Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

(2015) Ci-Xiu Li et al.   eLife

Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses

(2014) R. Tokarz et al.   JOURNAL OF VIROLOGY

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs inArabidopsis

(2014) Mengji Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts

(2014) Laurence Josset et al.   RNA Biology

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

(2014) J. T. Ladner et al.   mBio

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

(2013) S. N. Naccache et al.   JOURNAL OF VIROLOGY

RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence

(2013) Nathan Pumplin et al.   NATURE REVIEWS MICROBIOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Autologous Antibody Capture to Enrich Immunogenic Viruses for Viral Discovery

(2013) Bas B. Oude Munnink et al.   PLoS One

Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

(2013) Shelley Cook et al.   PLoS One

Antiviral RNA Interference in Mammalian Cells

(2013) P. V. Maillard et al.   SCIENCE

Identification of RNase L-Dependent, 3'-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells

(2013) E. Girardi et al.   mBio

Economic and Disease Burden of Dengue in Southeast Asia

(2013) Donald S. Shepard et al.   PLoS Neglected Tropical Diseases

Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection

(2013) Joao Trindade Marques et al.   PLoS Pathogens

Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes

(2012) Z. N. Adelman et al.   INSECT MOLECULAR BIOLOGY

Broad RNA Interference-Mediated Antiviral Immunity and Virus-Specific Inducible Responses in Drosophila

(2012) C. Kemp et al.   JOURNAL OF IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Arbovirus-Derived piRNAs Exhibit a Ping-Pong Signature in Mosquito Cells

(2012) Nicolas Vodovar et al.   PLoS One

Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma

(2012) Elaine M. Morazzani et al.   PLoS Pathogens

The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

(2011) Peter Arensburger et al.   BMC GENOMICS

RNA-Based Immunity Terminates Viral Infection in Adult Drosophila in the Absence of Viral Suppression of RNA Interference: Characterization of Viral Small Interfering RNA Populations in Wild-Type and Mutant Flies

(2011) Y.-H. Han et al.   JOURNAL OF VIROLOGY

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu et al.   PLoS One

Identification of a Novel Marine Fish Virus, Singapore Grouper Iridovirus-Encoded MicroRNAs Expressed in Grouper Cells by Solexa Sequencing

(2011) Yang Yan et al.   PLoS One

Discovery of DNA Viruses in Wild-Caught Mosquitoes Using Small RNA High throughput Sequencing

(2011) Maijuan Ma et al.   PLoS One

Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection

(2011) X. Peng et al.   mBio

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

RNAi-mediated immunity provides strong protection against the negative-strand RNA vesicular stomatitis virus in Drosophila

(2010) S. Mueller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

(2010) Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

(2009) Colin D. Malone et al.   CELL

The role of RNAi and microRNAs in animal virus replication and antiviral immunity

(2009) J. L. Umbach et al.   GENES & DEVELOPMENT

Drosophila A virus is an unusual RNA virus with a T=3 icosahedral core and permuted RNA-dependent RNA polymerase

(2009) R. L. Ambrose et al.   JOURNAL OF GENERAL VIROLOGY

Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

(2009) Appolinaire Djikeng et al.   PLoS One

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

(2009) Jan F. Kreuze et al.   VIROLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Novel virus discovery in field-collected mosquito larvae using an improved system for rapid determination of viral RNA sequences (RDV ver4.0)

(2008) Takuya Yamao et al.   ARCHIVES OF VIROLOGY

Mechanism of Induction and Suppression of Antiviral Immunity Directed by Virus-Derived Small RNAs in Drosophila

(2008) Roghiyh Aliyari et al.   Cell Host & Microbe

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

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

Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes

(2008) K. M. Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Identification of Known and New RNA Viruses from Animal Tissues

(2008) Joseph G. Victoria et al.   PLoS Pathogens