Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

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

Gut Virome Sequencing in Children With Early Islet Autoimmunity: Figure 1

(2015) Lenka Kramná et al.   DIABETES CARE

Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples

(2015) Toon Rosseel et al.   JOURNAL OF VIROLOGICAL METHODS

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent

(2015) Linlin Li et al.   JOURNAL OF VIROLOGICAL METHODS

Soil microbiome responses to the short-term effects of Amazonian deforestation

(2015) Acacio A. Navarrete et al.   MOLECULAR ECOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Origins and evolution of viruses of eukaryotes: The ultimate modularity

(2015) Eugene V. Koonin et al.   VIROLOGY

Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses

(2015) Nádia Conceição-Neto et al.   Virology Journal

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions

(2015) Cheryl-Emiliane T. Chow et al.   Frontiers in Microbiology

Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan, China

(2015) Han Xia et al.   PLoS One

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

(2015) Monika A. Gorzelak et al.   PLoS One

Viral Metagenomics Reveal Blooms of Anelloviruses in the Respiratory Tract of Lung Transplant Recipients

(2014) J. C. Young et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium

(2014) Jana Sachsenröder et al.   PLoS One

Feline fecal virome reveals novel and prevalent enteric viruses

(2014) Terry Fei Fan Ng et al.   VETERINARY MICROBIOLOGY

Viral metagenomic analysis of feces of wild small carnivores

(2014) Rogier Bodewes et al.   Virology Journal

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

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

First Isolation of Mimivirus in a Patient With Pneumonia

(2013) Hanene Saadi et al.   CLINICAL INFECTIOUS DISEASES

Shan Virus: A New Mimivirus Isolated from the Stool of a Tunisian Patient with Pneumonia

(2013) Hanene Saadi et al.   INTERVIROLOGY

Evidence of the megavirome in humans

(2013) Philippe Colson et al.   JOURNAL OF CLINICAL VIROLOGY

Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

(2013) Richard J. Hall et al.   JOURNAL OF VIROLOGICAL METHODS

Novel Hybrid Parvovirus-Like Virus, NIH-CQV/PHV, Contaminants in Silica Column-Based Nucleic Acid Extraction Kits

(2013) H. Smuts et al.   JOURNAL OF VIROLOGY

AIDS Alters the Commensal Plasma Virome

(2013) L. Li et al.   JOURNAL OF VIROLOGY

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

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

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

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

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

(2012) Jana Sachsenröder et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

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

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

Intestinal Microbiota of Dogs and Cats: a Bigger World than We Thought

(2011) Jan S. Suchodolski   VETERINARY CLINICS OF NORTH AMERICA-SMALL ANIMAL PRACTICE

The Fecal Viral Flora of Wild Rodents

(2011) Tung G. Phan et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Real-time quantitative PCR based sensitive detection and genotype discrimination of Pepino mosaic virus

(2009) Ion Gutiérrez-Aguirre et al.   JOURNAL OF VIROLOGICAL METHODS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY

An international inter-laboratory ring trial to evaluate a real-time PCR assay for the detection of bovine herpesvirus 1 in extended bovine semen

(2007) Jianning Wang et al.   VETERINARY MICROBIOLOGY