Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus

High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles

(2017) Michiel van de Waterbeemd et al.   NATURE METHODS

Role of Mitochondrial Membrane Spherules in Flock House Virus Replication

(2016) James R. Short et al.   JOURNAL OF VIROLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

A Defective Interfering Influenza RNA Inhibits Infectious Influenza Virus Replication in Human Respiratory Tract Cells: A Potential New Human Antiviral

(2016) Claire Smith et al.   Viruses-Basel

ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs

(2015) Andrew Routh et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Immunostimulatory Defective Viral Genomes from Respiratory Syncytial Virus Promote a Strong Innate Antiviral Response during Infection in Mice and Humans

(2015) Yan Sun et al.   PLoS Pathogens

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Defective Interfering Influenza Virus RNAs: Time To Reevaluate Their Clinical Potential as Broad-Spectrum Antivirals?

(2014) N. J. Dimmock et al.   JOURNAL OF VIROLOGY

A first look at the Oxford Nanopore MinION sequencer

(2014) Alexander S. Mikheyev et al.   Molecular Ecology Resources

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Solid phase click ligation for the synthesis of very long oligonucleotides

(2013) Jieqiong Qiu et al.   CHEMICAL COMMUNICATIONS

Sequence Analysis of In Vivo Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus

(2013) K. Saira et al.   JOURNAL OF VIROLOGY

RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila

(2013) Bertsy Goic et al.   NATURE IMMUNOLOGY

Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data

(2013) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

Continuous Influenza Virus Production in Cell Culture Shows a Periodic Accumulation of Defective Interfering Particles

(2013) Timo Frensing et al.   PLoS One

Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity

(2013) Karla Tapia et al.   PLoS Pathogens

Identification and Manipulation of the Molecular Determinants Influencing Poliovirus Recombination

(2013) Charles Runckel et al.   PLoS Pathogens

Packaging host RNAs in small RNA viruses

(2012) Andrew Routh et al.   CELL CYCLE

Nucleotide-Resolution Profiling of RNA Recombination in the Encapsidated Genome of a Eukaryotic RNA Virus by Next-Generation Sequencing

(2012) Andrew Routh et al.   JOURNAL OF MOLECULAR BIOLOGY

Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus

(2012) A. Routh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Internally deleted WNV genomes isolated from exotic birds in New Mexico: Function in cells, mosquitoes, and mice

(2012) Kendra N. Pesko et al.   VIROLOGY

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Defective Interfering Viral Particles in Acute Dengue Infections

(2011) Dongsheng Li et al.   PLoS One

Molecular characterization of Drosophila cells persistently infected with Flock House virus

(2011) Juan Jovel et al.   VIROLOGY

A 3′ terminal stem–loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication

(2010) John J. Rosskopf et al.   VIRUS RESEARCH

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic Analysis of Hepatitis C Virus with Defective Genome and Its Infectivity in Vitro

(2009) K. Sugiyama et al.   JOURNAL OF VIROLOGY

Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution

(2009) Ann C. Palmenberg et al.   SCIENCE

Defective Interfering RNAs: Foes of Viruses and Friends of Virologists

(2009) Kunj Pathak et al.   Viruses-Basel

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

(2009) Ben Langmead et al.   GENOME BIOLOGY