Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus

Identification, Characterization, and Natural Selection of Mutations Driving Airborne Transmission of A/H5N1 Virus

(2014) Martin Linster et al.   CELL

A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory

(2014) D. Seifert et al.   GENETICS

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

(2014) Christopher J. R. Illingworth et al.   PLoS Computational Biology

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

(2014) Matthieu Foll et al.   PLoS Genetics

Predicting evolution from the shape of genealogical trees

(2014) Richard A Neher et al.   eLife

Improving pandemic influenza risk assessment

(2014) Colin A Russell et al.   eLife

Identifying Signatures of Selection in Genetic Time Series

(2013) A. F. Feder et al.   GENETICS

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

Genetic characterization of seasonal influenza A (H3N2) viruses in Ontario during 2010-2011 influenza season: high prevalence of mutations at antigenic sites

(2013) AliReza Eshaghi et al.   Influenza and Other Respiratory Viruses

Evolution of Equine Influenza Virus in Vaccinated Horses

(2013) P. R. Murcia et al.   JOURNAL OF VIROLOGY

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

Highly confined ions store charge more efficiently in supercapacitors

(2013) C. Merlet et al.   Nature Communications

Influenza Virus Reassortment Occurs with High Frequency in the Absence of Segment Mismatch

(2013) Nicolle Marshall et al.   PLoS Pathogens

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Inferring HIV Escape Rates from Multi-Locus Genotype Data

(2013) Taylor A. Kessinger et al.   Frontiers in Immunology

A method to infer positive selection from marker dynamics in an asexual population

(2012) Christopher J. R. Illingworth et al.   BIOINFORMATICS

Clonal Interference in the Evolution of Influenza

(2012) N. Strelkowa et al.   GENETICS

Prediction and prevention of the next pandemic zoonosis

(2012) Stephen S Morse et al.   LANCET

Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets

(2012) Masaki Imai et al.   NATURE

Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets

(2012) S. Herfst et al.   SCIENCE

The Potential for Respiratory Droplet-Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host

(2012) C. A. Russell et al.   SCIENCE

Distinguishing Driver and Passenger Mutations in an Evolutionary History Categorized by Interference

(2011) Christopher J. R. Illingworth et al.   GENETICS

Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection

(2011) V. V. Ganusov et al.   JOURNAL OF VIROLOGY

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

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

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy

(2011) S. R. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

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

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy et al.   PLoS Genetics

Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus

(2010) P. R. Murcia et al.   JOURNAL OF VIROLOGY

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Hemagglutinin Receptor Binding Avidity Drives Influenza A Virus Antigenic Drift

(2009) S. E. Hensley et al.   SCIENCE

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes

(2008) S. Kryazhimskiy et al.   JOURNAL OF VIROLOGY