Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance

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Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

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GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

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Adaptive laboratory evolution – principles and applications for biotechnology

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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

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Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

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Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

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Long-Term Dynamics of Adaptation in Asexual Populations

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The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

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Microbial evolution in vivo and in silico: methods and applications

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Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli

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Fast gapped-read alignment with Bowtie 2

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EcoCyc: fusing model organism databases with systems biology

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Multidimensional Optimality of Microbial Metabolism

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The Molecular Diversity of Adaptive Convergence

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Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

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Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

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Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic ActinobacteriumThermobifida fusca

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Microbial laboratory evolution in the era of genome-scale science

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Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

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Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

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Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

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Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

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The biomass objective function

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A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution

(2010) Pier-Luc Tremblay et al.   ENVIRONMENTAL MICROBIOLOGY

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

(2010) Shota Atsumi et al.   Molecular Systems Biology

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

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Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

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Genome evolution and adaptation in a long-term experiment with Escherichia coli

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Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

Aerobic Fermentation of D-Glucose by an Evolved Cytochrome Oxidase-Deficient Escherichia coli Strain

(2008) V. A. Portnoy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

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