Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

[1]  Richard E. Lenski,et al.  Tempo and mode of genome evolution in a 50,000-generation experiment , 2016, Nature.

[2]  T. Hwa,et al.  Overflow metabolism in Escherichia coli results from efficient proteome allocation , 2015, Nature.

[3]  M. Doebeli,et al.  Calibration and analysis of genome-based models for microbial ecology , 2015, eLife.

[4]  Joshua R. Nahum,et al.  Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli , 2015, bioRxiv.

[5]  Jeffrey E. Barrick,et al.  Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli , 2015, Genetics.

[6]  D. Oyarzún,et al.  Mechanistic links between cellular trade-offs, gene expression, and growth , 2015, Proceedings of the National Academy of Sciences.

[7]  James Y. Dai,et al.  Mucosal effects of tenofovir 1% gel , 2014, bioRxiv.

[8]  J. Krug,et al.  Empirical fitness landscapes and the predictability of evolution , 2014, Nature Reviews Genetics.

[9]  Alex H. Lang,et al.  Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. , 2014, Cell reports.

[10]  Orkun S. Soyer,et al.  Synthetic microbial communities , 2014, Current opinion in microbiology.

[11]  Richard E. Lenski,et al.  Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli , 2014, Science.

[12]  Nicholas Leiby,et al.  Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli , 2014, PLoS biology.

[13]  Michael J. Wiser,et al.  Long-Term Dynamics of Adaptation in Asexual Populations , 2013, Science.

[14]  Edward J. O'Brien,et al.  Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction , 2013, Molecular systems biology.

[15]  Orkun S. Soyer,et al.  Evolutionary systems biology: What it is and why it matters , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  Niels Klitgord,et al.  The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum , 2013, PLoS Comput. Biol..

[17]  F. Bruggeman,et al.  Community Flux Balance Analysis for Microbial Consortia at Balanced Growth , 2013, PloS one.

[18]  U. Riebesell,et al.  Adaptive evolution of a key phytoplankton species to ocean acidification , 2012 .

[19]  Roeland M. H. Merks,et al.  Redox balance is key to explaining full vs. partial switching to low-yield metabolism , 2012, BMC Systems Biology.

[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]  Roded Sharan,et al.  Competitive and cooperative metabolic interactions in bacterial communities. , 2011, Nature communications.

[22]  Balázs Papp,et al.  Systems-biology approaches for predicting genomic evolution , 2011, Nature Reviews Genetics.

[23]  Christoph Kaleta,et al.  Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach , 2011, Biosyst..

[24]  Daniel Segrè,et al.  Ecosystems biology of microbial metabolism. , 2011, Current opinion in biotechnology.

[25]  Richard E. Lenski,et al.  Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli , 2011, G3: Genes | Genomes | Genetics.

[26]  Radhakrishnan Mahadevan,et al.  Economics of membrane occupancy and respiro-fermentation , 2011, Molecular systems biology.

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

[28]  Tom M. Conrad,et al.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models , 2010, Molecular systems biology.

[29]  Adam M. Feist,et al.  The biomass objective function. , 2010, Current opinion in microbiology.

[30]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[31]  Ronan M. T. Fleming,et al.  Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide , 2010, EcoSal Plus.

[32]  A. Moya,et al.  Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance , 2010, PLoS pathogens.

[33]  R. Lenski,et al.  Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). , 2009, Journal of molecular biology.

[34]  B. Teusink,et al.  Shifts in growth strategies reflect tradeoffs in cellular economics , 2009, Molecular systems biology.

[35]  Ronan M. T. Fleming,et al.  Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..

[36]  David L Stern,et al.  Is Genetic Evolution Predictable? , 2009, Science.

[37]  D. Fell,et al.  Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.

[38]  R. Lenski,et al.  Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli , 2008 .

[39]  Michelle D. Brazas,et al.  Metabolic Changes Associated With Adaptive Diversification in Escherichia coli , 2008, Genetics.

[40]  Stephen C Stearns,et al.  The great opportunity: Evolutionary applications to medicine and public health , 2008, Evolutionary applications.

[41]  R. Beardmore,et al.  Constraints on microbial metabolism drive evolutionary diversification in homogeneous environments , 2007, Journal of evolutionary biology.

[42]  M. A. de Menezes,et al.  Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity , 2007, Proceedings of the National Academy of Sciences.

[43]  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.

[44]  H. Holzhütter,et al.  Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks , 2007, BMC Systems Biology.

[45]  Laura E. Green,et al.  The role of ecological theory in microbial ecology , 2007, Nature Reviews Microbiology.

[46]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[47]  Michael Doebeli,et al.  Adaptive Diversification in Genes That Regulate Resource Use in Escherichia coli , 2007, PLoS genetics.

[48]  U. Alon,et al.  A comprehensive library of fluorescent transcriptional reporters for Escherichia coli , 2006, Nature Methods.

[49]  A. Khodursky,et al.  Overflow Metabolism in Escherichia coli during Steady-State Growth: Transcriptional Regulation and Effect of the Redox Ratio , 2006, Applied and Environmental Microbiology.

[50]  Barbara M. Bakker,et al.  Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[51]  H. Holzhütter.  The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. , 2004, European journal of biochemistry.

[52]  S. Bonhoeffer,et al.  Evolution of Cross‐Feeding in Microbial Populations , 2004, The American Naturalist.

[53]  Michael Doebeli,et al.  EXPERIMENTAL EVIDENCE FOR SYMPATRIC ECOLOGICAL DIVERSIFICATION DUE TO FREQUENCY‐DEPENDENT COMPETITION IN ESCHERICHIA COLI , 2004, Evolution; international journal of organic evolution.

[54]  Kenneth J. Kauffman,et al.  Advances in flux balance analysis. , 2003, Current opinion in biotechnology.

[55]  B. Palsson,et al.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.

[56]  David L. Kaplan,et al.  That shrinking feeling , 2002, Nature.

[57]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[58]  M. Covert,et al.  Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli * 210 , 2002, The Journal of Biological Chemistry.

[59]  M. Doebeli,et al.  A model for the evolutionary dynamics of cross-feeding polymorphisms in microorganisms , 2002, Population Ecology.

[60]  S. Bonhoeffer,et al.  Cooperation and Competition in the Evolution of ATP-Producing Pathways , 2001, Science.

[61]  B. Palsson,et al.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.

[62]  Daniel E Rozen,et al.  Long‐Term Experimental Evolution in Escherichia coli. VIII. Dynamics of a Balanced Polymorphism , 2000, The American Naturalist.

[63]  D. Button.  Nutrient Uptake by Microorganisms according to Kinetic Parameters from Theory as Related to Cytoarchitecture , 1998, Microbiology and Molecular Biology Reviews.

[64]  J. Adams,et al.  Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. , 1998, Molecular biology and evolution.

[65]  J. Klima,et al.  Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis , 1998, Applied and Environmental Microbiology.

[66]  R. Lenski,et al.  LONG‐TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA COLI. VII. MECHANISMS MAINTAINING GENETIC VARIABILITY WITHIN POPULATIONS , 1997, Evolution; international journal of organic evolution.

[67]  S. Elena,et al.  FREQUENCY‐DEPENDENT SELECTION IN A MAMMALIAN RNA VIRUS , 1997, Evolution; international journal of organic evolution.

[68]  R. Lenski,et al.  Tests of Ecological Mechanisms Promoting the Stable Coexistence of Two Bacterial Genotypes , 1996 .

[69]  B. Palsson,et al.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.

[70]  R. Rosenzweig,et al.  Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. , 1994, Genetics.

[71]  R. Lenski,et al.  Epistatic effects of promoter and repressor functions of the Tn10 tetracycline‐resistance operon on the fitness of Escherichia coli , 1994, Molecular ecology.

[72]  R. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.

[73]  R. Heinrich,et al.  Mathematical analysis of enzymic reaction systems using optimization principles. , 1991, European journal of biochemistry.

[74]  W. Holms,et al.  Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. , 1989, Journal of general microbiology.

[75]  Adam M. Feist,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox , 2007, Nature Protocols.