Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change

Dynamics of Adaptation in Experimental Yeast Populations Exposed to Gradual and Abrupt Change in Heavy Metal Concentration

(2016) Florien A. Gorter et al.   AMERICAN NATURALIST

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Sex speeds adaptation by altering the dynamics of molecular evolution

(2016) Michael J. McDonald et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Rate of novel host invasion affects adaptability of evolving RNA virus lineages

(2015) Valerie J. Morley et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

(2015) Antonio V. Bordería et al.   PLoS Pathogens

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

Strong Epistatic Interactions within a Single Protein

(2014) Mariona Parera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

Environment Determines Epistatic Patterns for a ssDNA Virus

(2013) S. Brian Caudle et al.   GENETICS

Evolutionary rescue from extinction is contingent on a lower rate of environmental change

(2013) Haley A. Lindsey et al.   NATURE

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Viral population analysis and minority-variant detection using short read next-generation sequencing

(2013) S. J. Watson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Chikungunya Virus 3′ Untranslated Region: Adaptation to Mosquitoes and a Population Bottleneck as Major Evolutionary Forces

(2013) Rubing Chen et al.   PLoS Pathogens

Clonal Interference in the Evolution of Influenza

(2012) N. Strelkowa et al.   GENETICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010

(2012) Rafael Lozano et al.   LANCET

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

Emergent Neutrality in Adaptive Asexual Evolution

(2011) Stephan Schiffels et al.   GENETICS

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

(2011) José M. Cuevas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

(2011) Darin R. Rokyta et al.   PLoS Genetics

Many Possible Worlds: Expanding the Ecological Scenarios in Experimental Evolution

(2010) Sinéad Collins   Evolutionary Biology

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

(2010) J. da Silva et al.   GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ADAPTATION TO DIFFERENT RATES OF ENVIRONMENTAL CHANGE INCHLAMYDOMONAS

(2009) Sinéad Collins et al.   EVOLUTION

The Genetic Basis of Phenotypic Adaptation I: Fixation of Beneficial Mutations in the Moving Optimum Model

(2009) M. Kopp et al.   GENETICS

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model

(2009) Michael Kopp et al.   GENETICS

Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2

(2009) A. J. Betancourt   GENETICS

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

ENVIRONMENTAL HETEROGENEITY ENHANCES CLONAL INTERFERENCE

(2008) Paulo R. A. Campos et al.   EVOLUTION

Beneficial Fitness Effects Are Not Exponential for Two Viruses

(2008) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE

Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come?

(2008) Xavier de Lamballerie et al.   Virology Journal