Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing

(2018) Michael R. Wilson et al.   JAMA Neurology

Severe Respiratory Viral Infections

(2017) James M. Walter et al.   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

Bacterial Topography of the Healthy Human Lower Respiratory Tract

(2017) Robert P. Dickson et al.   mBio

Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis

(2016) Santtu Heinonen et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society

(2016) Andre C. Kalil et al.   CLINICAL INFECTIOUS DISEASES

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

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics

(2016) Timothy E. Sweeney et al.   Science Translational Medicine

Host gene expression classifiers diagnose acute respiratory illness etiology

(2016) Ephraim L. Tsalik et al.   Science Translational Medicine

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

(2016) Thuy Doan et al.   Genome Medicine

S. aureus blocks efferocytosis of neutrophils by macrophages through the activity of its virulence factor alpha toxin

(2016) Taylor S. Cohen et al.   Scientific Reports

DiagnosingBalamuthia mandrillarisEncephalitis With Metagenomic Deep Sequencing

(2015) Michael R. Wilson et al.   ANNALS OF NEUROLOGY

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

Moving Toward Prime Time: Host Signatures for Diagnosis of Respiratory Infections

(2015) Ephraim L. Tsalik et al.   JOURNAL OF INFECTIOUS DISEASES

Superiority of Transcriptional Profiling Over Procalcitonin for Distinguishing Bacterial From Viral Lower Respiratory Tract Infections in Hospitalized Adults

(2015) Nicolas M. Suarez et al.   JOURNAL OF INFECTIOUS DISEASES

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Clostridium difficile Infection

(2015) Daniel A. Leffler et al.   NEW ENGLAND JOURNAL OF MEDICINE

Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults

(2015) Seema Jain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Polymicrobial community-acquired pneumonia: An emerging entity

(2015) Catia Cillóniz et al.   RESPIROLOGY

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

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

Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid

(2014) R. P. Dickson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The co-pathogenesis of influenza viruses with bacteria in the lung

(2014) Jonathan A. McCullers   NATURE REVIEWS MICROBIOLOGY

Multistate Point-Prevalence Survey of Health Care–Associated Infections

(2014) Shelley S. Magill et al.   NEW ENGLAND JOURNAL OF MEDICINE

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

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

The current epidemiology and clinical decisions surrounding acute respiratory infections

(2014) Aimee K. Zaas et al.   TRENDS IN MOLECULAR MEDICINE

Antibiotic treatment failure in four common infections in UK primary care 1991-2012: longitudinal analysis

(2014) C. J. Currie et al.   BMJ-British Medical Journal

New microbiota found in sputum from patients with community-acquired pneumonia

(2013) Chunyan Chen et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Metagenomic identification of viral pathogens

(2013) Kyle Bibby   TRENDS IN BIOTECHNOLOGY

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis

(2012) N. A. Abreu et al.   Science Translational Medicine

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

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

Microbiota regulates immune defense against respiratory tract influenza A virus infection

(2011) T. Ichinohe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EDF-1 contributes to the regulation of nitric oxide release in VEGF-treated human endothelial cells

(2010) Marzia Leidi et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

CD36 ligands promote sterile inflammation through assembly of a Toll-like receptor 4 and 6 heterodimer

(2009) Cameron R Stewart et al.   NATURE IMMUNOLOGY

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

How Large a Training Set is Needed to Develop a Classifier for Microarray Data?

(2008) K. K. Dobbin et al.   CLINICAL CANCER RESEARCH