MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

(2014) Kym Lowry et al.   PLoS Pathogens

A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission

(2014) Eugene V. Ryabov et al.   PLoS Pathogens

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

Identification and Manipulation of the Molecular Determinants Influencing Poliovirus Recombination

(2013) Charles Runckel et al.   PLoS Pathogens

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

The Recent Recombinant Evolution of a Major Crop Pathogen, Potato virus Y

(2012) Johan Christiaan Visser et al.   PLoS One

Global Honey Bee Viral Landscape Altered by a Parasitic Mite

(2012) S. J. Martin et al.   SCIENCE

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

Why do RNA viruses recombine?

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

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

(2011) Li C. Xia et al.   PLoS One

Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples

(2011) Ting Gong et al.   PLoS One

Replication of Varroa destructor virus 1 (VDV-1) and a Varroa destructor virus 1–deformed wing virus recombinant (VDV-1–DWV) in the head of the honey bee

(2011) Naama Zioni et al.   VIROLOGY

Varroa destructor is an effective vector of Israeli acute paralysis virus in the honeybee, Apis mellifera

(2010) G. Di Prisco et al.   JOURNAL OF GENERAL VIROLOGY

Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies

(2010) J. Moore et al.   JOURNAL OF GENERAL VIROLOGY

Analysis of Genetic Diversity and Sites of Recombination in Human Rhinovirus Species C

(2010) C. L. McIntyre et al.   JOURNAL OF VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Deformed wing virus

(2009) Joachim R. de Miranda et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology

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

Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future

(2008) S. ALIZON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Safety Concerns with Regard to Live Attenuated Flavivirus Vaccines

(2008) Stephen J. Seligman et al.   JOURNAL OF INFECTIOUS DISEASES

Venereal and vertical transmission of deformed wing virus in honeybees (Apis mellifera L.)

(2008) J.R. de Miranda et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium

(2008) Yoshinori Tomoyasu et al.   GENOME BIOLOGY