iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

(2016) Alexander Crits-Christoph et al.   ENVIRONMENTAL MICROBIOLOGY

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

(2015) Jacob H. Munson-McGee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome

(2015) Geoffrey D. Hannigan et al.   mBio

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

(2014) B. L. Hurwitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

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

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The global virome: not as big as we thought?

(2013) J Cesar Ignacio-Espinoza et al.   Current Opinion in Virology

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

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

(2012) Simon Roux et al.   PLoS One

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

(2009) Thomas Rattei et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

(2009) Appolinaire Djikeng et al.   PLoS One

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION