A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.

[1]  Axel Kowald,et al.  Systems Biology - a Textbook , 2016 .

[2]  Ali R. Zomorrodi,et al.  d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. , 2014, ACS synthetic biology.

[3]  Alina A. von Davier,et al.  Cross-Validation , 2014 .

[4]  P. Mendes,et al.  Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks , 2013, PloS one.

[5]  Partho Sen,et al.  Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways , 2013, BMC Systems Biology.

[6]  D. Broomhead,et al.  A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes , 2013, FEBS letters.

[7]  Ali R. Zomorrodi,et al.  Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. , 2013, Biotechnology journal.

[8]  Keng C. Soh,et al.  Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. , 2013, Biotechnology journal.

[9]  P. Mendes,et al.  Large-Scale Metabolic Models: From Reconstruction to Differential Equations , 2013 .

[10]  Yukako Tohsato,et al.  Parameter optimization and sensitivity analysis for large kinetic models using a real-coded genetic algorithm. , 2013, Gene.

[11]  P I Barton,et al.  A reliable simulator for dynamic flux balance analysis , 2013, Biotechnology and bioengineering.

[12]  Antje Chang,et al.  BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA , 2012, Nucleic Acids Res..

[13]  Rudiyanto Gunawan,et al.  Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles , 2012, Metabolites.

[14]  Radhakrishnan Mahadevan,et al.  The design of long‐term effective uranium bioremediation strategy using a community metabolic model , 2012, Biotechnology and bioengineering.

[15]  Paula Jouhten,et al.  Metabolic modelling in the development of cell factories by synthetic biology , 2012, Computational and structural biotechnology journal.

[16]  O. Demin,et al.  Kinetic modelling of central carbon metabolism in Escherichia coli , 2012, The FEBS journal.

[17]  Sang Yup Lee,et al.  Recent advances in reconstruction and applications of genome-scale metabolic models. , 2012, Current opinion in biotechnology.

[18]  R. Mahadevan,et al.  Ensemble Modeling of Cancer Metabolism , 2012, Front. Physio..

[19]  J. Liao,et al.  Metabolic ensemble modeling for strain engineers , 2012, Biotechnology journal.

[20]  Costas D. Maranas,et al.  OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities , 2012, PLoS Comput. Biol..

[21]  Marc Hafner,et al.  Efficient characterization of high-dimensional parameter spaces for systems biology , 2011, BMC Systems Biology.

[22]  Zachary L. Fowler,et al.  Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. , 2011, Metabolic engineering.

[23]  Gonzalo Guillén-Gosálbez,et al.  Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models , 2011, BMC Systems Biology.

[24]  V. Hatzimanikatis,et al.  Modeling of uncertainties in biochemical reactions , 2011, Biotechnology and bioengineering.

[25]  Radhakrishnan Mahadevan,et al.  Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments , 2011, The ISME Journal.

[26]  Ahmad A. Mannan,et al.  Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification , 2010, Microbial cell factories.

[27]  Daniel Segrè,et al.  Environments that Induce Synthetic Microbial Ecosystems , 2010, PLoS Comput. Biol..

[28]  Jack T Pronk,et al.  Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae. , 2010, Metabolic engineering.

[29]  Ljubisa Miskovic,et al.  Production of biofuels and biochemicals: in need of an ORACLE. , 2010, Trends in biotechnology.

[30]  Radhakrishnan Mahadevan,et al.  Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. , 2010, Biotechnology journal.

[31]  M. Soledad Diaz,et al.  Global sensitivity analysis in dynamic metabolic networks , 2010, Comput. Chem. Eng..

[32]  Hiroshi Miyano,et al.  Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production. , 2010, Journal of biotechnology.

[33]  Eugénio C. Ferreira,et al.  Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations , 2010, Biosyst..

[34]  J. Liao,et al.  Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt. , 2010, Biophysical journal.

[35]  A. M. Colón,et al.  A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network of Petunia hybrida. , 2010, The Plant journal : for cell and molecular biology.

[36]  Eva Balsa-Canto,et al.  An iterative identification procedure for dynamic modeling of biochemical networks , 2010, BMC Systems Biology.

[37]  Neil Swainston,et al.  Towards a genome-scale kinetic model of cellular metabolism , 2010, BMC Systems Biology.

[38]  Neema Jamshidi,et al.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. , 2010, Biophysical journal.

[39]  James C. Liao,et al.  Ensemble modeling and related mathematical modeling of metabolic networks , 2009 .

[40]  J. Liao,et al.  Ensemble Modeling for Aromatic Production in Escherichia coli , 2009, PloS one.

[41]  James C Liao,et al.  Ensemble modeling for strain development of L-lysine-producing Escherichia coli. , 2009, Metabolic engineering.

[42]  J. Rabinowitz,et al.  Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli , 2009, Nature chemical biology.

[43]  Jan Schellenberger,et al.  Use of Randomized Sampling for Analysis of Metabolic Networks* , 2009, Journal of Biological Chemistry.

[44]  Andreas Zell,et al.  Modeling metabolic networks in C . glutamicum : a comparison of rate laws in combination with various parameter optimization strategies , 2009 .

[45]  J. Liao,et al.  Ensemble modeling of metabolic networks. , 2008, Biophysical journal.

[46]  Eberhard O. Voit,et al.  System estimation from metabolic time-series data , 2008, Bioinform..

[47]  R. Steuer,et al.  The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks , 2007, Molecular systems biology.

[48]  D. Broomhead,et al.  Something from nothing − bridging the gap between constraint‐based and kinetic modelling , 2007, The FEBS journal.

[49]  A. Sorribas,et al.  Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations , 2007, Biotechnology and Bioengineering.

[50]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[51]  Pei Yee Ho,et al.  Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations , 2007, Science.

[52]  R. Sharan,et al.  A genome-scale computational study of the interplay between transcriptional regulation and metabolism , 2007, Molecular systems biology.

[53]  D. Stahl,et al.  Metabolic modeling of a mutualistic microbial community , 2007, Molecular systems biology.

[54]  V. Hatzimanikatis,et al.  Thermodynamics-based metabolic flux analysis. , 2007, Biophysical journal.

[55]  E. Klipp,et al.  Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data , 2006, Theoretical Biology and Medical Modelling.

[56]  Thilo Gross,et al.  Structural kinetic modeling of metabolic networks , 2006, Proceedings of the National Academy of Sciences.

[57]  H. Mori,et al.  Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[58]  E. Klipp,et al.  Biochemical networks with uncertain parameters. , 2005, Systems biology.

[59]  Masaru Tomita,et al.  Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH3 under those limiting continuous cultures , 2005 .

[60]  G. Stephanopoulos,et al.  Tuning genetic control through promoter engineering. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[61]  J. Heijnen Approximative kinetic formats used in metabolic network modeling , 2005, Biotechnology and bioengineering.

[62]  U. Sauer,et al.  Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast , 2005, Genome Biology.

[63]  B. Palsson,et al.  k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. , 2005, Biophysical journal.

[64]  A. Barabasi,et al.  Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.

[65]  Carmen G. Moles,et al.  Parameter estimation in biochemical pathways: a comparison of global optimization methods. , 2003, Genome research.

[66]  R. Mahadevan,et al.  The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.

[67]  J. Heijnen,et al.  Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. , 2003, Metabolic engineering.

[68]  Farren J. Isaacs,et al.  Prediction and measurement of an autoregulatory genetic module , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[69]  B. Palsson,et al.  Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli , 2003, Journal of bacteriology.

[70]  C. Chassagnole,et al.  Dynamic modeling of the central carbon metabolism of Escherichia coli. , 2002, Biotechnology and bioengineering.

[71]  B. Palsson,et al.  Regulation of gene expression in flux balance models of metabolism. , 2001, Journal of theoretical biology.

[72]  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.

[73]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[74]  M. Reuss,et al.  In VivoDynamics of the Pentose Phosphate Pathway inSaccharomyces cerevisiae , 1999 .

[75]  J E Bailey,et al.  Application of mathematical tools for metabolic design of microbial ethanol production. , 1998, Biotechnology and bioengineering.

[76]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae : I. Experimental observations. , 1997, Biotechnology and bioengineering.

[77]  J E Bailey,et al.  MCA has more to say. , 1996, Journal of theoretical biology.

[78]  J. Bailey,et al.  Analysis and design of metabolic reaction networks via mixed‐integer linear optimization , 1996 .

[79]  M. Reuss,et al.  In vivo analysis of glucose-induced fast changes in yeast adenine nucleotide pool applying a rapid sampling technique. , 1993, Analytical biochemistry.

[80]  M. Savageau Biochemical systems analysis. III. Dynamic solutions using a power-law approximation , 1970 .

[81]  Dennis Eichmann,et al.  Metabolic Engineering Principles And Methodologies , 2016 .

[82]  M. Araúzo-Bravo,et al.  Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations , 2004, Applied Microbiology and Biotechnology.

[83]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[84]  M. Reuss,et al.  In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. , 1999, Metabolic engineering.

[85]  J. Nielsen,et al.  Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates. , 1997, The Biochemical journal.

[86]  A. Cornish-Bowden Fundamentals of Enzyme Kinetics , 1979 .