Quantifying influenza virus diversity and transmission in humans

Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units

(2015) Marine Combe et al.   Cell Host & Microbe

Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

(2014) Andrew Varble et al.   Cell Host & Microbe

Co-infection With Pandemic H1N1 and Seasonal H3N2 Influenza Viruses

(2013) Nelson Lee   ANNALS OF INTERNAL MEDICINE

Genomewide Analysis of Reassortment and Evolution of Human Influenza A(H3N2) Viruses Circulating between 1968 and 2011

(2013) K. B. Westgeest et al.   JOURNAL OF VIROLOGY

Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission

(2013) C. Viboud et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain

(2013) Sarah L Fordyce et al.   Virology Journal

Antigenically intact hemagglutinin in circulating avian and swine influenza viruses and potential for H3N2 pandemic

(2013) Kannan Tharakaraman et al.   Scientific Reports

Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks

(2013) Joseph Hughes et al.   PLoS Pathogens

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Pathogenicity and Transmission in Pigs of the Novel A(H3N2)v Influenza Virus Isolated from Humans and Characterization of Swine H3N2 Viruses Isolated in 2010-2011

(2012) P. Kitikoon et al.   JOURNAL OF VIROLOGY

Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community

(2011) Leo L.M. Poon et al.   JOURNAL OF CLINICAL VIROLOGY

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic

(2010) E. Ghedin et al.   JOURNAL OF VIROLOGY

Comparative Epidemiology of Pandemic and Seasonal Influenza A in Households

(2010) Benjamin J. Cowling et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reassortant between Human-Like H3N2 and Avian H5 Subtype Influenza A Viruses in Pigs: A Potential Public Health Risk

(2010) Yanlong Cong et al.   PLoS One

Structural Basis of Preexisting Immunity to the 2009 H1N1 Pandemic Influenza Virus

(2010) R. Xu et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Single-Reaction Genomic Amplification Accelerates Sequencing and Vaccine Production for Classical and Swine Origin Human Influenza A Viruses

(2009) B. Zhou et al.   JOURNAL OF VIROLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Viral genome sequencing by random priming methods

(2008) Appolinaire Djikeng et al.   BMC GENOMICS

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY