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

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

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Genomes of Abundant and Widespread Viruses from the Deep Ocean

(2016) Carolina Megumi Mizuno et al.   mBio

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea

(2016) Mario López-Pérez et al.   Frontiers in Microbiology

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

(2016) Simon Roux et al.   PeerJ

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process ofE. coliphage HK97

(2015) Nichole Cumby et al.   MOLECULAR MICROBIOLOGY

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics

(2015) Carolina Megumi Mizuno et al.   mBio

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

(2015) Simon Roux et al.   eLife

Marine Microbial Metagenomics: From Individual to the Environment

(2014) Ching-Hung Tseng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

(2014) Chris L Dupont et al.   ISME Journal

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

(2014) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

(2014) Jinglie Zhou et al.   JOURNAL OF VIROLOGY

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Evidence for metaviromic islands in marine phages

(2014) Carolina Megumi Mizuno et al.   Frontiers in Microbiology

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome

(2014) Rachel Marine et al.   Microbiome

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

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

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

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

(2013) Rohit Ghai et al.   Scientific Reports

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

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

(2012) Y. Peng et al.   BIOINFORMATICS

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

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

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

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt 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

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

(2010) Rohit Ghai et al.   ISME Journal

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Explaining microbial population genomics through phage predation

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

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal