazat JP. Building a computer simulation of threonine synthesis in Escherichia coli. ICSB 2nd International Conference on Systems Biology, "The Future of Biology in the 21st Century", November 4-7, 2001, California Institute of Technology (2001).

Feng D, Ho D, Lau KK, Siu WC. GLLS for optimally sampled continuous dynamic system modeling: theory and algorithm. Comput. Methods Programs Biomed. 59: 31-43 (1999).

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).

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

Fischer HP. Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnol. Annu. Rev. 11: 1-68 (2005).

Floquet N, Mouilleron S, Daher R, Maigret B, Badet B, Badet-Denisot MA. Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): molecular dynamics simulations and kinetic studies of protein mutants. FEBS Lett. 581: 2981-2987 (2007).

Folcarelli S, Venerini F, Battistoni A, O'neill P, Rotilio G, Desideri A. Toward the engineering of a super efficient enzyme. Biochem. Biophys. Res. Commun. 256: 425-428 (1999).

Fourcaud T, Ji JN, Zhang ZQ, Stokes A. Understanding the impact of root morphology on overturning mechanisms: a modelling approach. Ann. Bot. (Lond.) 101: 1267-1280 (2008).

Fourcaud T, Zhang X, Stokes A, Lambers H, Korner C. Plant growth modelling and applications: the increasing importance of plant architecture in growth models. Ann. Bot. (Lond.) 101: 1053-1063 (2008).

Fu J, Swertz MA, Keurentjes JJ, Jansen RC. MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nat. Protoc. 2: 685-694 (2007).

Gao W, Wesely ML, Doskey PV. Numerical modeling of the turbulent-diffusion and chemistry of NOx, O3, isoprene, and other reactive trace gases in and above a forest canopy. J. Geophys. Res. 98: 18339-18353 (1993).

Garcia J, Shea J, Alvarez-Vasquez F, Qureshi A, Luberto C, Voit EO, Del Poeta M. Mathematical modeling of pathogenicity of Cryptococcus neoformans. Mol. Syst. Biol. 4: 183 (2008).

Gardner CL, Jerome JW, Eisenberg RS. Electrodiffusion model simulation of rectangular current pulses in a voltage-biased biological channel. J. Theor. Biol. 219: 291-299 (2002).

Garfinkel D. The role of computer simulation in biochemistry. Comput. Biomed. Res. 2: i-ii (1968).

Genard M, Gouble B. ETHY. A theory of fruit climacteric ethylene emission. Plant Physiol. 139: 531-545 (2005).

Genoud T, Buchala AJ, Chua NH, Metraux JP. Phytochrome signalling modulates the SA-perceptive pathway in Arabidopsis. Plant J. 31: 87-95 (2002).

Genoud T, Trevino Santa Cruz MB, Metraux JP. Numeric simulation of plant signaling networks. Plant Physiol. 126: 1430-1437 (2001).

Gielen B, De Boeck HJ, Lemmens CMHM, Valcke R, Nijs I, Ceulemans R. Grassland species will not necessarily benefit from future elevated air temperatures: a chlorophyll fluorescence approach to study autumn physiology. Physiol. Plant. 125: 52-63 (2005).

Gomez-Jimenez S, Urias-Reyes AA, Vazquez-Ortiz F, Hernandez-Watanabe G. Ammonia efflux rates and free amino acid levels in Litopenaeus vannamei postlarvae during sudden salinity changes. Aquaculture 233: 573-581 (2004).

Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D. Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol. Biosyst. 4: 148-159 (2008).

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).

Gonze D, Leloup JC, Goldbeter A. Theoretical models for circadian rhythms in Neurospora and Drosophila. C. R. Acad. Sci. III 323: 57-67 (2000).

Goryanin I, Hodgman TC, Selkov E. Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15: 749-758 (1999).

Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar AJ, Hall A. The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell 18: 1177-1187 (2006).

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

Graber R, Kasper P, Malashkevich VN, Sandmeier E, Berger P, Gehring H, Jansonius JN, Christen P. Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme. Eur. J. Biochem. 232: 686-690 (1995).

Grafahrend-Belau E, Schreiber F, Koschutzki D, Junker BH. Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 149: 585-598 (2009).

Grantz DA, Zhang X, Carlson T. Observations and model simulations link stomatal inhibition to impaired hydraulic conductance following ozone exposure in cotton. Plant Cell Environ. 22: 1201-1210 (1999).

Graus M, Schnitzler JP, Hansel A, Cojocariu C, Rennenberg H, Wisthaler A, Kreuzwieser J. Transient release of oxygenated volatile organic compounds during light-dark transitions in grey poplar leaves. Plant Physiol. 135: 1967-1975 (2004).

Greco WR. The role of simulation in biomathematical modeling. Bull. Math. Biol. 48: 241-251 (1986).

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

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).

Hammer GL, Sinclair TR, Chapman SC, van Oosterom E. On systems thinking, systems biology, and the in silico plant. Plant Physiol. 134: 909-911 (2004).

Hansen J, Sato M, Ruedy R, Lo K, Lea DW, Medina-Elizade M. Global temperature change. Proc. Natl. Acad. Sci. U.S.A. 103: 14288-14293 (2006).

Hardegree SP. Predicting germination response to temperature. III. Model validation under field-variable temperature conditions. Ann. Bot. (Lond.) 98: 827-834 (2006).

Hartigan MD, Crompton LA, Reynolds CK, Wray-Cahen D, Lomax MA, France J. An integrative model of amino acid metabolism in the liver of the lactating dairy cow. J. Theor. Biol. 228: 271-289 (2004).

Hashido M, Ikeguchi M, Kidera A. Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett. 579: 5549-5552 (2005).

Hatzimanikatis V, Lee KH, Bailey JE. A mathematical description of regulation of the G1-S transition of the mammalian cell cycle. Biotechnol. Bioeng. 65: 631-637 (1999).

Haunschild MD, Freisleben B, Takors R, Wiechert W. Investigating the dynamic behavior of biochemical networks using model families. Bioinformatics 21: 1617-1625 (2005).

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. Mathematical models of metabolic systems: general principles and control of glycolysis and membrane transport in erythrocytes. Biomed. Biochim. Acta 44: 913-927 (1985).

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).

Henkes GJ, Thorpe MR, Minchin PE, Schurr U, Rose US. Jasmonic acid treatment to part of the root system is consistent with simulated leaf herbivory, diverting recently-assimilated carbon towards untreated roots within an hour. Plant Cell Environ. 31: 1229-1236 (2008).

Henton SM, Greaves AJ, Piller GJ, Minchin PE. Revisiting the Munch pressure-flow hypothesis for long-distance transport of carbohydrates: modelling the dynamics of solute transport inside a semipermeable tube. J. Exp. Bot. 53: 1411-1419 (2002).

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).

Herring PA, McKnight BL, Jackson JH. Channeling behavior and activity models for Escherichia coli K-12 acetohydroxy acid synthases at physiological substrate levels. Biochem. Biophys. Res. Commun. 207: 48-54 (1995).

Hikosaka K, Nabeshima E, Hiura T. Seasonal changes in the temperature response of photosynthesis in canopy leaves of Quercus crispula in a cool-temperate forest. Tree Physiol. 27: 1035-1041 (2007).

Hofestadt R, Mavrovouniotis M, Collado-Vides J, Loffler M. Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. October 22-27, 1995. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany. Bioessays 18: 333-335 (1996).

Hofestadt R, Meineke F. Interactive modelling and simulation of biochemical networks. Comput. Biol. Med. 25: 321-334 (1995).

Hofestadt R, Thelen S. Quantitative modeling of biochemical networks. In Silico Biol. 1: 39-53 (1998).

Hofmeyr JH. Steady-state modelling of metabolic pathways: a guide for the prospective simulator. Comput. Appl. Biosci. 2: 5-11 (1986).

Hofmeyr JH, Cornish-Bowden A. The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models. Comput. Appl. Biosci. 13: 377-385 (1997).

Hofmeyr JH, Cornish-Bowden A. Quantitative assessment of regulation in metabolic systems. Eur. J. Biochem. 200: 223-236 (1991).

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).

Hong Y, Hu HY, Li FM. Physiological and biochemical effects of allelochemical ethyl 2-methyl acetoacetate (EMA) on cyanobacterium Microcystis aeruginosa. Ecotoxicol. Environ. Saf. 71: 527-534 (2008).

Hoon Yang T, Wittmann C, Heinzle EE. Metabolic network simulation using logical loop algorithm and Jacobian matrix. Metab. Eng. 6: 256-267 (2004).

Hopkins JC, Leipold RJ. On the dangers of adjusting the parameters values of mechanism-based mathematical models. J. Theor. Biol. 183: 417-427 (1996).

Huang W, Kim J, Jha S, Aboul-Ela F. A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res. Aug 31 [Epub ahead of print] (2009).

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H. Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project. Syst. Biol. 1: 41-53 (2004).

Hulme EC. Simulation of biochemical systems. J. Theor. Biol. 31: 131-137 (1971).

Humphries SW, Long SP. WIMOVAC: a software package for modelling the dynamics of plant leaf and canopy photosynthesis. Comput. Appl. Biosci. 11: 361-371 (1995).

Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U.S.A. 103: 16666-16671 (2006).

Ingalls BP. Autonomously oscillating biochemical systems: parametric sensitivity of extrema and period. Syst. Biol. 1: 62-70 (2004).

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

Jain E, Jain K. Integrated bioinformatics - high-throughput interpretation of pathways and biology Trends Biotechnol. 19: 157-158 (2001).

Jakobsson E. Computer simulation studies of biological membranes: progress, promise and pitfalls. Trends Biochem. Sci. 22: 339-344 (1997).

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).

Jeong E, Nagasaki M, Saito A, Miyano S. Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol. 7: 623-638 (2007).

Jochem FJ, Smith GJ, Gao Y, Zimmerman RC, Cabello-Pasini A, Kohrs DG, Alberte RS. Cytometric quantification of nitrate reductase by immunolabeling in the marine diatom Skeletonema costatum. Cytometry 39: 173-178 (2000).

Juty NS, Spence HD, Hotz HR, Tang H, Goryanin I, Hodgman TC. Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform. 2: 223-232 (2001).

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).

Kargacin GJ. Responses of Ca2+-binding proteins to localized, transient changes in intracellular [Ca2+]. J. Theor. Biol. 221: 245-258 (2003).

Kaukonen M, Soderhjelm P, Heimdal J, Ryde U. QM/MM-PBSA method to estimate free energies for reactions in proteins. J. Phys. Chem. B. 112: 12537-12548 (2008).

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).

Khannapho C, Zhao H, Bonde BK, Kierzek AM, Avignone-Rossa CA, Bushell ME. Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Metab. Eng. 10: 227-233 (2008).

Kim J, Saidel GM, Kalhan SC. A computational model of adipose tissue metabolism: evidence for intracellular compartmentation and differential activation of lipases. J. Theor. Biol. 251: 523-540 (2008).

Kim JI, Varner JD, Ramkrishna D. A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables. Biotechnol. Prog. 24: 993-1006 (2008).

Kim Y, Ye Q, Reinhardt H, Steudle E. Further quantification of the role of internal unstirred layers during the measurement of transport coefficients in giant internodes of Chara by a new stop-flow technique. J. Exp. Bot. 57: 4133-4144 (2006).

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

Kirchhoff H. Molecular crowding and order in photosynthetic membranes. Trends Plant Sci. 13: 201-207 (2008).

Kirschbaum MUF, Kuppers M, Schneider H, Giersch C, Noe S. Modelling photosynthesis in fluctuating light with inclusion of stomatal conductance, biochemical activation and pools of key photosynthetic intermediates. Planta 204: 16-26 (1998).

Klipp E, Liebermeister W. Mathematical modeling of intracellular signaling pathways. BMC Neurosci. 7 Suppl. 1: S10 (2006).

Klipp E, Liebermeister W, Wierling C. Inferring dynamic properties of biochemical reaction networks from structural knowledge. Genome Inform. 15: 125-137 (2004).

Klipp E, Nordlander B, Kruger R, Gennemark P, Hohmann S. Integrative model of the response of yeast to osmotic shock. Nature Biotechnol. 23: 975-982 (2005).

Knipfer T, Das D, Steudle E. During measurements of root hydraulics with pressure probes, the contribution of unstirred layers is minimized in the pressure relaxation mode: comparison with pressure clamp and high-pressure flowmeter. Plant Cell Environ. 30: 845-860 (2007).

Knipfer T, Steudle E. Root hydraulic conductivity measured by pressure clamp is substantially affected by internal unstirred layers. J. Exp. Bot. 59: 2071-2084 (2008).

Kobayashi T, Chen L, Aihara K. Modeling genetic switches with positive feedback loops. J. Theor. Biol. 221: 379-399 (2003).

Koh BT, Tan RB, Yap MG. Genetically structured mathematical modeling of trp attenuator mechanism. Biotechnol. Bioeng. 58: 502-509 (1998).

Kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V. Design principles of a bacterial signalling network. Nature 438: 504-507 (2005).

Kolmodin K, Aqvist J. Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase. FEBS Lett. 456: 301-305 (1999).

Korzeniewski B. Regulation of ATP supply during muscle contraction: theoretical studies. Biochem. J. 330: 1189-1195 (1998).

Kremling A, Gilles ED. The organization of metabolic reaction networks II. Signal processing in hierarchical structured functional units. Metab. Eng. 3: 138-150 (2001).

Kromer JO, Wittmann C, Schroder H, Heinzle E. Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 8: 353-369 (2006).

Kuhlemeier C. Phyllotaxis. Trends Plant Sci. 12: 143-150 (2007).

Kuparinen A. Mechanistic models for wind dispersal. Trends Plant Sci. 11: 296-301 (2006).

Kuthan H. A mathematical model of single target site location by Brownian movement in subcellular compartments. J. Theor. Biol. 221: 79-87 (2003).

Kutschera U. The growing outer epidermal wall: design and physiological role of a composite structure. Ann. Bot. (Lond.) 101: 615-621 (2008).

Lahoz-Beltra R. Evolving hardware as model of enzyme evolution. Biosystems 61: 15-25 (2001).

Lai CT, Katul G, Butnor J, Siqueira M, Ellsworth D, Maier C, Johnsen K, Mckeand S, Oren R. Modelling the limits on the response of net carbon exchange to fertilization in a south-eastern pine forest. Plant Cell Environ. 25: 1095-1119 (2002).

Lai N, Saidel GM, Iorio M, Cabrera ME. Non-invasive estimation of metabolic flux and blood flow in working muscle: effect of blood-tissue distribution. Adv. Exp. Med. Biol. 645: 155-160 (2009).

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

Lan Y, Papoian GA. Evolution of complex probability distributions in enzyme cascades. J. Theor. Biol. 248: 537-545 (2007).

Lawlor DW. Carbon and nitrogen assimilation in relation to yield: mechanisms are the key to understanding production systems. J. Exp. Bot. 53: 773-787 (2002).

Lazar D. Chlorophyll a fluorescence rise induced by high light illumination of dark-adapted plant tissue studied by means of a model of photosystem II and considering photosystem II heterogeneity. J. Theor. Biol. 220: 469-503 (2003).

Lazzeri L, Manici LM. Allelopathic effect of glucosinolate-containing plant green manure on Pythium sp and total fungal population in soil. Hortscience 36: 1283-1289 (2001).

Le Bot J, Adamowicz S, Robin P. Modelling plant nutrition of horticultural crops: a review. Scientia Horticulturae 74: 47-82 (1998).

Le Fevre F, Smidtas S, Combe C, Durot M, d'Alche-Buc F, Schachter V. CycSim- an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics. 25: 1987-1988 (2009).

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

Lebreton CM, Visscher PM, Haley CS, Semikhodskii A, Quarrie SA. A nonparametric bootstrap method for testing close linkage vs. pleiotropy of coincident quantitative trait loci. Genetics 150: 931-943 (1998).

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 JH, Heuvelink E. Simulation of leaf area development based on dry matter partitioning and specific leaf area for cut chrysanthemum. Ann. Bot. (Lond.) 91: 319-327 (2003).

Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl. Environ. Microbiol. 71: 7880-7887 (2005).

Lee SY, Lee DY, Hong SH, Kim TY, Yun H, Oh YG, Park S. MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform. Ser. Workshop Genome Inform. 14: 23-33 (2003).

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

Li J, Kuang Y, Mason CC. Modeling the glucose-insulin regulatory system and ultradian insulin secretory oscillations with two explicit time delays. J. Theor. Biol. 242: 722-735 (2006).

Li Y, Dash RK, Kim J, Saidel GM, Cabrera ME. Role of NADH/NAD+ transport activity and glycogen store on skeletal muscle energy metabolism during exercise: in silico studies. Am. J. Physiol. Cell Physiol. 296: C25-C46 (2009).

Liao JC, Oh MK. Toward predicting metabolic fluxes in metabolically engineered strains. Metab. Eng. 1: 214-223 (1999).

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: integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med. Model. 3: 42 (2006).

Lillo C, Meyer C, Ruoff P. The nitrate reductase circadian system. The central clock dogma contra multiple oscillatory feedback loops. Plant Physiol. 125: 1554-1557 (2001).

Liu ET. Integrative biology and systems biology. Mol. Syst. Biol. 1: 2005.0004 (2005).

Lobit P, Genard M, Soing P, Habib R. Modelling malic acid accumulation in fruits: relationships with organic acids, potassium, and temperature. J. Exp. Bot. 57: 1471-1483 (2006).

Lobit P, Genard M, Wu BH, Soing P, Habib R. Modelling citrate metabolism in fruits: responses to growth and temperature. J. Exp. Bot. 54: 2489-2501 (2003).

Loew LM, Schaff JC. The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol. 19: 401-406 (2001).

Lu M, Zhou L, Stanley WC, Cabrera ME, Saidel GM, Yu X. Role of the malate-aspartate shuttle on the metabolic response to myocardial ischemia. J. Theor. Biol. 254: 466-475 (2008).

Lumb JR. Computer simulation of biological systems. Current trends. Mol. Cell Biochem. 73: 91-98 (1987).

Luo RY, Liao S, Tao GY, Li YY, Zeng S, Li YX, Luo Q. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol. Syst. Biol. 2: 2006.0031 (2006).

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312 (2004).

Luttge U. The tonoplast functioning as the master switch for circadian regulation of Crassulacean acid metabolism. Planta 211: 761-769 (2000).

Luttge U, Beck F. Endogenous rhythms and chaos in Crassulacean acid metabolism. Planta 188: 28-38 (1992).

Ma Y, Wen M, Guo Y, Li B, Cournede PH, de Reffye P. Parameter optimization and field validation of the functional-structural model GREENLAB for maize at different population densities. Ann. Bot. (Lond.) 101: 1185-1194 (2008).

Maclagan RGAR, Malardier-Jugroot C, Whitehead MA, Lever M. Theoretical studies of the interaction of water with compensatory and noncompensatory solutes for proteins. J. Phys. Chem. A 108: 2514-2519 (2004).

Macol C, Dutta M, Stec B, Tsuruta H, Kantrowitz ER. The 80s loop of the catalytic chain of Escherichia coli aspartate transcarbamoylase is critical for catalysis and homotropic cooperativity. Protein Sci. 8: 1305-1313 (1999).

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

Majewski RA, Domach MM. Consideration of the gain, enzymatic capacity utilization, and response time properties of metabolic networks as a function of operating point and structure. Biosystems 18: 15-22 (1985).

Mantzaris NV, Liou J-J, Daoutidis P, Srienc F. Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration. J. Biotechnol. 71: 157-174 (1999).

Mao L, Resat H. Probabilistic representation of gene regulatory networks. Bioinformatics 20: 2258-2269 (2004).

Marabotti A, Cozzini P, Mozzarelli A. Novel allosteric effectors of the tryptophan synthase alpha(2)beta(2) complex identified by computer-assisted molecular modeling. Biochim. Biophys. Acta 1476: 287-299 (2000).

Martienssen RA, Rabinowicz PD, O'Shaughnessy A, McCombie WR. Sequencing the maize genome. Curr. Opin. Plant Biol. 7: 102-107 (2004).

Martre P, Porter JR, Jamieson PD, Triboi E. Modeling grain nitrogen accumulation and protein composition to understand the sink/source regulations of nitrogen remobilization for wheat. Plant Physiol. 133: 1959-1967 (2003).

Marx KA, Zhou T, Warren M, Braunhut SJ. Quartz crystal microbalance study of endothelial cell number dependent differences in initial adhesion and steady-state behavior: evidence for cell-cell cooperativity in initial adhesion and spreading. Biotechnol. Prog. 19: 987-999 (2003).

Mason GF, Rothman DL. Basic principles of metabolic modeling of NMR (13)C isotopic turnover to determine rates of brain metabolism in vivo. Metab. Eng. 6: 75-84 (2004).

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

Mayle FE, Beerling DJ, Gosling WD, Bush MB. Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 359: 499-514 (2004).

McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 27: 199-224 (1998).

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

McDowell LM, Klug CA, Beusen DD, Schaefer J. Ligand geometry of the ternary complex of 5-enolpyruvylshikimate-3-phosphate synthase from rotational-echo double-resonance NMR. Biochemistry 35: 5395-5403 (1996).

McMaster GS, White JW, Hunt LA, Jamieson PD, Dhillon SS, Ortiz-Monasterio JI. Simulating the influence of vernalization, photoperiod and optimum temperature on wheat developmental rates. Ann. Bot. (Lond.) 102: 561-569 (2008).

McNamara JP, Baldwin RL. Estimation of parameters describing lipid metabolism in lactation: challenge of existing knowledge described in a model of metabolism. J. Dairy Sci. 83: 128-143 (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).

Mehra S, Hu WS, Karypis G. A Boolean algorithm for reconstructing the structure of regulatory networks. Metab. Eng. 6: 326-339 (2004).

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).

Mendes P. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22: 361-363 (1997).

Mendes P. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9: 563-571 (1993).

Mendes P, Camacho D, de la Fuente A. Modelling and simulation for metabolomics data analysis. Biochem. Soc. Trans. 33: 1427-1429 (2005).

Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol. Biol. 500: 17-59 (2009).

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. Numerical optimization and simulation for rational metabolic engineering. In (C Larsson, IL Pahlman, L Gustaffson eds) "BioThermoKinetics in the Post Genomic Era", Chalmers Reproservice, Goteborg, pp. 345-349 (1998).

Mendes P, Kell DB. Computer simulation of biochemical kinetics. In "BioThermoKinetics of the living cell" (HV Westerhoff, JL Snoep, FE Sluse, JE Wijker, BN Kholodenko eds), BioThermoKinetics Press, Amsterdam, pp. 254-257 (1996).

Mendes P, Kell DB. On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool. Acta Biotheor. 41: 63-73 (1993).

Mendes P, Kell DB, Welch GR. Metabolic channelling in organized enzyme systems: experiments and models. Adv. Mol. Cell. Biol. 11: 1-19 (1995).

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

Mendes P, Kell DB, Westerhoff HV. Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim. Biophys. Acta 1289: 175-186 (1996).

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

Meng TC, Somani S, Dhar P. Modeling and simulation of biological systems with stochasticity. In Silico Biol. 4: 0024 (2004).

Meric PA, Wise MJ. Quantitative, scalable discrete-event simulation of metabolic pathways. Ismb 7: 187-194 (1999).

Merzlyak MN, Melo TB, Naqvi KR. Effect of anthocyanins, carotenoids, and flavonols on chlorophyll fluorescence excitation spectra in apple fruit: signature analysis, assessment, modelling, and relevance to photoprotection. J. Exp. Bot. 59: 349-359 (2008).

Messana I, Misiti F, el-Sherbini S, Giardina B, Castagnola M. Quantitative determination of the main glucose metabolic fluxes in human erythrocytes by 13C- and 1H-MR spectroscopy. J. Biochem. Biophys. Methods 39: 63-84 (1999).

Meyers S, Friedland P. Knowledge-based simulation of genetic regulation in bacteriophage lambda. Nucleic Acids Res. 12: 1-9 (1984).

Mihalas GI, Macovievici G, Simon Z, Mihalas G, Balea G, Lungeanu D. MOBISIM--package for simulation in molecular biology. Stud. Health Technol. Inform. 68: 617-620 (1999).

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).

Moing A, Escobar-Gutierrez A, Gaudillere JP. Modeling carbon export out of mature peach leaves. Plant Physiol. 106: 591-600 (1994).

Mollney M, Wiechert W, Kownatzki D, de Graaf AA. Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66: 86-103 (1999).

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

Moya-Garcia AA, Ruiz-Pernia J, Martí S, Sanchez-Jimenez F, Tunon I. Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study. J. Biol. Chem. 283: 12393-12401 (2008).

Muchow RC. Effect of water and nitrogen supply on radiation interception and biomass accumulation of kenaf (Hibiscus cannabinus) in a semiarid tropical environment. Field Crop. Res. 28: 281-293 (1992).

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: computer simulation and Metabolic Control Analysis. Biochem. J. 342: 597-604 (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).

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 JM, Sexton DM, Barnett DN, Jones GS, Webb MJ, Collins M, Stainforth DA. Quantification of modelling uncertainties in a large ensemble of climate change simulations. Nature 430: 768-772 (2004).

Mutalik VK, Venkatesh KV. A theoretical steady state analysis indicates that induction of Escherichia coli glnALG operon can display all-or-none behavior. Biosystems 90: 1-19 (2007).

Nagasaki M, Saito A, Li C, Jeong E, Miyano S. Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2: 53 (2008).

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).

Naito Y, Ohno H, Seno S, Oguchi Y, Sano A, Nakajima H, Tomita M. A simulation model of diabetes using E-Cell system. Genome Informatics 12: 310-311 (2001).

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J. Bioinform. Comput. Biol. 4: 335-355 (2006).

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Proc. IEEE Comput. Syst. Bioinform. Conf. 2005: 279-288 (2005).

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

Namjoshi AA, Ramkrishna D. Multiplicity and stability of steady states in continuous bioreactors: dissection of cybernetic models. Chem. Eng. Sci. 56: 5593-5607 (2001).

Niinemets U, Diaz-Espejo A, Flexas J, Galmes J, Warren CR. Role of mesophyll diffusion conductance in constraining potential photosynthetic productivity in the field. J. Exp. Bot. 60: 2249-2270 (2009).

Niinemets U, Reichstein M, Staudt M, Seufert G, Tenhunen JD. Stomatal constraints may affect emission of oxygenated monoterpenoids from the foliage of Pinus pinea. Plant Physiol. 130: 1371-1385 (2002).

Niinemets U, Sonninen E, Tobias M. Canopy gradients in leaf intercellular CO2 mole fractions revisited: interactions between leaf irradiance and water stress need consideration. Plant Cell Environ. 27: 569-583 (2004).

Niinemets U, Tenhunen JD, Harley PC, Steinbrecher R. A model of isoprene emission based on energetic requirements for isoprene synthesis and leaf photosynthetic properties for Liquidambar and Quercus. Plant Cell Environ. 22: 1319-1335 (1999).

Nijhout HF, Gregory JF, Fitzpatrick C, Cho E, Lamers KY, Ulrich CM, Reed MC. A mathematical model gives insights into the effects of vitamin B-6 deficiency on 1-carbon and glutathione metabolism. J. Nutr. 139: 784-791 (2009).

Nikolov NT, Massman WJ, Schoettle AW. Coupling biochemical and biophysical processes at the leaf level - an equilibrium photosynthesis model for leaves of C3 plants. Ecological Modelling 80: 205-235 (1995).

Noble D. Will genomics revolutionise pharmaceutical R&D? Trends Biotechnol. 21: 333-337 (2003).

Noh K, Wahl A, Wiechert W. Computational tools for isotopically instationary (13)C labeling experiments under metabolic steady state conditions. Metab. Eng. 8: 554-577 (2006).

Noh K, Wiechert W. Experimental design principles for isotopically in stationary 13C labeling experiments. Biotechnol. Bioeng. 94: 234-251 (2006).

Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst. Biol. 2: 71 (2008).

Noordewier MO, Warren PV. Gene expression microarrays and the integration of biological knowledge. Trends Biotechnol. 19: 412-415 (2001).

Normand F, Habib R, Chadoeuf J. A stochastic flowering model describing an asynchronically flowering set of trees. Ann. Bot. (Lond.) 90: 405-415 (2002).

Nowak W, Cody V, Wojtczak A. Computer modeling studies of the structural role of NADPH binding to active site mutants of human dihydrofolate reductase in complex with piritrexim. Acta Biochim. Pol. 48: 903-916 (2001).

Ohashi K, Thomson JD. Trapline foraging by pollinators: its ontogeny, economics and possible consequences for plants. Ann. Bot. (Lond.) 103: 1365-1378 (2009).

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).

Okamoto H, Ichikawa K. Switching characteristics of a model for biochemical-reaction networks describing autophosphorylation versus dephosphorylation of Ca2+/calmodulin-dependent protein kinase II. Biol. Cybern. 82: 35-47 (2000).

Okamoto M, Hayashi K. Homeostatic capability of rate-sensitive feedback system: mathematical model. Am. J. Physiol. 247: R927-R931 (1984).

Oliveira JS, Bailey CG, Jones-Oliveira JB, Dixon DA. An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull. Math. Biol. 63: 1163-1196 (2001).

Ow DS, Lee DY, Yap MG, Oh SK. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol. Prog. 25: 61-67 (2009).

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

Palma PN, Lagoutte B, Krippahl L, Moura JJ, Guerlesquin F. Synechocystis ferredoxin/ferredoxin-NADP(+)-reductase/NADP+ complex: structural model obtained by NMR-restrained docking. FEBS Lett. 579: 4585-4590 (2005).

Palsson B. The challenges of in silico biology. Nat. Biotechnol. 18: 1147-1150 (2000).

Palsson E, Othmer HG. A model for individual and collective cell movement in Dictyostelium discoideum. Proc. Natl. Acad. Sci. U.S.A. 97: 10448-10453 (2000).

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).

Perrin RM, Wigge PA. Physiology and metabolism: Web alert. Curr. Opin. Plant Biol. 4: 177-178 (2001).

Petricka JJ, Clay NK, Nelson TM. Vein patterning screens and the defectively organized tributaries (dot) mutants in Arabidopsis thaliana. Plant J. 56: 251-263 (2008).

Pfundel E, Nagel E, Meister A. Analyzing the light energy distribution in the photosynthetic apparatus of C4 plants using highly purified mesophyll and bundle-sheath thylakoids. Plant Physiol. 112: 1055-1070 (1996).

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).

Piazza M, Feng XJ, Rabinowitz JD, Rabitz H. Diverse metabolic model parameters generate similar methionine cycle dynamics. J. Theor. Biol. 251: 628-639 (2008).

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).

Poolman MG, Fell DA, Thomas S. Modelling photosynthesis and its control. J. Exp. Bot. 51: 319-328 (2000).

Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 21: 162-169 (2003).

Prusinkiewicz P, Rolland-Lagan AG. Modeling plant morphogenesis. Curr. Opin. Plant Biol. 9: 83-88 (2006).

Quereix A, Dewar RC, Gaudillere JP, Dayau S, Valancogne C. Sink feedback regulation of photosynthesis in vines: measurements and a model. J. Exp. Bot. 52: 2313-2322 (2001).

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

Ramkrishna D, Schell J. On self-similar growth. J. Biotechnol. 71: 255-258 (1999).

Ramputh AL, Bown AW. Rapid gamma-aminobutyric acid synthesis and the inhibition of the growth and development of oblique banded leaf roller larvae. Plant Physiol. 111: 1349-1352 (1996).

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).

Rey H, Dauzat J, Chenu K, Barczi JF, Dosio GA, Lecoeur J. Using a 3-D virtual sunflower to simulate light capture at organ, plant and plot levels: contribution of organ interception, impact of heliotropism and analysis of genotypic differences. Ann. Bot. (Lond.) 101: 1139-1151 (2008).

Riederer M, Daiss A, Gilbert N, Kohle H. Semi-volatile organic compounds at the leaf/atmosphere interface: numerical simulation of dispersal and foliar uptake. J. Exp. Bot. 53: 1815-1823 (2002).

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).

Robert C, Bancal MO, Lannou C, Ney B. Quantification of the effects of Septoria tritici blotch on wheat leaf gas exchange with respect to lesion age, leaf number, and leaf nitrogen status. J. Exp. Bot. 57: 225-234 (2006).

Robert C, Bancal MO, Nicolas P, Lannou C, Ney B. Analysis and modelling of effects of leaf rust and Septoria tritici blotch on wheat growth. J. Exp. Bot. 55: 1079-1094 (2004).

Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Patil K, Nielsen J, Rocha I. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 9: 499 (2008).

Roche O, Field MJ. Theoretical study of the conformation of the lipoamide arm in a mutant H protein. Proteins 45: 237-240 (2001).

Rodrigues ML, Scott KA, Sansom MS, Pereira IA, Archer M. Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA. J. Mol. Biol. 381: 341-350 (2008).

Rosenblatt J. The mathematics behind modeling. Adv. Exp. Med. Biol. 445: 115-129 (1998).

Rossi JA. An informatics approach to complex research problems. Dynamic process modeling. Comput. Nurs. 9: 7-14 (1991).

Rost U, Kummer U. Visualisation of biochemical network simulations with SimWiz. Syst. Biol. 1: 184-189 (2004).

Roth-Nebelsick A. Computer-based studies of diffusion through stomata of different architecture. Ann. Bot. (Lond.) 100: 23-32 (2007).

Roy A, Parker RS. Dynamic modeling of free fatty acid, glucose, and insulin: an extended "minimal model". Diabetes Technol. Ther. 8: 617-626 (2006).

Ruiz-Ramos M, Minguez MI. ALAMEDA, a structural-functional model for faba bean crops: morphological parameterization and verification. Ann. Bot. (Lond.) 97: 377-388 (2006).

Sack L, Streeter CM, Holbrook NM. Hydraulic analysis of water flow through leaves of sugar maple and red oak. Plant Physiol. 134: 1824-1833 (2004).

Sahle S, Mendes P, Hoops S, Kummer U. A new strategy for assessing sensitivities in biochemical models. Philos. Transact. A. Math. Phys. Eng. Sci. 366: 3619-3631 (2008).

Samuel SA, Weng G. Characterization of a branch of the phylogenetic tree. J. Theor. Biol. 220: 457-468 (2003).

Sandberg L, Edholm O. A fast and simple method to calculate protonation states in proteins. Proteins 36: 474-483 (1999).

Sandhu KS, Pandey S, Maiti S, Pillai B. GASCO: genetic algorithm simulation for codon optimization. In Silico Biol. 8: 187-192 (2008).

Santillan M, Mackey MC. Dynamic regulation of the tryptophan operon: a modeling study and comparison with experimental data. Proc. Natl. Acad. Sci. U.S.A. 98: 1364-1369 (2001).

Sauer U, Cameron DC, Bailey JE. Metabolic capacity of Bacillus subtilis for the production of purine nucleosides, riboflavin, and folic acid. Biotechnol. Bioeng. 59: 227-238 (1998).

Schaff J, Loew LM. The virtual cell. Pac. Symp. Biocomput. 1999: 228-239 (1999).

Schaller G, Meyer-Hermann M. A modelling approach towards epidermal homoeostasis control. J. Theor. Biol. 247: 554-573 (2007).

Schittko U, Preston CA, Baldwin IT. Eating the evidence? Manduca sexta larvae can not disrupt specific jasmonate induction in Nicotiana attenuata by rapid consumption. Planta 210: 343-346 (2000).

Schmidhuber J, Tubiello FN. Global food security under climate change. Proc. Natl. Acad. Sci. U.S.A. 104: 19703-19708 (2007).

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

Schmidt K, Norregaard LC, Pedersen B, Meissner A, Duus JO, Nielsen JO, Villadsen J. Quantification of intracellular metabolic fluxes from fractional enrichment and 13C-13C coupling constraints on the isotopomer distribution in labeled biomass components. Metab. Eng. 1: 166-179 (1999).

Schouten RE, Carvalho SM, Heuvelink E, Van Kooten O. Modelling of temperature-controlled internode elongation applied to chrysanthemum. Ann. Bot. (Lond.) 90: 353-359 (2002).

Schutyser MA, Briels WJ, Rinzema A, Boom RM. Numerical simulation and PEPT measurements of a 3D conical helical-blade mixer: A high potential solids mixer for solid-state fermentation. Biotechnol. Bioeng. 84: 29-39 (2003).

Schwender J, Ohlrogge JB, Shachar-Hill Y. A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. J. Biol. Chem. 278: 29442-29453 (2003).

Seginer I. A dynamic model for nitrogen-stressed lettuce. Ann. Bot. (Lond.) 91: 623-635 (2003).

Seginer I, Bleyaert P, Breugelmans M. Modelling ontogenetic changes of nitrogen and water content in lettuce. Ann. Bot. (Lond.) 94: 393-404 (2004).

Selivanov VA, Marin S, Lee PW, Cascante M. Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis. Bioinformatics 22: 2806-2812 (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).

Selvarasu S, Ow DS, Lee SY, Lee MM, Oh SK, Karimi IA, Lee DY. Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis. Biotechnol. Bioeng. 102: 923-934 (2009).

Selvarasu S, Wong VV, Karimi IA, Lee DY. Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling. Biotechnol. Bioeng. 102: 1494-1504 (2009).

Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol. Bioeng. 101: 1036-1052 (2008).

Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol. Bioeng. 101: 1053-1071 (2008).

Serra R, Villani M, Graudenzi A, Kauffman SA. Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. J. Theor. Biol. 246: 449-460 (2007).

Shanklin T, Roper K, Yegneswaran PK, Marten MR. Selection of bioprocess simulation software for industrial applications. Biotechnol. Bioeng. 72: 483-489 (2001).

Sheridan R, Jackson GA, LR, Ward J, Dunnill P. Rational engineering of the TOL meta-cleavage pathway. Biotechnol. Bioeng. 58: 240-249 (1998).

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

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).

Silva FV, Martins RC, Silva CL. Design and optimization of hot-filling pasteurization conditions: cupuacu (Theobroma grandiflorum) fruit pulp case study. Biotechnol. Prog. 19: 1261-1268 (2003).

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).

Sinibaldi R, Casieri C, Melchionna S, Onori G, Segre AL, Viel S, Mannina L, De Luca F. The role of water coordination in binary mixtures. A study of two model amphiphilic molecules in aqueous solutions by molecular dynamics and NMR. J. Phys. Chem. B. Condens. Matter Mater. Surf. Interfaces Biophys. 110: 8885-8892 (2006).

Siso-Nadal F, Ollivier JF, Swain PS. Facile: a command-line network compiler for systems biology. BMC Syst. Biol. 1: 36 (2007).

Small JR, Kacser H. Responses of metabolic systems to large changes in enzyme activities and effectors. 2. The linear treatment of branched pathways and metabolite concentrations. Assessment of the general non-linear case. Eur. J. Biochem. 213: 625-640 (1993).

Smith JE, Heath LS. Identifying influences on model uncertainty: An application using a forest carbon budget model. Environ. Manage. 27: 253-267 (2001).

Smith MA, King PJ, Grimm B. Transient-state kinetic analysis of Synechococcus glutamate 1-semialdehyde aminotransferase. Biochemistry 37: 319-329 (1998).

Smith RS, Bayer EM. Auxin transport-feedback models of patterning in plants. Plant Cell Environ. 32: 1258-1271 (2009).

Smith RS, Guyomarc'h S, Mandel T, Reinhardt D, Kuhlemeier C, Prusinkiewicz P. A plausible model of phyllotaxis. Proc. Natl. Acad. Sci. U.S.A. 103: 1301-1306 (2006).

Smolen P, Baxter DA, Byrne JH. Modeling transcriptional control in gene networks--methods, recent results, and future directions. Bull. Math. Biol. 62: 247-292 (2000).

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).

Soyer OS, Bonhoeffer S. Evolution of complexity in signaling pathways. Proc. Natl. Acad. Sci. U.S.A. 103: 16337-16342 (2006).

Spyrakis F, Raboni S, Cozzini P, Bettati S, Mozzarelli A. Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit. Biochim. Biophys. Acta 1764: 1102-1109 (2006).

Srinivasan V, Ciddi V, Bringi V, Shuler ML. Metabolic inhibitors, elicitors, and precursors as tools for probing yield limitation in taxane production by Taxus chinensis cell cultures. Biotechnol. Prog. 12: 457-465 (1996).

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

Stadler T, Arunyawat U, Stephan W. Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178: 339-350 (2008).

Steel C, Henchman M. Understanding the quadrupole mass filter through computer simulation. J. Chem. Educ. 75: 1049-1054 (1998).

Stephanopoulos G, Simpson TW. Flux amplification in complex metabolic networks. Chem. Eng. Sci. 52: 2607-2627 (1997).

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).

Stoffers HJ, Sonnhammer EL, Blommestijn GJ, Raat NJ, Westerhoff HV. METASIM: object-oriented modelling of cell regulation. Comput. Appl. Biosci. 8: 443-449 (1992).

Streck NA, Weiss A, Xue Q, Baenziger PS. Incorporating a chronology response into the prediction of leaf appearance rate in winter wheat. Ann. Bot. (Lond.) 92: 181-190 (2003).

Sugimoto T. Darwinian evolution does not rule out the gaia hypothesis. J. Theor. Biol. 218: 447-455 (2002).

Sun X, Jin L, Xiong M. Extended Kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks. PLoS ONE 3: e3758 (2008).

Szilagyi Z, Fenselau C. Molecular dynamics simulation of metallothionein-drug complexes. Drug Metab. Dispos. 28: 174-179 (2000).

Takahashi K, Arjunan SN, Tomita M. Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico. FEBS Lett. 579: 1783-1788 (2005).

Talasaz AH, Nemat-Gorgani M, Liu Y, Stahl P, Dutton RW, Ronaghi M, Davis RW. Prediction of protein orientation upon immobilization on biological and nonbiological surfaces. Proc. Natl. Acad. Sci. U.S.A. 103: 14773-14778 (2006).

Talbot A, Neuman MR, Saidel GM, Jacobsen E. Dynamic model of oxygen transport for transcutaneous PO2 analysis. Ann. Biomed. Eng. 24: 294-304 (1996).

Thomas S, Fell DA. Design of metabolic control for large flux changes. J. Theor. Biol. 182: 285-298 (1996).

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).

Thompson D, Lazennec C, Plateau P, Simonson T. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Proteins 71: 1450-1460 (2008).

Tomek P, Lazar D, Ilik P, Naus J. On the intermediate steps between the O and P steps in chlorophyll alpha fluorescence rise measured at different intensities of exciting light. Aust. J. Plant Physiol. 28: 1151-1160 (2001).

Tomita M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19: 205-210 (2001).

Tomita M, Hashimoto K, Takahashi K, Shimizu T, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA. E-CELL: software environment for whole cell simulation. Genome Inform. Ser. Workshop Genome Inform. 8: 147-155 (1997).

Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA 3rd. E-CELL: software environment for whole-cell simulation. Bioinformatics 15: 72-84 (1999).

Topham CM. Computer simulations of the kinetics of irreversible enzyme inhibition by an unstable inhibitor. Biochem. J. 240: 817-820 (1986).

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).

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. Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl. Acad. Sci. U.S.A. 88: 7328-7232 (1991).

Uchiyama K, Shioya S. Modeling and optimization of a-amylase production in a recombinant yeast fed-batch culture taking into account of the cell cycle population distribution. J. Biotechnol. 71: 133-141 (1999).

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

Valero E, Gonzalez-Sanchez MI, Macia H, Garcia-Carmona F. Computer simulation of the dynamic behavior of the glutathione-ascorbate redox cycle in chloroplasts. Plant Physiol. 149: 1958-1969 (2009).

van Aalten DM, Grotewold E, Joshua-Tor L. Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant. Methods 14: 318-328 (1998).

van Beek JH, Hauschild AC, Hettling H, Binsl TW. Robust modelling, measurement and analysis of human and animal metabolic systems. Philos. Transact. A. Math. Phys. Eng. Sci. 367: 1971-1992 (2009).

van Breukelen B, Barendregt A, Heck AJ, van den Heuvel RH. Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra. Rapid Commun. Mass Spectrom. 20: 2490-2496 (2006).

Van der Weerd L, Claessens MMAE, Efde C, Van As H. Nuclear magnetic resonance imaging of membrane permeability changes in plants during osmotic stress. Plant Cell Environ. 25: 1539-1549 (2002).

Van Dien SJ, Lidstrom ME. Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol. Bioeng. 78: 296-312 (2002).

van Gunsteren WF, Mark AE. On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204: 947-961 (1992).

van Riel NA, Giuseppin ML, Verrips CT. Dynamic optimal control of homeostasis: an integrative system approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae. Metab. Eng. 2: 49-68 (2000).

Van Winden WA, Van Gulik WM, Schipper D, Verheijen PJ, Krabben P, Vinke JL, Heijnen JJ. Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation. Biotechnol. Bioeng. 83: 75-92 (2003).

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).

Vasil'ev S, Bruce D. Optimization and evolution of light harvesting in photosynthesis: the role of antenna chlorophyll conserved between photosystem II and photosystem I. Plant Cell 16: 3059-3068 (2004).

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).

Verkest A, Manes CL, Vercruysse S, Maes S, Van Der Schueren E, Beeckman T, Genschik P, Kuiper M, Inze D, De Veylder L. The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes. Plant Cell 17: 1723-1736 (2005).

Vesala T, Holtta T, Peramaki M, Nikinmaa E. Refilling of a hydraulically isolated embolized xylem vessel: model calculations. Ann. Bot. (Lond.) 91: 419-428 (2003).

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, 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).

Vitkup D, Ringe D, Petsko GA, Karplus M. Solvent mobility and the protein 'glass' transition. Nat. Struct. Biol. 7: 34-38 (2000).

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

Voit EO, Del Signore M. Assessment of effects of experimental imprecision on optimized biochemical systems. Biotechnol. Bioeng. 74: 443-448 (2001).

Volder A, Smart DR, Bloom AJ, Eissenstat DM. Rapid decline in nitrate uptake and respiration with age in fine lateral roots of grape: implications for root efficiency and competitive effectiveness. New Phytol. 165: 493-501 (2005).

Vrbka L, Vondrasek J, Jagoda-Cwiklik B, Vacha R, Jungwirth P. Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces. Proc. Natl. Acad. Sci. U.S.A. 103: 15440-1544 (2006).

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

Walk TC, Van Erp E, Lynch JP. Modelling applicability of fractal analysis to efficiency of soil exploration by roots. Ann. Bot. (Lond.) 94: 119-128 (2004).

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

Wang CX, Wang L, Thomas CR. Modelling the mechanical properties of single suspension-cultured tomato cells. Ann. Bot. (Lond.) 93: 443-453 (2004).

Wang Q, Chen X, Yang Y, Zhao X. Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production. Appl. Microbiol. Biotechnol. 73: 887-894 (2006).

Wann M, Raper CD Jr. A dynamic model for plant growth: validation study under changing temperatures. Ann. Bot. (Lond.) 53: 45-52 (1984).

Wedler FC, Ley BW. Kinetic and regulatory mechanisms for (Escherichia coli) homoserine dehydrogenase-I. Equilibrium isotope exchange kinetics. J. Biol. Chem. 268: 4880-4888 (1993).

Wedler FC, Ley BW. Homoserine dehydrogenase-I (Escherichia coli): action of monovalent ions on catalysis and substrate association-dissociation. Arch. Biochem. Biophys. 301: 416-423 (1993).

Wei H, Atkins CA, Layzell DB. Adenylate gradients and Ar:O2 effects on legume nodules. II. Changes in the subcellular adenylate pools. Plant Physiol. 134: 1775-1783 (2004).

Wei H, Atkins CA, Layzell DB. Adenylate gradients and Ar:O2 effects on legume nodules: I. Mathematical models. Plant Physiol. 134: 801-812 (2004).

Weinstein AM. Insights from mathematical modeling of renal tubular function in vivo, in vitro and mathematical analysis of renal tubule function. Exp. Nephrol. 5: 462-468 (1998).

Werner C, Ryel RJ, Correia O, Beyschlag W. Effects of photoinhibition on whole-plant carbon gain assessed with a photosynthesis model. Plant Cell Environ. 24: 27-40 (2001).

Werner I, Bacher A, Eisenreich W. Retrobiosynthetic NMR studies with 13C-labeled glucose. Formation of gallic acid in plants and fungi. J. Biol. Chem. 272: 25474-25482 (1997).

Werten PJL, Remigy HW, de Groot BL, Fotiadis D, Philippsen A, Stahlberg H, Grubmuller H, Engel A. Progress in the analysis of membrane protein structure and function. FEBS Lett. 529: 65-72 (2002).

Wiechert W. 13C metabolic flux analysis. Metab. Eng. 3: 195-206 (2001).

Wiechert W. Modeling and simulation: tools for metabolic engineering. J. Biotechnol. 94: 37-63 (2002).

Wiechert W. An introduction to 13C metabolic flux analysis. Genet. Eng. (N.Y.) 24: 215-238 (2002).

Wiechert W, de Graaf AA. Bidirectional reaction steps in metabolic networks. 1. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55: 101-117 (1997).

Wiechert W, Mollney M, Isermann N, Wurzel M, de Graaf AA. Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. Biotechnol. Bioeng. 66: 69-85 (1999).

Wiechert W, Mollney M, Petersen S, de Graaf AA. A universal framework for 13C metabolic flux analysis. Metab. Eng. 3: 265-283 (2001).

Wiechert W, Noh K. From stationary to instationary metabolic flux analysis. Adv. Biochem. Eng. Biotechnol. 92: 145-172 (2005).

Wiechert W, Wurzel M. Metabolic isotopomer labeling systems. Part I: global dynamic behavior. Math Biosci. 169: 173-205 (2001).

Wille A, Gruissem W, Buhlmann P, Hennig L. EVE (external variance estimation) increases statistical power for detecting differentially expressed genes. Plant J. 52: 561-569 (2007).

Williams JP, Khan MU, Wong D. Computer simulation model for the biosynthesis of galactosyldiacylglycerols and fatty acid desaturation in plants. Determination of rates of desaturase activity in monogalactosyldiacylglycerol. Plant Physiol. 101: 977-983 (1993).

Winkler E, Stocklin J. Sexual and vegetative reproduction of Hieracium pilosella L. under competition and disturbance: a grid-based simulation model. Ann. Bot. (Lond.) 89: 525-536 (2002).

Winz RA, Baldwin IT. Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. IV. Insect-induced … Plant Physiol. 125: 2189-2202 (2001).

Wissuwa M. How do plants achieve tolerance to phosphorus deficiency? Small causes with big effects. Plant Physiol. 133: 1947-1958 (2003).

Wittmann C, Heinzle E. Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62: 739-750 (1999).

Woehl E, Dunn MF. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase alpha-, beta-, and alpha beta-reactions. Biochemistry 38: 7131-7141 (1999).

Wolf J, Sohn H, Heinrich R, Kuriyama H. Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae. FEBS Lett. 499: 230-234 (2001).

Wu J, Voit E. Hybrid modeling in biochemical systems theory by means of functional petri nets. J. Bioinform. Comput. Biol. 7: 107-134 (2009).

Wuensche A. Genomic regulation modeled as a network with basins of attraction. Pac. Symp. Biocomput. 1998: 89-102 (1998).

Wurthner JU, Mukhopadhyay AK, Peimann CJ. A cellular automaton model of cellular signal transduction. Comput. Biol. Med. 30: 1-21 (2000).

Wyka TP, Bohn A, Duarte HM, Kaiser F, Luttge UE. Perturbations of malate accumulation and the endogenous rhythms of gas exchange in the Crassulacean acid metabolism plant Kalanchoe daigremontiana: testing the tonoplast-as-oscillator model. Planta 219: 705-713 (2004).

Xu B, Jahic M, Enfors SO. Modeling of overflow metabolism in batch and fed-batch cultures of Escherichia coli. Biotechnol. Prog. 15: 81-90 (1999).

Xu X, Cui ZF. Modeling of the co-transport of cryoprotective agents in a porous medium as a model tissue. Biotechnol. Prog. 19: 972-981 (2003).

Xu Z, Sun X, Yu S. Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach. BMC Bioinformatics 10 Suppl. 1: S62 (2009).

Yamamoto H, Yoshida M, Okuyama T. Growth stress controls negative gravitropism in woody plant stems. Planta 216: 280-292 (2002).

Yamamoto R, Fujii S, Tanimoto E, Nevins DJ. Computer simulation of osmotic expansion and shrinkage in okra hypocotyl segments. Biorheology 37: 213-223 (2000).

Yan L, Ropella GE, Park S, Roberts MS, Hunt CA. Modeling and simulation of hepatic drug disposition using a physiologically based, multi-agent in silico liver. Pharm. Res. 25: 1023-1036 (2008).

Yang CR. An enzyme-centric approach for modelling non-linear biological complexity. BMC Syst. Biol. 2: 70 (2008).

Yang J, Wongsa S, Kadirkamanathan V, Billings SA, Wright PC. Metabolic flux distribution analysis by 13C-tracer experiments using the Markov chain-Monte Carlo method. Biochem. Soc. Trans. 33: 1421-1422 (2005).

Yang J, Zhu J, Williams RW. Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23: 1527-1536 (2007).

Yang TH, Bolten CJ, Coppi MV, Sun J, Heinzle E. Numerical bias estimation for mass spectrometric mass isotopomer analysis. Anal. Biochem. 388: 192-203 (2009).

Yang TH, Heinzle E, Wittmann C. Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling. Comput. Biol. Chem. 29: 121-133 (2005).

Yang Z, Midmore DJ. A model for the circadian oscillations in expression and activity of nitrate reductase in higher plants. Ann. Bot. (Lond.) 96: 1019-1026 (2005).

Yaniv Y, Stanley WC, Saidel GM, Cabrera ME, Landesberg A. The role of Ca2+ in coupling cardiac metabolism with regulation of contraction: in silico modeling. Ann. N. Y. Acad. Sci. 1123: 69-78 (2008).

Yin X, Goudriaan J, Lantinga EA, Vos J, Spiertz HJ. A flexible sigmoid function of determinate growth. Ann. Bot. (Lond.) 91: 361-371 (2003).

Yin X, Lantinga EA, Schapendonk AH, Zhong X. Some quantitative relationships between leaf area index and canopy nitrogen content and distribution. Ann. Bot. (Lond.) 91: 893-903 (2003).

You L, Yin J. Patterns of regulation from mRNA and protein time series. Metab. Eng. 2: 210-217 (2000).

Yu Q. Simulation of the physiological responses of C3 plant leaves to environmental factors by a model which combines stomatal conductance, photosynthesis and transpiration. Acta Bot. Sin. 40: 740-754 (1998).

Yu Q, Zhang Y, Liu Y, Shi P. Simulation of the stomatal conductance of winter wheat in response to light, temperature and CO2 changes. Ann. Bot. (Lond.) 93: 435-441 (2004).

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).

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

Zeng ZB. Precision mapping of quantitative trait loci. Genetics 136: 1457-1468 (1994).

Zhang LB, Zhu Q, Wu ZQ, Ross-Ibarra J, Gaut BS, Ge S, Sang T. Selection on grain shattering genes and rates of rice domestication. New Phytol. Aug 5 [Epub ahead of print] (2009).

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 H, Singh NJ, Kim KS. Homology modeling and molecular dynamics study of chorismate synthase from Shigella flexneri. J. Mol. Graph Model. 25: 434-441 (2006).

Zhu XG, de Sturler E, Long SP. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm. Plant Physiol. 145: 513-526 (2007).

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, Ort DR, Whitmarsh J, Long SP. The slow reversibility of photosystem II thermal energy dissipation on transfer from high to low light may cause large losses in carbon gain by crop canopies: a theoretical analysis. J. Exp. Bot. 55: 1167-1175 (2004).

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, Reichling P, Valladares F. A simulation study on the importance of size-related changes in leaf morphology and physiology for carbon gain in an epiphytic bromeliad. Ann. Bot. (Lond.) 90: 437-443 (2002).

Number of references = 526