{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:38:39Z","timestamp":1767181119934,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007319","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T00:00:00Z","timestamp":1569283200000}}],"reference-count":97,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T00:00:00Z","timestamp":1568073600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000076","name":"Directorate for Biological Sciences","doi-asserted-by":"publisher","award":["1615646"],"award-info":[{"award-number":["1615646"]}],"id":[{"id":"10.13039\/100000076","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Center For Bioenergy Innovation"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007319","type":"journal-article","created":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T13:28:41Z","timestamp":1568122121000},"page":"e1007319","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1494-4566","authenticated-orcid":true,"given":"Charles J.","family":"Foster","sequence":"first","affiliation":[]},{"given":"Saratram","family":"Gopalakrishnan","sequence":"additional","affiliation":[]},{"given":"Maciek R.","family":"Antoniewicz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1508-1398","authenticated-orcid":true,"given":"Costas D.","family":"Maranas","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,9,10]]},"reference":[{"key":"pcbi.1007319.ref001","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ymben.2017.06.003","article-title":"Engineering biological systems using automated biofoundries","volume":"42","author":"R Chao","year":"2017","journal-title":"Metab Eng"},{"issue":"7","key":"pcbi.1007319.ref002","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1007\/s11427-015-4866-8","article-title":"Building biological foundries for next-generation synthetic biology","volume":"58","author":"R Chao","year":"2015","journal-title":"Sci China Life Sci"},{"key":"pcbi.1007319.ref003","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.copbio.2018.01.027","article-title":"Advances in analytical tools for high throughput strain engineering","volume":"54","author":"E Marcellin","year":"2018","journal-title":"Curr Opin Biotechnol"},{"issue":"4","key":"pcbi.1007319.ref004","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1021\/acssynbio.6b00293","article-title":"Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry","volume":"6","author":"R Chao","year":"2017","journal-title":"ACS Synth Biol"},{"key":"pcbi.1007319.ref005","doi-asserted-by":"crossref","first-page":"15187","DOI":"10.1038\/ncomms15187","article-title":"Automated multiplex genome-scale engineering in yeast","volume":"8","author":"T Si","year":"2017","journal-title":"Nat Commun"},{"issue":"6","key":"pcbi.1007319.ref006","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/bit.10803","article-title":"Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization","volume":"84","author":"AP Burgard","year":"2003","journal-title":"Biotechnol Bioeng"},{"key":"pcbi.1007319.ref007","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1002\/bit.260260210","article-title":"Equations and Calculations for Fermentations of Butyric Acid Bacteria","volume":"26","author":"ET Papoutsakis","year":"1984","journal-title":"Biotechnol Bioeng"},{"issue":"3","key":"pcbi.1007319.ref008","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nbt.1614","article-title":"What is flux balance analysis?","volume":"28","author":"JD Orth","year":"2010","journal-title":"Nat Biotechnol"},{"issue":"23","key":"pcbi.1007319.ref009","doi-asserted-by":"crossref","first-page":"15112","DOI":"10.1073\/pnas.232349399","article-title":"Analysis of optimality in natural and perturbed metabolic networks","volume":"99","author":"D Segre","year":"2002","journal-title":"PNAS"},{"issue":"2","key":"pcbi.1007319.ref010","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1002\/(SICI)1097-0290(19970420)54:2<91::AID-BIT1>3.0.CO;2-Q","article-title":"Effects of Spatiotemporal Variations on Metabolic Control: Approximate Analysis Using (Log)Linear kinetic Models","volume":"54","author":"V Hatzimanikatis","year":"1996","journal-title":"Biotechnol Bioeng"},{"issue":"17","key":"pcbi.1007319.ref011","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1016\/j.febslet.2013.06.043","article-title":"A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes","volume":"587","author":"K Smallbone","year":"2013","journal-title":"FEBS Lett"},{"key":"pcbi.1007319.ref012","doi-asserted-by":"crossref","first-page":"29635","DOI":"10.1038\/srep29635","article-title":"Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach","volume":"6","author":"PA Saa","year":"2016","journal-title":"Sci Rep"},{"key":"pcbi.1007319.ref013","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1046\/j.1432-1327.2000.01527.x","article-title":"Can yeast glycolysis be understood in terms of in vitro kinetics of the constitutent enzymes? Testing biochemistry","volume":"267","author":"B Teusink","year":"2000","journal-title":"Eur J Biochem"},{"key":"pcbi.1007319.ref014","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.ymben.2014.05.014","article-title":"A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data","volume":"25","author":"A Khodayari","year":"2014","journal-title":"Metab Eng"},{"issue":"9","key":"pcbi.1007319.ref015","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1002\/biot.201200270","article-title":"Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks","volume":"8","author":"AR Zomorrodi","year":"2013","journal-title":"Biotechnol J"},{"key":"pcbi.1007319.ref016","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1186\/s13068-017-0792-2","article-title":"Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations","volume":"10","author":"S Dash","year":"2017","journal-title":"Biotechnol Biofuels"},{"issue":"2","key":"pcbi.1007319.ref017","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.jbiosc.2017.09.005","article-title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","volume":"125","author":"H Kurata","year":"2018","journal-title":"J Biosci Bioeng"},{"key":"pcbi.1007319.ref018","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/msb.2008.8","article-title":"Formulating genome-scale kinetic models in the post-genome era","volume":"4","author":"N Jamshidi","year":"2008","journal-title":"Mol Syst Biol"},{"issue":"2","key":"pcbi.1007319.ref019","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.bpj.2009.09.064","article-title":"Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models","volume":"98","author":"N Jamshidi","year":"2010","journal-title":"Biophys J"},{"issue":"4","key":"pcbi.1007319.ref020","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.cels.2015.10.003","article-title":"Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics","volume":"1","author":"A Bordbar","year":"2015","journal-title":"Cell Syst"},{"key":"pcbi.1007319.ref021","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/0895-7177(88)90553-5","article-title":"Introduction to S-systems and the underlying power-law formalism","volume":"11","author":"MA Savageau","year":"1988","journal-title":"Mathl Comput Modelling"},{"issue":"5","key":"pcbi.1007319.ref022","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1002\/bit.20558","article-title":"Approximative kinetic formats used in metabolic network modeling","volume":"91","author":"JJ Heijnen","year":"2005","journal-title":"Biotechnol Bioeng"},{"issue":"2","key":"pcbi.1007319.ref023","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1006\/mben.2001.0216","article-title":"The mathematics of metabolic control analysis revisited","volume":"4","author":"D Visser","year":"2002","journal-title":"Metab Eng"},{"issue":"4","key":"pcbi.1007319.ref024","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.ymben.2004.07.001","article-title":"Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics","volume":"6","author":"D Visser","year":"2004","journal-title":"Metab Eng"},{"issue":"3","key":"pcbi.1007319.ref025","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/S1096-7176(03)00025-9","article-title":"Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics","volume":"5","author":"D Visser","year":"2003","journal-title":"Metabolic Engineering"},{"issue":"4","key":"pcbi.1007319.ref026","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1002\/bit.20772","article-title":"The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening","volume":"95","author":"M Noble","year":"2006","journal-title":"Biotechnol Bioeng"},{"issue":"3","key":"pcbi.1007319.ref027","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1142\/S0219720006002259","article-title":"An automated procedure for the extraction of metabolic network information from time series data","volume":"4","author":"S Marino","year":"2006","journal-title":"Journal of Bioinformatics and Computational Biology"},{"key":"pcbi.1007319.ref028","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.compchemeng.2014.06.011","article-title":"Gobal optimization of hybrid kinetic\/FBA models via outer-approximation","volume":"72","author":"C Pozo","year":"2015","journal-title":"Computers & Chemical Engineering"},{"issue":"3","key":"pcbi.1007319.ref029","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1049\/iet-syb:20060064","article-title":"S-system parameter estimation for noisy metabolic profiles using Newton-flow analysis","volume":"1","author":"Z Kutalik","year":"2007","journal-title":"IET Systems Biology"},{"issue":"12","key":"pcbi.1007319.ref030","doi-asserted-by":"crossref","first-page":"5606","DOI":"10.1529\/biophysj.108.135442","article-title":"Ensemble modeling of metabolic networks","volume":"95","author":"LM Tran","year":"2008","journal-title":"Biophys J"},{"key":"pcbi.1007319.ref031","first-page":"25","article-title":"Using Ant Colony Optimization (ACO) on Kinetic Modeling of the Acetoin Production in Lactococcus Lactis C7","volume":"477","author":"NFB Saidin","year":"2013","journal-title":"Studies in Computational Intelligence"},{"key":"pcbi.1007319.ref032","doi-asserted-by":"crossref","first-page":"13806","DOI":"10.1038\/ncomms13806","article-title":"A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains","volume":"7","author":"A Khodayari","year":"2016","journal-title":"Nat Commun"},{"key":"pcbi.1007319.ref033","doi-asserted-by":"crossref","unstructured":"Greene J, Waechter A, Tyo K, Broadbelt LJ. Eliminating dependent variables and guaranteeing local stability enhances metabolic ensemble modeling performance. in review. 2017.","DOI":"10.1016\/j.bpj.2017.07.018"},{"key":"pcbi.1007319.ref034","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ymben.2014.06.006","article-title":"Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways","volume":"25","author":"Y Lee","year":"2014","journal-title":"Metab Eng"},{"issue":"4","key":"pcbi.1007319.ref035","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.ymben.2006.01.004","article-title":"Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements","volume":"8","author":"MR Antoniewicz","year":"2006","journal-title":"Metab Eng"},{"issue":"5824","key":"pcbi.1007319.ref036","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1126\/science.1132067","article-title":"Multiple high-throughput analyses monitor the response of E. coli to perturbations","volume":"316","author":"N Ishii","year":"2007","journal-title":"Science"},{"issue":"3","key":"pcbi.1007319.ref037","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.ymben.2007.01.003","article-title":"Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol","volume":"9","author":"MR Antoniewicz","year":"2007","journal-title":"Metab Eng"},{"issue":"1","key":"pcbi.1007319.ref038","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.copbio.2010.01.011","article-title":"Metabolic flux analysis in eukaryotes","volume":"21","author":"J Niklas","year":"2010","journal-title":"Curr Opin Biotechnol"},{"key":"pcbi.1007319.ref039","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.ymben.2013.08.006","article-title":"COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis","volume":"20","author":"RW Leighty","year":"2013","journal-title":"Metab Eng"},{"key":"pcbi.1007319.ref040","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.ymben.2015.08.006","article-title":"13C metabolic flux analysis at a genome-scale","volume":"32","author":"S Gopalakrishnan","year":"2015","journal-title":"Metab Eng"},{"issue":"6311","key":"pcbi.1007319.ref041","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf2786","article-title":"Systems-level analysis of mechanisms regulating yeast metabolic flux","volume":"354","author":"SR Hackett","year":"2016","journal-title":"Science"},{"issue":"5","key":"pcbi.1007319.ref042","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.ymben.2012.06.003","article-title":"Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis","volume":"14","author":"RW Leighty","year":"2012","journal-title":"Metab Eng"},{"issue":"5","key":"pcbi.1007319.ref043","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1002\/bit.21675","article-title":"Metabolic flux analysis in Escherichia coli by integrating isotopic dynamic and isotopic stationary 13C labeling data","volume":"99","author":"J Schaub","year":"2008","journal-title":"Biotechnol Bioeng"},{"key":"pcbi.1007319.ref044","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1006\/mben.1999.0114","article-title":"Quantification of Intracellular Metbolic Fluxes from Fractional Enrichment and 13-13C Coupling Constraints on the Isotopomer Distribution in Labeled Biomass Components","volume":"1","author":"K Schmidt","year":"1999","journal-title":"Metab Eng"},{"issue":"2","key":"pcbi.1007319.ref045","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.jbiotec.2006.11.015","article-title":"Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments","volume":"129","author":"K Noh","year":"2007","journal-title":"J Biotechnol"},{"issue":"6","key":"pcbi.1007319.ref046","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1002\/(SICI)1097-0290(19970920)55:6<831::AID-BIT2>3.0.CO;2-H","article-title":"Modeling Isotopomer Distributions in Biochemical Networks Using Isotopomer Mapping Matrices","volume":"55","author":"K Schmidt","year":"1997","journal-title":"Biotechnol Bioeng"},{"issue":"3","key":"pcbi.1007319.ref047","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.jbiotec.2009.07.010","article-title":"Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells","volume":"144","author":"CM Metallo","year":"2009","journal-title":"J Biotechnol"},{"issue":"6","key":"pcbi.1007319.ref048","doi-asserted-by":"crossref","first-page":"R49","DOI":"10.1186\/gb-2005-6-6-r49","article-title":"Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast","volume":"6","author":"LM Blank","year":"2005","journal-title":"Genome Biol"},{"issue":"3","key":"pcbi.1007319.ref049","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1006\/mben.2002.0226","article-title":"Metabolic Flux Analysis in Synechocystis Using Isotope Distribution from 13C-Labeled Glucose","volume":"4","author":"C Yang","year":"2002","journal-title":"Metabolic Engineering"},{"issue":"2","key":"pcbi.1007319.ref050","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1007\/s00253-001-0839-x","article-title":"13 C-NMR analysis of glucose metabolism during citric acid production by Aspergillus niger","volume":"58","author":"A Peksel","year":"2002","journal-title":"Applied Microbiology and Biotechnology"},{"issue":"19","key":"pcbi.1007319.ref051","doi-asserted-by":"crossref","first-page":"5413","DOI":"10.1128\/JB.00713-12","article-title":"Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis","volume":"194","author":"L Liu","year":"2012","journal-title":"J Bacteriol"},{"issue":"2","key":"pcbi.1007319.ref052","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.ymben.2009.09.002","article-title":"Metabolic flux analysis in mammalian cell culture","volume":"12","author":"LE Quek","year":"2010","journal-title":"Metab Eng"},{"issue":"2","key":"pcbi.1007319.ref053","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1006\/mben.2001.0209","article-title":"Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy","volume":"4","author":"S Flores","year":"2002","journal-title":"Metab Eng"},{"key":"pcbi.1007319.ref054","doi-asserted-by":"crossref","unstructured":"Shimizu K. Metabolic Flux Analysis Based on 13C-Labeling Experiments and Integration of the Information with Gene and Protein Expression Patterns. Recent Progress of Biochemical and Biomedical Engineering in Japan II. Advances in Biochemical Engineering\/Biotechnology2004. p. 1\u201349.","DOI":"10.1007\/b94204"},{"issue":"87","key":"pcbi.1007319.ref055","first-page":"1","article-title":"Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis","volume":"11","author":"Y Usui","year":"2012","journal-title":"Microbial Cell Factories"},{"issue":"3","key":"pcbi.1007319.ref056","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1002\/biot.201000282","article-title":"Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis","volume":"6","author":"SB Crown","year":"2011","journal-title":"Biotechnol J"},{"issue":"5","key":"pcbi.1007319.ref057","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1002\/biot.201300477","article-title":"13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions","volume":"9","author":"L You","year":"2014","journal-title":"Biotechnol J"},{"issue":"1","key":"pcbi.1007319.ref058","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.ymben.2006.09.001","article-title":"Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions","volume":"9","author":"MR Antoniewicz","year":"2007","journal-title":"Metab Eng"},{"key":"pcbi.1007319.ref059","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.ymben.2018.03.008","article-title":"Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models","volume":"47","author":"S Gopalakrishnan","year":"2018","journal-title":"Metab Eng"},{"issue":"2","key":"pcbi.1007319.ref060","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1104\/pp.18.01357","article-title":"Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient (13)C-Labeling Data","volume":"179","author":"JI Hendry","year":"2019","journal-title":"Plant Physiol"},{"key":"pcbi.1007319.ref061","doi-asserted-by":"crossref","unstructured":"Gopalakrishnan S, Dash S, Maranas CD. K-FIT: An accelerated kinetic parameterization algorithm using stead-state fluxomic data. bioRxiv. 2019.","DOI":"10.1101\/612994"},{"key":"pcbi.1007319.ref062","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.ymben.2016.06.001","article-title":"Optimal tracers for parallel labeling experiments and (13)C metabolic flux analysis: A new precision and synergy scoring system","volume":"38","author":"SB Crown","year":"2016","journal-title":"Metab Eng"},{"issue":"11","key":"pcbi.1007319.ref063","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1016\/j.celrep.2017.08.066","article-title":"Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity","volume":"20","author":"E Reznik","year":"2017","journal-title":"Cell Rep"},{"key":"pcbi.1007319.ref064","article-title":"Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli\u2019s Rapid Response to Oxidative Stress","author":"D Christodoulou","year":"2018","journal-title":"Cell Syst"},{"key":"pcbi.1007319.ref065","doi-asserted-by":"crossref","first-page":"14316","DOI":"10.1038\/ncomms14316","article-title":"Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli","volume":"8","author":"CP Long","year":"2017","journal-title":"Nat Commun"},{"issue":"D1","key":"pcbi.1007319.ref066","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkw952","article-title":"BRENDA in 2017: new perspectives and new tools in BRENDA","volume":"45","author":"S Placzek","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pcbi.1007319.ref067","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkw1003","article-title":"The EcoCyc database: reflecting new knowledge about Escherichia coli K-12","volume":"45","author":"IM Keseler","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007319.ref068","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.ymben.2019.08.003","article-title":"Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism","volume":"55","author":"CP Long","year":"2019","journal-title":"Metab Eng"},{"issue":"2","key":"pcbi.1007319.ref069","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1016\/j.bej.2008.01.001","article-title":"Metabolic engineering of Escherichia coli for the production of malic acid","volume":"40","author":"SY Moon","year":"2008","journal-title":"Biochemical Engineering Journal"},{"issue":"3","key":"pcbi.1007319.ref070","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1128\/AEM.00973-08","article-title":"Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli","volume":"75","author":"TS Moon","year":"2009","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"pcbi.1007319.ref071","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1128\/AEM.67.1.148-154.2001","article-title":"Mutation of the ptsG gene results in increased production of succinate in fermentation of glucose by Escherichia coli","volume":"67","author":"R Chatterjee","year":"2001","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"pcbi.1007319.ref072","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s11427-012-4304-0","article-title":"Metabolic engineering and flux analysis of Corynebacterium glutamicum for L-serine production","volume":"55","author":"S Lai","year":"2012","journal-title":"Sci China Life Sci"},{"key":"pcbi.1007319.ref073","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/msb4100196","article-title":"Systems metabolic engineering of Escherichia coli for L-threonine production","volume":"3","author":"KH Lee","year":"2007","journal-title":"Mol Syst Biol"},{"key":"pcbi.1007319.ref074","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1475-2859-6-30","article-title":"Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine","volume":"6","author":"JL Baez-Viveros","year":"2007","journal-title":"Microb Cell Fact"},{"key":"pcbi.1007319.ref075","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.ymben.2014.02.004","article-title":"Systematic metabolic engineering of Escherichia coli for high-yield production of fuel bio-chemical 2,3-butanediol","volume":"23","author":"Y Xu","year":"2014","journal-title":"Metab Eng"},{"issue":"5","key":"pcbi.1007319.ref076","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.ymben.2011.06.008","article-title":"Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA","volume":"13","author":"P Xu","year":"2011","journal-title":"Metab Eng"},{"issue":"5","key":"pcbi.1007319.ref077","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1002\/bit.23044","article-title":"Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering","volume":"108","author":"JH Park","year":"2011","journal-title":"Biotechnol Bioeng"},{"issue":"3","key":"pcbi.1007319.ref078","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1007\/s00284-010-9817-9","article-title":"Evaluation of genetic manipulation strategies on D-lactate production by Escherichia coli","volume":"62","author":"L Zhou","year":"2011","journal-title":"Curr Microbiol"},{"key":"pcbi.1007319.ref079","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.ymben.2016.05.006","article-title":"Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism","volume":"37","author":"CP Long","year":"2016","journal-title":"Metab Eng"},{"issue":"2","key":"pcbi.1007319.ref080","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1042\/bj0190338","article-title":"A note on the kinetics of enzyme action","volume":"19","author":"GE Briggs","year":"1925","journal-title":"Biochem J"},{"key":"pcbi.1007319.ref081","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ymben.2014.06.006","article-title":"Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways","volume":"25","author":"Y Lee","year":"2014","journal-title":"Metabolic Engineering"},{"key":"pcbi.1007319.ref082","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-21736-9","volume-title":"All of Statistics A Concise Course in Statistical Inference","author":"L Wasserman","year":"2004"},{"key":"pcbi.1007319.ref083","volume-title":"An Introduction to Statistical Methods and Data Analysis","author":"LR Ott","year":"2010","edition":"6 ed"},{"issue":"10","key":"pcbi.1007319.ref084","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1021\/j150544a010","article-title":"A schematic method of driving the rate laws for enzyme catalyzed reactions","volume":"60","author":"EL King","year":"1956","journal-title":"J Phys Chem"},{"issue":"7","key":"pcbi.1007319.ref085","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/nchembio.2077","article-title":"Metabolite concentrations, fluxes and free energies imply efficient enzyme usage","volume":"12","author":"JO Park","year":"2016","journal-title":"Nat Chem Biol"},{"key":"pcbi.1007319.ref086","first-page":"76","article-title":"Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model","volume":"2","author":"A Khodayari","year":"2014","journal-title":"Front Bioeng Biotechnol"},{"issue":"2","key":"pcbi.1007319.ref087","doi-asserted-by":"crossref","first-page":"e1005396","DOI":"10.1371\/journal.pcbi.1005396","article-title":"Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli","volume":"13","author":"P Millard","year":"2017","journal-title":"PLoS Comput Biol"},{"issue":"15","key":"pcbi.1007319.ref088","doi-asserted-by":"crossref","first-page":"4062","DOI":"10.1021\/jp4118858","article-title":"Macromolecular crowding effect upon in vitro enzyme kinetics: mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase","volume":"118","author":"C Balcells","year":"2014","journal-title":"J Phys Chem B"},{"issue":"2","key":"pcbi.1007319.ref089","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.bpj.2019.06.017","article-title":"Particle-based simulation reveals macromolecular crowding effects on the Michaelis-Menten mechanism","volume":"117","author":"DR Weilandt","year":"2019","journal-title":"Biophysical Journal"},{"issue":"38","key":"pcbi.1007319.ref090","doi-asserted-by":"crossref","first-page":"15838","DOI":"10.1074\/jbc.M117.792119","article-title":"Quantifying enzyme activity in living cells","volume":"292","author":"A Zotter","year":"2017","journal-title":"J Biol Chem"},{"issue":"4","key":"pcbi.1007319.ref091","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.bbapap.2009.11.013","article-title":"Non-linear effects of macromolecular crowding on enzymatic activity of multi-copper oxidase","volume":"1804","author":"I Pozdnyakova","year":"2010","journal-title":"Biochim Biophys Acta"},{"issue":"1","key":"pcbi.1007319.ref092","doi-asserted-by":"crossref","DOI":"10.1038\/srep31007","article-title":"Macromolecular crowding explains overflow metabolism in cells","volume":"6","author":"A Vazquez","year":"2016","journal-title":"Scientific Reports"},{"issue":"1","key":"pcbi.1007319.ref093","first-page":"3","article-title":"Macromolecular Crowding upon In-vivo-like Enzyme-Kinetics: Effect of Enzyme-Obstacle Size Ratio","volume":"24","author":"C Balcells","year":"2015","journal-title":"New Front Chem"},{"key":"pcbi.1007319.ref094","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.copbio.2014.02.006","article-title":"Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook","volume":"28","author":"CP Long","year":"2014","journal-title":"Curr Opin Biotechnol"},{"issue":"11","key":"pcbi.1007319.ref095","doi-asserted-by":"crossref","first-page":"e1005167","DOI":"10.1371\/journal.pcbi.1005167","article-title":"The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization","volume":"12","author":"E Noor","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"pcbi.1007319.ref096","doi-asserted-by":"crossref","first-page":"e1006010","DOI":"10.1371\/journal.pcbi.1006010","article-title":"Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield","volume":"14","author":"MT Wortel","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pcbi.1007319.ref097","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nbt.3418","article-title":"The quantitative and condition-dependent Escherichia coli proteome","volume":"34","author":"A Schmidt","year":"2016","journal-title":"Nat Biotechnol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007319","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T00:00:00Z","timestamp":1569283200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007319","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,19]],"date-time":"2021-01-19T18:35:46Z","timestamp":1611081346000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007319"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,9,10]]},"references-count":97,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2019,9,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007319","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,10]]}}}