Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics

The Deep Viriosphere: Assessing the Viral Impact on Microbial Community Dynamics in the Deep Subsurface

(2013) R. E. Anderson et al.   Reviews in Mineralogy & Geochemistry

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

(2012) Bonnie L. Hurwitz et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system

(2012) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

Metagenomic Exploration of Viruses throughout the Indian Ocean

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

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

(2011) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes

(2011) Vera Tai et al.   PLoS One

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

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Carrying photosynthesis genes increases ecological fitness of cyanophagein silico

(2009) Ferdi L. Hellweger   ENVIRONMENTAL MICROBIOLOGY

Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm

(2009) William J Brazelton et al.   ISME Journal

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Explaining microbial population genomics through phage predation

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

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

(2009) Barbara J. Campbell et al.   PLoS Genetics

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria

(2008) Thorben Dammeyer et al.   CURRENT BIOLOGY

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

(2008) Shannon J Williamson et al.   ISME Journal

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

(2008) Jason G. Bragg et al.   PLoS One