Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

The predictability of molecular evolution during functional innovation

(2014) D. Blank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

(2014) J. Plucain et al.   SCIENCE

Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli

(2014) Nicholas Leiby et al.   PLOS BIOLOGY

Efflux pumps of Gram-negative bacteria: what they do, how they do it, with what and how to deal with them

(2014) Leonard Amaral et al.   Frontiers in Pharmacology

Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance

(2013) Corwin Miller et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparative genomics and transcriptomics analysis of experimentally evolvedEscherichia coli MC1000 in complex environments

(2013) Pilar Eliana Puentes-Téllez et al.   ENVIRONMENTAL MICROBIOLOGY

Putrescine catabolism is a metabolic response to several stresses inEscherichia coli

(2013) Barbara L. Schneider et al.   MOLECULAR MICROBIOLOGY

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Nutritional Basis for Colonization Resistance by Human Commensal Escherichia coli Strains HS and Nissle 1917 against E. coli O157:H7 in the Mouse Intestine

(2013) Rosalie Maltby et al.   PLoS One

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

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

The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

(2013) Dan M. Park et al.   PLoS Genetics

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

(2012) Pilar Eliana Puentes-Téllez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum

(2012) Gerda Saxer et al.   PLoS One

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance

(2012) K. Walkiewicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks

(2012) A. A. M. Al Mamun et al.   SCIENCE

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Biogenic ammonia modifies antibiotic resistance at a distance in physically separated bacteria

(2011) Steve P. Bernier et al.   MOLECULAR MICROBIOLOGY

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

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

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

EFFECTS OF TEMPERATURE ON THE FITNESS COST OF RESISTANCE TO BACTERIOPHAGE T4 INESCHERICHIA COLI.

(2009) Michael A. Quance et al.   EVOLUTION

Role of RpoS in Virulence of Pathogens

(2009) T. Dong et al.   INFECTION AND IMMUNITY

Polyamines Are Not Required for Aerobic Growth of Escherichia coli: Preparation of a Strain with Deletions in All of the Genes for Polyamine Biosynthesis

(2009) M. K. Chattopadhyay et al.   JOURNAL OF BACTERIOLOGY

Spatial structure leads to ecological breakdown and loss of diversity

(2009) G. Saxer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS