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Phage or foe: an insight into the impact of viral predation on microbial communities

(2018) Lucía Fernández et al.   ISME Journal

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

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Biological species in the viral world

(2018) Louis-Marie Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

(2018) Maria de la Cruz Peña et al.   Viruses-Basel

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

(2018) Pakorn Aiewsakun et al.   Microbiome

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

(2018) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

(2017) Welkin H. Pope et al.   mBio

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

(2017) Simon Roux et al.   Nature Communications

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

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Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

(2016) Mart Krupovic et al.   ARCHIVES OF VIROLOGY

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2016) Benjamin Bolduc et al.   ISME Journal

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

(2016) Jaime Iranzo et al.   JOURNAL OF VIROLOGY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

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Virus-mediated archaeal hecatomb in the deep seafloor

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Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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The global ocean microbiome

(2015) M. A. Moran   SCIENCE

Structure and function of the global ocean microbiome

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Patterns and ecological drivers of ocean viral communities

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A structured annotation frame for the transposable phages: A new proposed family “Saltoviridae” within the Caudovirales

(2015) Chantal Hulo et al.   VIROLOGY

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

(2015) Welkin H Pope et al.   eLife

Challenges in RNA virus bioinformatics

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Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

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Molecular Bases and Role of Viruses in the Human Microbiome

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Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

NCBI Viral Genomes Resource

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Unification of the Globally Distributed Spindle-Shaped Viruses of the Archaea

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Real Time Classification of Viruses in 12 Dimensions

(2013) Chenglong Yu et al.   PLoS One

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Going viral: next-generation sequencing applied to phage populations in the human gut

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IntScore: a web tool for confidence scoring of biological interactions

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Genome-based phylogeny of dsDNA viruses by a novel alignment-free method

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Bacteria-Phage Antagonistic Coevolution in Soil

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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

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Classification of Myoviridae bacteriophages using protein sequence similarity

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Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

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Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools

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The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE