Illumina sequencing of clinical samples for virus detection in a public health laboratory

Genomic Insights into Zika Virus Emergence and Spread

(2018) Nathan D. Grubaugh et al.   CELL

Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases

(2018) Julianne R. Brown et al.   JOURNAL OF INFECTION

Emerging recombinant noroviruses identified by clinical and waste water screening

(2018) Jennifer H. Lun et al.   Emerging Microbes & Infections

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Towards a Universal Molecular Microbiological Test

(2017) Richard J. N. Allcock et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Recombination events and variability among full-length genomes of co-circulating molluscum contagiosum virus subtypes 1 and 2

(2017) Alberto López-Bueno et al.   JOURNAL OF GENERAL VIROLOGY

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel

(2016) Erin H. Graf et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens

(2016) Anh To Nguyen et al.   Virology Journal

The resurgence of mumps and pertussis

(2016) Martine Sabbe et al.   Human Vaccines & Immunotherapeutics

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing

(2015) Samia N. Naccache et al.   CLINICAL INFECTIOUS DISEASES

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

The use of next generation sequencing in the diagnosis and typing of respiratory infections

(2015) Fiona Thorburn et al.   JOURNAL OF CLINICAL VIROLOGY

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

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

Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa

(2015) Matthew H. Stremlau et al.   PLoS Neglected Tropical Diseases

Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis

(2015) M.-L. Frémond et al.   Journal of the Pediatric Infectious Diseases Society

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

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

Deep Sequencing to Identify the Causes of Viral Encephalitis

(2014) Benjamin K. Chan et al.   PLoS One

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

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

(2012) Fredrik Lysholm et al.   PLoS One

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

(2012) Nathan L. Yozwiak et al.   PLoS Neglected Tropical Diseases

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

Vector Competence of Australian Mosquitoes for Chikungunya Virus

(2009) Andrew F. van den Hurk et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections

(2008) C. Y. Chiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA