First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes

The phenotypic signature of adaptation to thermal stress in Escherichia coli

(2015) Shaun M. Hug et al.   BMC EVOLUTIONARY BIOLOGY

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

(2014) Troy E. Sandberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Different tradeoffs result from alternate genetic adaptations to a common environment

(2014) A. Rodriguez-Verdugo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

The Genomic Landscape of Compensatory Evolution

(2014) Béla Szamecz et al.   PLOS BIOLOGY

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress

(2013) Alejandra Rodríguez-Verdugo et al.   BMC EVOLUTIONARY BIOLOGY

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation inEscherichia coli

(2013) Erik M. Quandt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Sean Michael Carroll et al.   PLoS Genetics

Isolation and Characterization of RNA PolymeraserpoBMutations That Alter Transcription Slippage during Elongation inEscherichia coli

(2012) Yan Ning Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Global Metabolomic Responses of Escherichia coli to Heat Stress

(2012) Yangfang Ye et al.   JOURNAL OF PROTEOME RESEARCH

Competition between Transposable Elements and Mutator Genes in Bacteria

(2012) T. Feher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

(2012) Gerrit Brandis et al.   MOLECULAR MICROBIOLOGY

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

New insights into bacterial adaptation through in vivo and in silico experimental evolution

(2012) Thomas Hindré et al.   NATURE REVIEWS MICROBIOLOGY

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis

(2012) Y. S. Polikanov et al.   SCIENCE

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

The RpoS-Mediated General Stress Response inEscherichia coli

(2010) Aurelia Battesti et al.   Annual Review of Microbiology

The Heat Shock Response: Life on the Verge of Death

(2010) Klaus Richter et al.   MOLECULAR CELL

Metabolomic and transcriptomic stress response of Escherichia coli

(2010) Szymon Jozefczuk et al.   Molecular Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport

(2010) Feng Long et al.   NATURE

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

Causes and evolutionary significance of genetic convergence

(2010) Pascal-Antoine Christin et al.   TRENDS IN GENETICS

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

(2010) Natacha Opalka et al.   PLOS BIOLOGY

Transition from Positive to Neutral in Mutation Fixation along with Continuing Rising Fitness in Thermal Adaptive Evolution

(2010) Toshihiko Kishimoto et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Global discovery of adaptive mutations

(2009) Hani Goodarzi et al.   NATURE METHODS

Impact of Individual Mutations on Increased Fitness in Adaptively Evolved Strains of Escherichia coli

(2008) M. K. Applebee et al.   JOURNAL OF BACTERIOLOGY

Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

(2008) T. S. Gunasekera et al.   JOURNAL OF BACTERIOLOGY

Thermal Probing of E. coli RNA Polymerase Off-Pathway Mechanisms

(2008) Yara X. Mejia et al.   JOURNAL OF MOLECULAR BIOLOGY

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS