Classification and quantification of bacteriophage taxa in human gut metagenomes

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi 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

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

(2013) Ivan Vujkovic-Cvijin et al.   Science Translational Medicine

Estimation of viral richness from shotgun metagenomes using a frequency count approach

(2013) Heather K Allen et al.   Microbiome

Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens

(2012) Ben Busby et al.   ENVIRONMENTAL MICROBIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

(2012) Cesar O Flores et al.   ISME Journal

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Role of the intestinal microbiome in health and disease: from correlation to causation

(2012) Willem M de Vos et al.   NUTRITION REVIEWS

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

A composite bacteriophage alters colonization by an intestinal commensal bacterium

(2012) B. A. Duerkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Lactococcal 936-type phages and dairy fermentation problems: from detection to evolution and prevention

(2012) Jennifer Mahony et al.   Frontiers in Microbiology

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

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

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

(2010) Kimberly P Tucker et al.   ISME Journal

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae

(2010) Margarida Carrolo et al.   PLoS One

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

(2009) Xiaoxue Wang et al.   ISME Journal

New dimensions of the virus world discovered through metagenomics

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

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

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