The stepwise assembly of the neonatal virome is modulated by breastfeeding

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

(2019) Erik L. Clarke et al.   Microbiome

Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics

(2019) Kevin R. Theis et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

Bidirectional transfer of anelloviridae lineages between graft and host during lung transplantation

(2018) A. A. Abbas et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes

(2018) Aimee M. Baumann-Dudenhoeffer et al.   NATURE MEDICINE

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Viral communities of the human gut: metagenomic analysis of composition and dynamics

(2017) Varun Aggarwala et al.   Mobile DNA

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction

(2016) A. A. Abbas et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Global, regional, and national causes of under-5 mortality in 2000–15: an updated systematic analysis with implications for the Sustainable Development Goals

(2016) Li Liu et al.   LANCET

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Viruses Causing Gastroenteritis: The Known, The New and Those Beyond

(2016) Bas Oude Munnink et al.   Viruses-Basel

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation

(2016) Christel Chehoud et al.   mBio

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

(2015) Efrem S Lim et al.   NATURE MEDICINE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

PHACTS, a computational approach to classifying the lifestyle of phages

(2012) Katelyn McNair et al.   BIOINFORMATICS

ERE database: A database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome

(2012) Damian Kao et al.   GENOMICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emv2, the only endogenous ecotropic murine leukemia virus of C57BL/6J mice

(2012) George R Young et al.   Retrovirology

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

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

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

Diagnosis of viral gastroenteritis by simultaneous detection of Adenovirus group F, Astrovirus, Rotavirus group A, Norovirus genogroups I and II, and Sapovirus in two internally controlled multiplex real-time PCR assays

(2010) Noortje M. van Maarseveen et al.   JOURNAL OF CLINICAL VIROLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

(2009) D A Hill et al.   Mucosal Immunology

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY