Effects of genotype on rates of substitution during experimental evolution

The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations

(2014) Evgeni M. Frenkel et al.   GENETICS

Testing the Role of Genetic Background in Parallel Evolution Using the Comparative Experimental Evolution of Antibiotic Resistance

(2014) Tom Vogwill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Microbiological effects of sublethal levels of antibiotics

(2014) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success

(2014) Liam S. Redgrave et al.   TRENDS IN MICROBIOLOGY

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

(2014) Susan F. Bailey et al.   Nature Communications

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation

(2013) Richard A. Neher   Annual Review of Ecology Evolution and Systematics

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

(2013) L. Perfeito et al.   EVOLUTION

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Codon Usage Determines the Mutational Robustness, Evolutionary Capacity, and Virulence of an RNA Virus

(2012) Adam S. Lauring et al.   Cell Host & Microbe

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

(2012) JEREMY R. DETTMAN et al.   MOLECULAR ECOLOGY

Genealogies of rapidly adapting populations

(2012) R. A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

(2012) B. H. Good et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

(2012) Alex Wong et al.   PLoS Genetics

THE LENGTH OF ADAPTIVE WALKS IS INSENSITIVE TO STARTING FITNESS IN ASPERGILLUS NIDULANS

(2011) Danna R. Gifford et al.   EVOLUTION

Cost of Antibiotic Resistance and the Geometry of Adaptation

(2011) Ana Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Selection of Resistant Bacteria at Very Low Antibiotic Concentrations

(2011) Erik Gullberg et al.   PLoS Pathogens

Prevalence of Antimicrobial-Resistant Pathogens in Canadian Hospitals: Results of the Canadian Ward Surveillance Study (CANWARD 2008)

(2010) G. G. Zhanel et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution

(2010) Itay Mayrose et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

(2010) N. Lartillot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

(2010) J. E. Barrick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation sequencing as a tool to study microbial evolution

(2010) MICHAEL A. BROCKHURST et al.   MOLECULAR ECOLOGY

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

Beneficial mutations and the dynamics of adaptation in asexual populations

(2010) P. D. Sniegowski et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Watching the clock: Studying variation in rates of molecular evolution between species

(2010) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis

(2009) B. M. Hall et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Genetics of Adaptation for Eight Microvirid Bacteriophages

(2009) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2009) Jeffrey E. Barrick et al.   NATURE

Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa

(2009) A. R. Hall et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174

(2008) Kim M Pepin et al.   BMC EVOLUTIONARY BIOLOGY

The Distribution of Beneficial and Fixed Mutation Fitness Effects Close to an Optimum

(2008) Guillaume Martin et al.   GENETICS

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence

(2008) J. P. Bollback et al.   GENETICS

Clonal Interference, Multiple Mutations and Adaptation in Large Asexual Populations

(2008) C. A. Fogle et al.   GENETICS

The fixation probability of beneficial mutations

(2008) Z Patwa et al.   Journal of the Royal Society Interface

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

Mechanism of action of and resistance to quinolones

(2008) Anna Fàbrega et al.   Microbial Biotechnology