Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

Engineering redox balance through cofactor systems

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Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

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Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations

(2014) Hsin-Hung Chou et al.   PLoS Genetics

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Development of an Optimized Medium, Strain and High-Throughput Culturing Methods for Methylobacterium extorquens

(2013) Nigel F. Delaney et al.   PLoS One

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology

(2013) Sean Michael Carroll et al.   PLoS Genetics

COFACTOR MODIFICATION ANALYSIS: A COMPUTATIONAL FRAMEWORK TO IDENTIFY COFACTOR SPECIFICITY ENGINEERING TARGETS FOR STRAIN IMPROVEMENT

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Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems

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13C-flux Analysis Reveals NADPH-balancing Transhydrogenation Cycles in Stationary Phase of Nitrogen-starvingBacillus subtilis

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EcoGene 3.0

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Optimization of Gene Expression through Divergent Mutational Paths

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Protein Structural Modularity and Robustness Are Associated with Evolvability

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Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures

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Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants

(2011) Ruilian Yao et al.   Microbial Cell Factories

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity

(2011) C. Auriol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

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Ultrahigh Performance Liquid Chromatography−Tandem Mass Spectrometry Method for Fast and Robust Quantification of Anionic and Aromatic Metabolites

(2010) Joerg Martin Buescher et al.   ANALYTICAL CHEMISTRY

A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress

(2010) Bin Rui et al.   BMC Systems Biology

Entrez Gene: gene-centered information at NCBI

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

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Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

ASYMMETRIC, BIMODAL TRADE-OFFS DURING ADAPTATION OFMETHYLOBACTERIUMTO DISTINCT GROWTH SUBSTRATES

(2009) Ming-Chun Lee et al.   EVOLUTION

Different Biochemical Mechanisms Ensure Network-Wide Balancing of Reducing Equivalents in Microbial Metabolism

(2009) T. Fuhrer et al.   JOURNAL OF BACTERIOLOGY

Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes

(2009) F. William Studier et al.   JOURNAL OF MOLECULAR BIOLOGY

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

(2009) Stéphane Vuilleumier et al.   PLoS One

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation

(2009) Hsin-Hung Chou et al.   PLoS Genetics

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE