Temporal dynamics of uncultured viruses: a new dimension in viral diversity

Communication between viruses guides lysis–lysogeny decisions

(2017) Zohar Erez et al.   NATURE

Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly

(2016) Josef Komenda et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

(2016) Ovidiu Popa et al.   ISME Journal

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

(2016) Siobhan C. Watkins et al.   MARINE AND FRESHWATER RESEARCH

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

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

Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

(2016) Timofey Skvortsov et al.   PLoS One

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA

(2015) JC Green et al.   AQUATIC MICROBIAL ECOLOGY

The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

(2015) Danielle L. Peters et al.   BMC GENOMICS

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

(2015) Benjamin Bolduc et al.   ISME Journal

Population Dynamics of Cyanomyovirus in a Tropical Eutrophic Reservoir

(2015) Bee Hui Yeo et al.   MICROBES AND ENVIRONMENTS

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

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

(2015) Simon Roux et al.   eLife

Genetic diversity and temporal dynamics of phytoplankton viruses in East Lake, China

(2015) Mei-Niang Wang et al.   VIROLOGICA SINICA

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Linking Host Prokaryotic Physiology to Viral Lifestyle Dynamics in a Temperate Freshwater Lake (Lake Pavin, France)

(2014) S. Palesse et al.   MICROBIAL ECOLOGY

Coevolution can reverse predator-prey cycles

(2014) M. H. Cortez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and genome dynamics of marine cyanophages using metagenomic analyses

(2014) Yingfei Ma et al.   Environmental Microbiology Reports

New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

(2013) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

(2013) Ching-Hung Tseng et al.   ISME Journal

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

(2012) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Seasonality and monthly dynamics of marine myovirus communities

(2012) Cheryl-Emiliane T. Chow et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

(2012) Laura Fancello et al.   ISME Journal

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

(2012) Simon Roux et al.   PLoS One

Diverse CRISPRs Evolving in Human Microbiomes

(2012) Mina Rho et al.   PLoS Genetics

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons

(2010) Corinne F Maurice et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

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