Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX

Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis

(2017) Matthew Thoendel et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

(2017) Christian Milani et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

(2017) Stephen Hayes et al.   Viruses-Basel

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses

(2017) Konstantin Yarygin et al.   PLoS One

Bacteriophages as potential new mammalian pathogens

(2017) George V. Tetz et al.   Scientific Reports

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Sequencing Indicates That the Oropharyngeal Phageome of Individuals With Schizophrenia Differs From That of Controls

(2015) Robert H. Yolken et al.   SCHIZOPHRENIA BULLETIN

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Molecular Bases and Role of Viruses in the Human Microbiome

(2014) Shira R. Abeles et al.   JOURNAL OF MOLECULAR BIOLOGY

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Characterization of virus-like particles associated with the human faecal and caecal microbiota

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

The Human Microbiome: From Symbiosis to Pathogenesis

(2013) Emiley A. Eloe-Fadrosh et al.   Annual Review of Medicine

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Rapid evolution of the human gut virome

(2013) S. Minot 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative (Meta)genomic Analysis and Ecological Profiling of Human Gut-Specific Bacteriophage φB124-14

(2012) Lesley A. Ogilvie et al.   PLoS One

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

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

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

(2011) S. Minot et al.   GENOME RESEARCH

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY