Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

(2019) Ella T. Sieradzki et al.   Nature Communications

Numerous cultivated and uncultivated viruses encode ribosomal proteins

(2019) Carolina M. Mizuno et al.   Nature Communications

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe

(2018) Alfred Fillol-Salom et al.   ISME Journal

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

(2018) Nathan A. Ahlgren et al.   ISME Journal

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

(2017) David M Needham et al.   ISME Journal

Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone

(2017) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior

(2017) Elaine Luo et al.   mBio

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera

(2017) Samuel T. Wilson et al.   Nature Microbiology

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

Viruses Inhibit CO 2 Fixation in the Most Abundant Phototrophs on Earth

(2016) Richard J. Puxty et al.   CURRENT BIOLOGY

Viral metabolic reprogramming in marine ecosystems

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

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

Genomes of Abundant and Widespread Viruses from the Deep Ocean

(2016) Carolina Megumi Mizuno et al.   mBio

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Re-examination of the relationship between marine virus and microbial cell abundances

(2016) Charles H. Wigington et al.   Nature Microbiology

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

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea

(2015) Dawn B. Goldsmith et al.   PeerJ

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites

(2015) José R. Penadés et al.   Annual Review of Virology

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

Microbial oceanography and the Hawaii Ocean Time-series programme

(2014) David M. Karl et al.   NATURE REVIEWS MICROBIOLOGY

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

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

(2014) Julianne H. Grose et al.   VIROLOGY

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience

(2013) David M Needham et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

(2013) I. Kang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

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

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Seasonality and monthly dynamics of marine myovirus communities

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Development ofphoHas a Novel Signature Gene for Assessing Marine Phage Diversity

(2011) Dawn B. Goldsmith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features

(2011) Shellie R. Bench et al.   Frontiers in Microbiology

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

(2010) Alyson E. Santoro et al.   ENVIRONMENTAL MICROBIOLOGY

Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

(2010) H. Moreau et al.   JOURNAL OF VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

From small hosts come big viruses: the complete genome of a secondOstreococcus taurivirus, OtV-1

(2009) Karen D. Weynberg et al.   ENVIRONMENTAL MICROBIOLOGY

Diel rhythm of nitrogen and carbon metabolism in the unicellular, diazotrophic cyanobacteriumCrocosphaera watsoniiWH8501

(2009) Wiebke Mohr et al.   ENVIRONMENTAL MICROBIOLOGY

Abundances of crenarchaealamoAgenes and transcripts in the Pacific Ocean

(2009) Matthew J. Church et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Lysogenic virus–host interactions predominate at deep-sea diffuse-flow hydrothermal vents

(2008) Shannon J Williamson et al.   ISME Journal