Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes

Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching

(2016) Nathan D. Grubaugh et al.   Cell Host & Microbe

Determinants of Arbovirus Vertical Transmission in Mosquitoes

(2016) Sebastian Lequime et al.   PLoS Pathogens

Demographics of Natural Oral Infection of Mosquitos by Venezuelan Equine Encephalitis Virus

(2015) Serafín Gutiérrez et al.   JOURNAL OF VIROLOGY

Modulation of Flavivirus Population Diversity by RNA Interference

(2015) Doug E. Brackney et al.   JOURNAL OF VIROLOGY

Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints

(2015) October M. Sessions et al.   PLoS Neglected Tropical Diseases

Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission

(2015) Shuzhen Sim et al.   PLoS Neglected Tropical Diseases

Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness

(2015) Nathan D. Grubaugh et al.   PLoS Pathogens

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

Inference with viral quasispecies diversity indices: clonal and NGS approaches

(2014) Josep Gregori et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti

(2014) Gordana Rašić et al.   BMC GENOMICS

Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential

(2014) Kenneth A. Stapleford et al.   Cell Host & Microbe

Vertical transmission of arboviruses in mosquitoes: A historical perspective

(2014) Sebastian Lequime et al.   INFECTION GENETICS AND EVOLUTION

Arboviral Bottlenecks and Challenges to Maintaining Diversity and Fitness during Mosquito Transmission

(2014) Naomi Forrester et al.   Viruses-Basel

Vector Competence in West African Aedes aegypti Is Flavivirus Species and Genotype Dependent

(2014) Laura B. Dickson et al.   PLoS Neglected Tropical Diseases

Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models

(2014) Kathryn Rozen-Gagnon et al.   PLoS Pathogens

Variation in RNA Virus Mutation Rates across Host Cells

(2014) Marine Combe et al.   PLoS Pathogens

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

(2013) Anthony G Doran et al.   BMC BIOINFORMATICS

Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing

(2013) Robert Scott Cornman et al.   BMC GENOMICS

Factors shaping the adaptive landscape for arboviruses: implications for the emergence of disease

(2013) Lark L Coffey et al.   Future Microbiology

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses

(2013) Thanyalak Fansiri et al.   PLoS Genetics

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

(2013) Rubing Chen et al.   PLoS Pathogens

Cooperative interactions in the West Nile virus mutant swarm

(2012) Alexander T Ciota et al.   BMC EVOLUTIONARY BIOLOGY

Quantification of intrahost bottlenecks of West Nile virus in Culex pipiens mosquitoes using an artificial mutant swarm

(2012) Alexander T. Ciota et al.   INFECTION GENETICS AND EVOLUTION

Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity

(2012) Poornima Parameswaran et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Specificity of resistance to dengue virus isolates is associated with genotypes of the mosquito antiviral gene Dicer-2

(2012) L. Lambrechts et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Virus population bottlenecks during within-host progression and host-to-host transmission

(2012) Serafín Gutiérrez et al.   Current Opinion in Virology

Vector-Borne Transmission Imposes a Severe Bottleneck on an RNA Virus Population

(2012) Naomi L. Forrester et al.   PLoS Pathogens

High-Resolution Analysis of Intrahost Genetic Diversity in Dengue Virus Serotype 1 Infection Identifies Mixed Infections

(2011) K. T. D. Thai 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

West Nile Virus Genetic Diversity is Maintained during Transmission by Culex pipiens quinquefasciatus Mosquitoes

(2011) Doug E. Brackney et al.   PLoS One

Arbovirus high fidelity variant loses fitness in mosquitoes and mice

(2011) L. L. Coffey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative genetics of Aedes aegypti vector competence for dengue viruses: towards a new paradigm?

(2011) Louis Lambrechts   TRENDS IN PARASITOLOGY

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Quasispecies Theory and the Behavior of RNA Viruses

(2010) Adam S. Lauring et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic specificity and potential for local adaptation between dengue viruses and mosquito vectors

(2009) Louis Lambrechts et al.   BMC EVOLUTIONARY BIOLOGY

Dengue 1 Diversity and Microevolution, French Polynesia 2001–2006: Connection with Epidemiology and Clinics

(2009) Elodie Descloux et al.   PLoS Neglected Tropical Diseases

RNAi Targeting of West Nile Virus in Mosquito Midguts Promotes Virus Diversification

(2009) Doug E. Brackney et al.   PLoS Pathogens

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Large Bottleneck Size in Cauliflower Mosaic Virus Populations during Host Plant Colonization

(2008) Baptiste Monsion et al.   PLoS Pathogens