Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

(2019) L. E. Kafetzopoulou et al.   SCIENCE

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

(2019) Hayden C. Metsky et al.   NATURE BIOTECHNOLOGY

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

(2019) Steve Miller et al.   GENOME RESEARCH

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

(2019) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico

(2018) Julien Thézé et al.   Cell Host & Microbe

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

Evaluating Novel Diagnostics in an Outbreak Setting: Lessons Learned from Ebola

(2017) Nira R. Pollock et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Zika virus evolution and spread in the Americas

(2017) Hayden C. Metsky et al.   NATURE

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Emerging infectious diseases: A proactive approach

(2017) David E. Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AIDS, Avian flu, SARS, MERS, Ebola, Zika… what next?

(2017) Leslie A. Reperant et al.   VACCINE

Assay optimization for molecular detection of Zika virus

(2016) Victor M Corman et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology

(2016) Angela L. Rasmussen et al.   Cell Host & Microbe

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

(2016) Mohammad R. Hasan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

(2016) Silvia I. Sardi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Ebola virus disease diagnosis by real-time RT-PCR: A comparative study of 11 different procedures

(2016) Pascal Cherpillod et al.   JOURNAL OF CLINICAL VIROLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

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

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

Diagnostics in Ebola Virus Disease in Resource-Rich and Resource-Limited Settings

(2016) Robert J Shorten et al.   PLoS Neglected Tropical Diseases

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

A Pan-HIV Strategy for Complete Genome Sequencing

(2015) Michael G. Berg et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes

(2015) Sarah Temmam et al.   PLoS One

Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays

(2015) Shanmuga Sozhamannan et al.   Viruses-Basel

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Development and Evaluation of a Panel of Filovirus Sequence Capture Probes for Pathogen Detection by Next-Generation Sequencing

(2014) Jeffrey W. Koehler et al.   PLoS One

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

(2014) J. T. Ladner et al.   mBio

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

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

(2012) M. Kearse et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Appreciating HIV Type 1 Diversity: Subtype Differences in Env

(2009) Rebecca M. Lynch et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES