The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

(2013) Elke Allers et al.   ENVIRONMENTAL MICROBIOLOGY

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Real Time Metagenomics: Using k-mers to annotate metagenomes

(2012) Robert A. Edwards et al.   BIOINFORMATICS

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

(2012) Elke Allers 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

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

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

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

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Cultivated Single-Stranded DNA Phages That Infect Marine Bacteroidetes Prove Difficult To Detect with DNA-Binding Stains

(2011) Karin Holmfeldt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

(2011) Caroline S Fortunato et al.   ISME Journal

The Western English Channel contains a persistent microbial seed bank

(2011) J Gregory Caporaso et al.   ISME Journal

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen et al.   PLoS One

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning

(2011) Grieg F Steward et al.   Virology Journal

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

(2010) C. Andrews-Pfannkoch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

(2010) Matthew R. Henn et al.   PLoS One

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton

(2008) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

(2008) Shibu Yooseph et al.   BMC BIOINFORMATICS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

(2008) Shannon J Williamson et al.   ISME Journal

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

(2008) Shannon J. Williamson et al.   PLoS One

Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression

(2008) Lauren McDaniel et al.   PLoS One

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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