Expanding the Marine Virosphere Using Metagenomics

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

(2013) Jennifer R Brum et al.   ISME Journal

Previously unknown and highly divergent ssDNA viruses populate the oceans

(2013) Jessica M Labonté et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

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

(2013) Bonnie L. Hurwitz et al.   PLoS One

Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity

(2013) Tamara Smokvina et al.   PLoS One

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

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

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

(2013) Rohit Ghai et al.   Scientific Reports

Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids

(2012) Carolina Megumi Mizuno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

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

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

(2012) Aitor Gonzaga et al.   Genome Biology and Evolution

Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L

(2012) Ilnam Kang et al.   JOURNAL OF VIROLOGY

Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses

(2012) Inmaculada Garcia-Heredia et al.   PLoS One

Metagenomic Exploration of Viruses throughout the Indian Ocean

(2012) Shannon J. Williamson et al.   PLoS One

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges

(2011) Sijun Huang et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

(2011) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology

(2010) Alice McCarthy   CHEMISTRY & BIOLOGY

Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets

(2010) Ariella Alperovitch-Lavy et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing

(2010) Rohit Ghai et al.   ISME Journal

Complete Genome Sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a Representative of the SAR116 Clade in the Alphaproteobacteria

(2010) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

Insights into the function of the WhiB-like protein of mycobacteriophage TM4 - a transcriptional inhibitor of WhiB2

(2010) Jan Rybniker et al.   MOLECULAR MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price 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

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

(2009) Lejla Pašić et al.   BMC GENOMICS

Classification of Myoviridae bacteriophages using protein sequence similarity

(2009) Rob Lavigne et al.   BMC MICROBIOLOGY

Genomic analysis of multiple Roseophage SIO1 strains

(2009) Florent Angly et al.   ENVIRONMENTAL MICROBIOLOGY

Roles of viruses in the environment

(2009) Forest Rohwer et al.   ENVIRONMENTAL MICROBIOLOGY

The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’

(2009) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and Freshwaters

(2008) C. Chenard 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

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

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

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

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

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

(2008) Rob Lavigne et al.   RESEARCH IN MICROBIOLOGY