Unveiling the RNA virosphere associated with marine microorganisms

New insight into the RNA aquatic virosphere via viromics

(2018) Alexander Culley   VIRUS RESEARCH

Phytopathogenic fungus hosts a plant virus: A naturally occurring cross-kingdom viral infection

(2017) Ida Bagus Andika et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

(2017) Lisa Zeigler Allen et al.   mSystems

A new member of the family Totiviridae associated with arboreal ants (Camponotus nipponicus)

(2016) Satoshi Koyama et al.   ARCHIVES OF VIROLOGY

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance

(2016) Syun-ichi Urayama et al.   MICROBES AND ENVIRONMENTS

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Marine genomics goes viral

(2016) Linda Koch   NATURE REVIEWS GENETICS

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Environmental microbiology: Viral diversity on the global stage

(2016) Curtis A. Suttle   Nature Microbiology

Prevalence and complete genome characterization of turkey picobirnaviruses

(2015) Harsha Verma et al.   INFECTION GENETICS AND EVOLUTION

A simple and rapid method to purify viral dsRNA from plant and fungal tissue

(2015) Ryo Okada et al.   JOURNAL OF GENERAL PLANT PATHOLOGY

A New Fractionation and Recovery Method of Viral Genomes Based on Nucleic Acid Composition and Structure Using Tandem Column Chromatography

(2015) Syun-ichi Urayama et al.   MICROBES AND ENVIRONMENTS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

(2014) A. I. Culley et al.   mBio

Analysis of Double-Stranded RNA from Microbial Communities Identifies Double-Stranded RNA Virus-like Elements

(2014) Carolyn J. Decker et al.   Cell Reports

Epidemiology, Phylogeny, and Evolution of Emerging EntericPicobirnavirusesof Animal Origin and Their Relationship to Human Strains

(2014) Yashpal S. Malik et al.   Biomed Research International

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Are we missing half of the viruses in the ocean?

(2012) Grieg F Steward et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data

(2011) AKIFUMI S. TANABE   Molecular Ecology Resources

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Ecogenomics: using massively parallel pyrosequencing to understand virus ecology

(2010) MARILYN J. ROOSSINCK et al.   MOLECULAR ECOLOGY

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome packaging in influenza A virus

(2009) E. C. Hutchinson et al.   JOURNAL OF GENERAL VIROLOGY

Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

(2009) Appolinaire Djikeng et al.   PLoS One