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

Modeling of the GC content of the substituted bases in bacterial core genomes

(2018) Jon Bohlin et al.   BMC GENOMICS

Diagnostic Approach to Healthcare- and Device-associated CNS infections

(2018) Ryan M. Martin et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

(2018) Wei Gu et al.   Annual Review of Pathology-Mechanisms of Disease

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology

(2017) Robert Schlaberg et al.   JOURNAL OF INFECTIOUS DISEASES

The blood DNA virome in 8,000 humans

(2017) Ahmed Moustafa et al.   PLoS Pathogens

Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing

(2017) Kanokporn Mongkolrattanothai et al.   Journal of the Pediatric Infectious Diseases Society

From Sample to Multi-Omics Conclusions in under 48 Hours

(2016) Robert A. Quinn et al.   mSystems

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents

(2016) Michael R. Wilson et al.   mSystems

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

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

(2015) Alexander L. Greninger et al.   Genome Medicine

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

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

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

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents

(2014) S Motley et al.   BMC GENOMICS

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

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

Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

(2013) C. Cazanave et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

(2013) Stephen J. Salipante et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

(2012) Vincent Foulongne et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Detection of Murine Leukemia Virus or Mouse DNA in Commercial RT-PCR Reagents and Human DNAs

(2011) HaoQiang Zheng et al.   PLoS One

Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study

(2010) Julia Granerod et al.   LANCET INFECTIOUS DISEASES

Human anelloviruses and the central nervous system

(2010) Fabrizio Maggi et al.   REVIEWS IN MEDICAL VIROLOGY