Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum

Accurate viral population assembly from ultra-deep sequencing data

(2014) S. Mangul et al.   BIOINFORMATICS

Within-Host Whole-Genome Deep Sequencing and Diversity Analysis of Human Respiratory Syncytial Virus Infection Reveals Dynamics of Genomic Diversity in the Absence and Presence of Immune Pressure

(2014) Y. H. Grad et al.   JOURNAL OF VIROLOGY

High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution

(2014) Nicholas C. Wu et al.   Scientific Reports

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

(2013) Kerensa McElroy et al.   BMC GENOMICS

Genetics research: jumping into the deep end of the pool

(2013) NOAM SHOMRON   Genetics Research

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

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Sequencing approach to analyze the role of quasispecies for classical swine fever

(2013) Armin Töpfer et al.   VIROLOGY

A Roadmap to the Human Virome

(2013) Eric Delwart   PLoS Pathogens

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

(2012) John Archer et al.   BMC BIOINFORMATICS

The effect of strand bias in Illumina short-read sequencing data

(2012) Yan Guo et al.   BMC GENOMICS

Next-generation sequencing technology in clinical virology

(2012) M.R. Capobianchi et al.   CLINICAL MICROBIOLOGY AND INFECTION

Identification of Hepatitis C Virus Transmission Using a Next-Generation Sequencing Approach

(2012) A. Escobar-Gutierrez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Application of next-generation sequencing technologies in virology

(2012) A. D. Radford et al.   JOURNAL OF GENERAL VIROLOGY

Presence of Oseltamivir-Resistant Pandemic A/H1N1 Minor Variants Before Drug Therapy With Subsequent Selection and Transmission

(2012) Elodie Ghedin et al.   JOURNAL OF INFECTIOUS DISEASES

Ultradeep Sequencing Analysis of Population Dynamics of Virus Escape Mutants in RNAi-Mediated Resistant Plants

(2012) Fernando Martínez et al.   MOLECULAR BIOLOGY AND EVOLUTION

A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease

(2012) Rachel L Graham et al.   NATURE MEDICINE

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

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

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

(2012) Vincent Foulongne et al.   PLoS One

Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

(2012) John Archer et al.   PLoS One

Coxsackievirus B3 mutator strains are attenuated in vivo

(2012) N. F. Gnadig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative quasispecies theory-based model of virus escape mutation under immune selection

(2012) H.-J. Woo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

(2012) Li Yin et al.   Retrovirology

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

(2011) Luisa Barzon et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Variations of Coxsackievirus B3 Capsid Primary Structure, Ligands, and Stability Are Selected for in a Coxsackievirus and Adenovirus Receptor-Limited Environment

(2011) S. D. Carson et al.   JOURNAL OF VIROLOGY

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

(2011) Patrick Flaherty et al.   NUCLEIC ACIDS RESEARCH

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

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

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

(2011) Rowena A. Bull et al.   PLoS Pathogens

Mathematical Modeling of Ultradeep Sequencing Data Reveals that Acute CD8+ T-Lymphocyte Responses Exert Strong Selective Pressure in Simian Immunodeficiency Virus-Infected Macaques but Still Fail To Clear Founder Epitope Sequences

(2010) T. M. T. Love et al.   JOURNAL OF VIROLOGY

Viral Mutation Rates

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

Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing

(2010) C. F. Wright et al.   JOURNAL OF VIROLOGY

Host Alternation of Chikungunya Virus Increases Fitness while Restricting Population Diversity and Adaptability to Novel Selective Pressures

(2010) L. L. Coffey et al.   JOURNAL OF VIROLOGY

Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology

(2010) Stephanie M. Willerth et al.   PLoS One

Quasispecies Theory and the Behavior of RNA Viruses

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

Fidelity Variants of RNA Dependent RNA Polymerases Uncover an Indirect, Mutagenic Activity of Amiloride Compounds

(2010) Laura I. Levi et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Therapeutically targeting RNA viruses via lethal mutagenesis

(2008) Jason D Graci et al.   Future Virology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Hidden Virulence Determinants in a Viral Quasispecies In Vivo

(2008) M. Sanz-Ramos et al.   JOURNAL OF VIROLOGY

Arbovirus evolution in vivo is constrained by host alternation

(2008) L. L. Coffey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology