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

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

(2017) Eric C. Keen et al.   mBio

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

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

(2016) Magdalena Calusinska et al.   ENVIRONMENTAL 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

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

(2016) Eduardo Corel et al.   TRENDS IN MICROBIOLOGY

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

(2016) Jaime Iranzo et al.   mBio

Taxonomic reassessment of N4-like viruses using comparative genomics and proteomics suggests a new subfamily - “Enquartavirinae”

(2015) Johannes Wittmann et al.   ARCHIVES OF VIROLOGY

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Methods for virus classification and the challenge of incorporating metagenomic sequence data

(2015) P. Simmonds   JOURNAL OF GENERAL VIROLOGY

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

A Suggested New Bacteriophage Genus, “Kp34likevirus”, within the Autographivirinae Subfamily of Podoviridae

(2015) Harald Eriksson et al.   Viruses-Basel

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

(2015) Welkin H Pope et al.   eLife

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

(2015) Simon Roux et al.   eLife

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

(2015) Simon Roux et al.   Frontiers in Microbiology

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages

(2014) Yan D. Niu et al.   PLoS One

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

(2014) Julianne H. Grose et al.   VIROLOGY

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Three proposed new bacteriophage genera of staphylococcal phages: “3alikevirus”, “77likevirus” and “Phietalikevirus”

(2013) Diana Gutiérrez et al.   ARCHIVES OF VIROLOGY

Characterization and Genome Sequencing of Phage Abp1, a New phiKMV-Like Virus Infecting Multidrug-Resistant Acinetobacter baumannii

(2013) Guangtao Huang et al.   CURRENT MICROBIOLOGY

Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

(2013) Ho Bin Jang et al.   JOURNAL OF VIROLOGY

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

A new proposed taxon for double-stranded DNA viruses, the order “Ligamenvirales”

(2012) David Prangishvili et al.   ARCHIVES OF VIROLOGY

Identifying functional modules in interaction networks through overlapping Markov clustering

(2012) Y.-K. Shih et al.   BIOINFORMATICS

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

(2012) S. J. Labrie et al.   ENVIRONMENTAL MICROBIOLOGY

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Phylogenomic networks

(2011) Tal Dagan   TRENDS IN MICROBIOLOGY

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

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

Classification of Myoviridae bacteriophages using protein sequence similarity

(2009) Rob Lavigne et al.   BMC MICROBIOLOGY

Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism

(2009) Peter Redder et al.   ENVIRONMENTAL MICROBIOLOGY

Recombination and microdiversity in coastal marine cyanophages

(2009) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence ofSynechococcushost genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution

(2009) Andrew D. Millard et al.   ENVIRONMENTAL MICROBIOLOGY

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage

(2009) Adeline Goulet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

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

The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere

(2008) A. M. Comeau et al.   MOLECULAR BIOLOGY AND EVOLUTION