Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

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

Metagenomics and the Human Virome in Asymptomatic Individuals

(2016) Nicolás Rascovan et al.   Annual Review of Microbiology

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

(2016) Edward T. Mee et al.   VACCINE

Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains

(2015) Dagmara W. Lewandowska et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples

(2015) Nicole Fischer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

(2015) Nádia Conceição-Neto et al.   Scientific Reports

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

Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

(2015) Ka-Cheung Luk et al.   PLoS One

Exploring the Potential of Next-Generation Sequencing in Detection of Respiratory Viruses

(2014) S. Prachayangprecha et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans

(2014) Nicole E. Moore et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comprehensive Human Virus Screening Using High-Throughput Sequencing with a User-Friendly Representation of Bioinformatics Analysis: a Pilot Study

(2014) Tom J. Petty et al.   JOURNAL OF CLINICAL MICROBIOLOGY

New astrovirus in human feces from Burkina Faso

(2014) Tung Gia Phan et al.   JOURNAL OF CLINICAL VIROLOGY

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

(2014) Matthew Cotten et al.   PLoS One

A Method Enabling High-Throughput Sequencing of Human Cytomegalovirus Complete Genomes from Clinical Isolates

(2014) Steven Sijmons et al.   PLoS One

Viral metagenomic analysis of feces of wild small carnivores

(2014) Rogier Bodewes et al.   Virology Journal

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

Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

(2013) John L. Mokili et al.   PLoS One

Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool

(2013) John Law et al.   PLoS One

Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types

(2013) Hanna Johansson et al.   VIROLOGY

Virus discovery: one step beyond

(2013) Saskia L Smits et al.   Current Opinion in Virology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

(2012) Scott A. Handley et al.   CELL

Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing

(2012) Fredrik Lysholm et al.   PLoS One

Performance of VIDISCA-454 in Feces-Suspensions and Serum

(2012) Michel de Vries et al.   Viruses-Basel

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in 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

Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

(2011) J. Yang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Heart and Skeletal Muscle Inflammation of Farmed Salmon Is Associated with Infection with a Novel Reovirus

(2010) Gustavo Palacios et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

New Molecular Detection Tools Adapted to Emerging Rhinoviruses and Enteroviruses

(2009) C. Tapparel et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

(2009) J. G. Victoria et al.   JOURNAL OF VIROLOGY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

(2008) Stacy R. Finkbeiner et al.   PLoS Pathogens

Rapid Identification of Known and New RNA Viruses from Animal Tissues

(2008) Joseph G. Victoria et al.   PLoS Pathogens