Experimental and mathematical approaches to modeling plant metabolic networks.
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[1] Reinhart Heinrich,et al. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. , 1974, European journal of biochemistry.
[2] C Reder,et al. Metabolic control theory: a structural approach. , 1988, Journal of theoretical biology.
[3] C. Giersch. Control analysis of biochemical pathways: a novel procedure for calculating control coefficients, and an additional theorem for branched pathways. , 1988, Journal of theoretical biology.
[4] G. Pettersson,et al. A mathematical model of the Calvin photosynthesis cycle. , 1988, European journal of biochemistry.
[5] M. Stitt,et al. Decreased-activity mutants of phosphoglucose isomerase in the cytosol and chloroplast of Clarkia xantiana. Impact on mass-action ratios and fluxes to sucrose and starch, and estimation of Flux Control Coefficients and Elasticity Coefficients. , 1989, The Biochemical journal.
[6] I. Dry,et al. An analysis of the control of phosphorylation-coupled respiration in isolated plant mitochondria. , 1989, Plant physiology.
[7] G. Brown,et al. A 'top-down' approach to the determination of control coefficients in metabolic control theory. , 1990, European journal of biochemistry.
[8] L. Gross,et al. A dynamic model of photosynthesis in varying light taking account of stomatal conductance, C3-cycle intermediates, photorespiration and Rubisco activation , 1991 .
[9] A. Sherry,et al. 13C-NMR: a simple yet comprehensive method for analysis of intermediary metabolism. , 1991, Trends in biochemical sciences.
[10] A simple model describing the kinetics of the xanthophyll cycle. , 1991, Biophysical chemistry.
[11] J. Liao,et al. Determination of Flux Control Coefficients from transient metabolite concentrations. , 1992, The Biochemical journal.
[12] G. Collatz,et al. Coupled Photosynthesis-Stomatal Conductance Model for Leaves of C4 Plants , 1992 .
[13] Pedro Mendes,et al. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems , 1993, Comput. Appl. Biosci..
[14] J. Harwood,et al. Acetyl-CoA carboxylase exerts strong flux control over lipid synthesis in plants. , 1994, Biochimica et biophysica acta.
[15] Michael B. Coughenour,et al. Mathematical simulation of C4 grass photosynthesis in ambient and elevated CO2 , 1994 .
[16] A Metabolic Control Analysis of the Glutamine Synthetase/Glutamate Synthase Cycle in Isolated Barley (Hordeum vulgare L.) Chloroplasts , 1994, Plant physiology.
[17] George Stephanopoulos,et al. Modeling of Isotope Distributions and Intracellular Fluxes in Metabolic Networks Using Atom Mapping Matrices , 1994 .
[18] M. Kirschbaum. The sensitivity of C3 photosynthesis to increasing CO2 concentration: a theoretical analysis of its dependence on temperature and background CO2 concentration , 1994 .
[19] S. Schuster,et al. ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE , 1994 .
[20] M. Dieuaide-Noubhani,et al. Quantification of Compartmented Metabolic Fluxes in Maize Root Tips Using Isotope Distribution from 13C- or 14C-Labeled Glucose (*) , 1995, The Journal of Biological Chemistry.
[21] P. Hedden,et al. Constitutive expression of a fruit phytoene synthase gene in transgenic tomatoes causes dwarfism by redirecting metabolites from the gibberellin pathway , 1995 .
[22] K. Krab. Kinetic and regulatory aspects of the function of the alternative oxidase in plant respiration , 1995, Journal of bioenergetics and biomembranes.
[23] H. Kacser,et al. The control of flux. , 1995, Biochemical Society transactions.
[24] R. Heinrich,et al. The Regulation of Cellular Systems , 1996, Springer US.
[25] D. Fell. Understanding the Control of Metabolism , 1996 .
[26] J. Villadsen,et al. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. , 1997, Biotechnology and bioengineering.
[27] F. Botha,et al. Carbon Partitioning during Sucrose Accumulation in Sugarcane Internodal Tissue , 1997, Plant physiology.
[28] Robert W. Pearcy,et al. An improved dynamic model of photosynthesis for estimation of carbon gain in sunfleck light regimes , 1997 .
[29] C. Giersch,et al. Modelling photosynthesis in fluctuating light with inclusion of stomatal conductance, biochemical activation and pools of key photosynthetic intermediates , 1997, Planta.
[30] D. Fell,et al. Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): explanation for the low control coefficient of phosphofructokinase over respiratory flux. , 1997, The Biochemical journal.
[31] D. Fell,et al. Finite change analysis of glycolytic intermediates in tuber tissue of lines of transgenic potato (Solanum tuberosum) overexpressing phosphofructokinase. , 1997, The Biochemical journal.
[32] A Model for Photosynthetic Oscillations in Crassulacean Acid Metabolism (CAM). , 1997, Journal of theoretical biology.
[33] G. Pettersson. Control properties of the Calvin photosynthesis cycle at physiological carbon dioxide concentrations , 1997 .
[34] B. Blasius,et al. Thermodynamics and Energetics of the Tonoplast Membrane Operating as a Hysteresis Switch in an Oscillatory Model of Crassulacean Acid Metabolism , 1998, The Journal of Membrane Biology.
[35] B. Blasius,et al. Oscillatory model of crassulacean acid metabolism : structural analysis and stability boundaries with a discrete hysteresis switch , 1998 .
[36] Nguyen,et al. Contribution of malic enzyme, pyruvate kinase, phosphoenolpyruvate carboxylase, and the krebs cycle to respiration and biosynthesis and to intracellular pH regulation during hypoxia in maize root tips observed by nuclear magnetic resonance imaging and gas chromatography-mass spectrometry , 1998, Plant physiology.
[37] G. Stephanopoulos,et al. Metabolic Engineering: Principles And Methodologies , 1998 .
[38] T Szyperski,et al. 13C-NMR, MS and metabolic flux balancing in biotechnology research , 1998, Quarterly Reviews of Biophysics.
[39] L. Fridlyand,et al. Flux control of the malate valve in leaf cells. , 1998, Archives of biochemistry and biophysics.
[40] P. Raymond,et al. Unidirectional Steady State Rates of Central Metabolism Enzymes Measured Simultaneously in a Living Plant Tissue* , 1998, The Journal of Biological Chemistry.
[41] Independent Changes of ATP/ADP or DeltapH could cause Oscillations in Photosynthesis. , 1998, Journal of theoretical biology.
[42] L. Fridlyand,et al. Regulation of the Calvin cycle for CO2 fixation as an example for general control mechanisms in metabolic cycles. , 1999, Bio Systems.
[43] D. Ramkrishna,et al. Mathematical models of metabolic pathways. , 1999, Current opinion in biotechnology.
[44] J Villadsen,et al. Quantification of intracellular metabolic fluxes from fractional enrichment and 13C-13C coupling constraints on the isotopomer distribution in labeled biomass components. , 1999, Metabolic engineering.
[45] B. Palsson,et al. Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances , 1999, Biotechnology progress.
[46] D. Fell,et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.
[47] W. Wiechert,et al. Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. , 1999, Biotechnology and bioengineering.
[48] G. Kishore,et al. Metabolic engineering of Arabidopsis and Brassica for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer production , 1999, Nature Biotechnology.
[49] P. Dunnill,et al. Metabolic modeling as a tool for evaluating polyhydroxyalkanoate copolymer production in plants. , 1999, Metabolic engineering.
[50] Kruger,et al. Control of gluconeogenesis by isocitrate lyase in endosperm of germinating castor bean seedlings , 1999, The Plant journal : for cell and molecular biology.
[51] F. Beck,et al. Oscillatory model of crassulacean acid metabolism with a dynamic hysteresis switch , 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[52] P. Beyer,et al. Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. , 2000, Science.
[53] C Giersch. Mathematical modelling of metabolism. , 2000, Current opinion in plant biology.
[54] N. Kruger,et al. Strategies for metabolic flux analysis in plants using isotope labelling. , 2000, Journal of biotechnology.
[55] Metabolic control analysis of de novo sunflower fatty acid biosynthesis. , 2000, Biochemical Society transactions.
[56] Barbara M. Bakker,et al. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. , 2000, European journal of biochemistry.
[57] L. Fridlyand,et al. Regulation in metabolic systems under homeostatic flux control. , 2000, Archives of biochemistry and biophysics.
[58] C. Giersch,et al. Process-based modelling of isoprene emission by oak leaves. , 2000 .
[59] A. Hanson,et al. Choline import into chloroplasts limits glycine betaine synthesis in tobacco: analysis of plants engineered with a chloroplastic or a cytosolic pathway. , 2000, Metabolic engineering.
[60] L. Wackett. Metabolic engineering , 2009, Nature biotechnology.
[61] D. Fell,et al. Modelling photosynthesis and its control. , 2000, Journal of experimental botany.
[62] Y. Shachar-Hill,et al. Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco. , 2000, Plant physiology.
[63] Y. Shachar-Hill,et al. Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco. , 2000, Plant physiology.
[64] K. Burda,et al. A mathematical model describing kinetics of conversion of violaxanthin to zeaxanthin via intermediate antheraxanthin by the xanthophyll cycle enzyme violaxanthin de-epoxidase. , 2000, Journal of theoretical biology.
[65] B. Palsson,et al. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.
[66] B. Palsson,et al. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. , 2000, Biotechnology and bioengineering.
[67] A. Fernie,et al. Fructose 2,6-bisphosphate activates pyrophosphate: fructose-6-phosphate 1-phosphotransferase and increases triose phosphate to hexose phosphate cycling in heterotrophic cells , 2001, Planta.
[68] J. Rohwer,et al. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. , 2001, The Biochemical journal.
[69] A. Polle,et al. Dissecting the superoxide dismutase-ascorbate-glutathione-pathway in chloroplasts by metabolic modeling. Computer simulations as a step towards flux analysis. , 2001, Plant physiology.
[70] W. Eisenreich,et al. Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. Metabolic flux in developing maize kernels. , 2001, Plant physiology.
[71] W. Wiechert. 13C metabolic flux analysis. , 2001, Metabolic engineering.
[72] D. DellaPenna,et al. Plant metabolic engineering. , 2001, Plant physiology.
[73] Yair Shachar-Hill,et al. PROBING PLANT METABOLISM WITH NMR. , 2003, Annual review of plant physiology and plant molecular biology.
[74] W Wiechert,et al. A universal framework for 13C metabolic flux analysis. , 2001, Metabolic engineering.
[75] C. Cantrel,et al. Consequences of ω-6-Oleate Desaturase Deficiency on Lipid Dynamics and Functional Properties of Mitochondrial Membranes ofArabidopsis thaliana * , 2001, The Journal of Biological Chemistry.
[76] Consequences of omega -6-oleate desaturase deficiency on lipid dynamics and functional properties of mitochondrial membranes of Arabidopsis thaliana. , 2001, The Journal of biological chemistry.
[77] W. Eisenreich,et al. Starch Biosynthesis and Intermediary Metabolism in Maize Kernels. Quantitative Analysis of Metabolite Flux by Nuclear Magnetic Resonance1 , 2002, Plant Physiology.
[78] J. Harwood,et al. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly. , 2002, The Biochemical journal.
[79] P. Verheijen,et al. Cumulative bondomers: a new concept in flux analysis from 2D [13C,1H] COSY NMR data. , 2002, Biotechnology and bioengineering.
[80] Jörg Schwender,et al. Probing in Vivo Metabolism by Stable Isotope Labeling of Storage Lipids and Proteins in Developing Brassica napusEmbryos1 , 2002, Plant Physiology.
[81] J. Morgan,et al. Mathematical modeling of plant metabolic pathways. , 2002, Metabolic engineering.
[82] D. Rolin,et al. The Metabolic Architecture of Plant Cells , 2002, The Journal of Biological Chemistry.
[83] Jason A. Papin,et al. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. , 2002, Genome research.
[84] N. Misawa,et al. Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[85] S. Schuster,et al. Metabolic network structure determines key aspects of functionality and regulation , 2002, Nature.
[86] Apirak Hoonlor,et al. Modeling biological systems using Dynetica-a simulator of dynamic networks , 2003, Bioinform..
[87] J. Schwender,et al. A Flux Model of Glycolysis and the Oxidative Pentosephosphate Pathway in Developing Brassica napus Embryos* , 2003, Journal of Biological Chemistry.
[88] Masaru Tomita,et al. E-Cell 2: Multi-platform E-Cell simulation system , 2003, Bioinform..
[89] Steffen Klamt,et al. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps , 2003, Bioinform..
[90] Jason A. Papin,et al. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. , 2003, Biophysical journal.
[91] Gilles Curien,et al. A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana. , 2003, European journal of biochemistry.
[92] H. Miyagawa,et al. Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy. , 2003, Plant & cell physiology.
[93] Steffen Klamt,et al. Two approaches for metabolic pathway analysis? , 2003, Trends in biotechnology.
[94] D. Fell,et al. Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. , 2003, European journal of biochemistry.
[95] Hiroaki Kitano,et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .
[96] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[97] Jacky L. Snoep,et al. Web-based kinetic modelling using JWS Online , 2004, Bioinform..
[98] G. Edwards,et al. A mathematical model of C4 photosynthesis: The mechanism of concentrating CO2 in NADP-malic enzyme type species , 2004, Photosynthesis Research.
[99] Hao Zhu,et al. Cellware-a multi-algorithmic software for computational systems biology , 2004, Bioinform..
[100] Estimation of diffusive resistance of bundle sheath cells to CO2 from modeling of C4 photosynthesis , 1996, Photosynthesis Research.
[101] D. Grierson,et al. Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression , 1993, Plant Molecular Biology.
[102] Ganesh Sriram,et al. Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. , 2004, Metabolic engineering.
[103] Xinlu Chen,et al. Understanding in Vivo Benzenoid Metabolism in Petunia Petal Tissue1 , 2004, Plant Physiology.
[104] E. Schulze,et al. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with “antisense” rbcS , 1992, Planta.
[105] Ganesh Sriram,et al. Quantification of Compartmented Metabolic Fluxes in Developing Soybean Embryos by Employing Biosynthetically Directed Fractional 13C Labeling, Two-Dimensional [13C, 1H] Nuclear Magnetic Resonance, and Comprehensive Isotopomer Balancing1[w] , 2004, Plant Physiology.
[106] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[107] Mark Gerstein,et al. Analyzing cellular biochemistry in terms of molecular networks. , 2003, Annual review of biochemistry.
[108] Steffen Klamt,et al. Computation of elementary modes: a unifying framework and the new binary approach , 2004, BMC Bioinformatics.
[109] J. Schwender,et al. Understanding flux in plant metabolic networks. , 2004, Current opinion in plant biology.
[110] M. Kluge,et al. A dynamic computer model of the metabolic and regulatory processes in Crassulacean acid metabolism , 1984, Planta.
[111] E. Schulze,et al. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with ‘antisense’ rbcS , 1991, Planta.
[112] E. Schulze,et al. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with “antisense” rbcS , 1991, Planta.
[113] Lothar Willmitzer,et al. Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in (13)C labelled isotopes. , 2004, The Plant journal : for cell and molecular biology.
[114] J. Schwender,et al. Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds , 2004, Nature.
[115] J. Berry,et al. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species , 1980, Planta.
[116] J. Heijnen. Approximative kinetic formats used in metabolic network modeling , 2005, Biotechnology and bioengineering.
[117] Robert Urbanczik. SNA – a toolbox for the stoichiometric analysis of metabolic networks , 2005, BMC Bioinformatics.
[118] Bernhard O. Palsson,et al. Expa: a Program for Calculating Extreme Pathways in Biochemical Reaction Networks , 2005, Bioinform..
[119] Stefan Schuster,et al. YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities , 2005, BMC Bioinformatics.
[120] J. Harwood,et al. Metabolic control analysis reveals an important role for diacylglycerol acyltransferase in olive but not in oil palm lipid accumulation , 2005, The FEBS journal.
[121] Dominique Rolin,et al. A New Substrate Cycle in Plants. Evidence for a High Glucose-Phosphate-to-Glucose Turnover from in Vivo Steady-State and Pulse-Labeling Experiments with [13C]Glucose and [14C]Glucose1 , 2005, Plant Physiology.
[122] Lei Liu,et al. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria , 2006, BMC Genomics.
[123] Hamid Bolouri,et al. Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks , 2005, J. Bioinform. Comput. Biol..
[124] Mark Stitt,et al. Flux an important, but neglected, component of functional genomics. , 2005, Current opinion in plant biology.
[125] Sang Yup Lee,et al. MFAML: a standard data structure for representing and exchanging metabolic flux models , 2005, Bioinform..
[126] H. Miyagawa,et al. Metabolic flux analysis of the phenylpropanoid pathway in elicitor-treated potato tuber tissue. , 2005, Plant & cell physiology.
[127] Nicola Zamboni,et al. FiatFlux – a software for metabolic flux analysis from 13C-glucose experiments , 2005, BMC Bioinformatics.
[128] W. Eisenreich,et al. Metabolic flux analysis in complex isotopolog space. Recycling of glucose in tobacco plants. , 2005, Phytochemistry.
[129] Wolfgang Wiechert,et al. From stationary to instationary metabolic flux analysis. , 2005, Advances in biochemical engineering/biotechnology.
[130] W. Eisenreich,et al. Changes in flux pattern of the central carbohydrate metabolism during kernel development in maize. , 2005, Phytochemistry.
[131] B. M. Lange,et al. Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps. , 2005, Phytochemistry.
[132] Alisdair R Fernie,et al. Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. , 2005, The New phytologist.
[133] Hugh D. Spence,et al. Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.
[134] Thilo Gross,et al. Structural kinetic modeling of metabolic networks , 2006, Proceedings of the National Academy of Sciences.
[135] Vitaly A. Selivanov,et al. Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis , 2006, Bioinform..
[136] Mats Jirstrand,et al. Systems biology Systems Biology Toolbox for MATLAB : a computational platform for research in systems biology , 2006 .
[137] Mudita Singhal,et al. COPASI - a COmplex PAthway SImulator , 2006, Bioinform..
[138] J. Schwender,et al. Mitochondrial Metabolism in Developing Embryos of Brassica napus*♦ , 2006, Journal of Biological Chemistry.
[139] Rui Alves,et al. Tools for kinetic modeling of biochemical networks , 2006, Nature Biotechnology.
[140] Y. Shachar-Hill,et al. Measuring multiple fluxes through plant metabolic networks. , 2006, The Plant journal : for cell and molecular biology.
[141] Stefan Schuster,et al. Systems biology Metatool 5.0: fast and flexible elementary modes analysis , 2006 .
[142] W. Römisch,et al. Robustness of central carbohydrate metabolism in developing maize kernels. , 2006, Phytochemistry.
[143] R. Moreno-Sánchez,et al. Control of glutathione and phytochelatin synthesis under cadmium stress. Pathway modeling for plants. , 2006, Journal of theoretical biology.
[144] B. M. Lange,et al. Integrative analysis of metabolic networks: from peaks to flux models? , 2006, Current opinion in plant biology.
[145] N. Kruger,et al. The response of carbohydrate metabolism in potato tubers to low temperature. , 2006, Plant & cell physiology.
[146] Jacky L. Snoep,et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..
[147] Sang Yup Lee,et al. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks , 2006, Bioinform..
[148] M. Perrier,et al. Development of a kinetic metabolic model: application to Catharanthus roseus hairy root , 2006, Bioprocess and biosystems engineering.
[149] G. Stephanopoulos,et al. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. , 2007, Metabolic engineering.