Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities

Airway Platelet Activation Is Associated With Airway Eosinophilic Inflammation in Asthma

(2016) Angela S. Benton et al.   JOURNAL OF INVESTIGATIVE MEDICINE

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways

(2015) Ying Shen et al.   BIOINFORMATICS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Contrasting the Microbiomes From Healthy Volunteers and Patients With Chronic Rhinosinusitis

(2014) Rajeev Aurora et al.   JAMA Otolaryngology-Head & Neck Surgery

The nasal cavity microbiota of healthy adults

(2014) Christine M Bassis et al.   Microbiome

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples

(2014) Changjin Hong et al.   Microbiome

Increased Risk of Pneumonia and Bronchiolitis after Bacterial Colonization of the Airways as Neonates

(2013) Nadja H. Vissing et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Pathogenic Bacteria Colonizing the Airways in Asymptomatic Neonates Stimulates Topical Inflammatory Mediator Release

(2013) Nilofar V. Følsgaard et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The Role of the Lung Microbiome in Health and Disease. A National Heart, Lung, and Blood Institute Workshop Report

(2013) Yvonne J. Huang et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The Effects of Airway Microbiome on Corticosteroid Responsiveness in Asthma

(2013) Elena Goleva et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Characterization of the Molecular Interplay between Moraxella catarrhalis and Human Respiratory Tract Epithelial Cells

(2013) Stefan P. W. de Vries et al.   PLoS One

The Microbiome of the Middle Meatus in Healthy Adults

(2013) Vijay R. Ramakrishnan et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

(2012) Bo Liu et al.   PLoS One

Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease

(2011) Michael J. Docktor et al.   INFLAMMATORY BOWEL DISEASES

Psychrobacter isolates of human origin, other than Psychrobacter phenylpyruvicus, are predominantly Psychrobacter faecalis and Psychrobacter pulmonis, with emended description of P. faecalis

(2011) P. Deschaght et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Extracellular Cyclophilin Levels Associate with Parameters of Asthma in Phenotypic Clusters

(2011) Erik J. Stemmy et al.   JOURNAL OF ASTHMA

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

(2011) John R. Erb-Downward et al.   PLoS One

Overcoming Heterogeneity in Pediatric Asthma: Tobacco Smoke and Asthma Characteristics Within Phenotypic Clusters in an African American Cohort

(2010) Angela S. Benton et al.   JOURNAL OF ASTHMA

The Human Oral Microbiome

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

High Prevalence of Vitamin D Deficiency among Inner-City African American Youth with Asthma in Washington, DC

(2010) Robert J. Freishtat et al.   JOURNAL OF PEDIATRICS

Disordered Microbial Communities in Asthmatic Airways

(2010) Markus Hilty et al.   PLoS One

Nasal Epithelial Cells as Surrogates for Bronchial Epithelial Cells in Airway Inflammation Studies

(2008) Catherine M. McDougall et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

(2008) Jeffrey M Dick   GEOCHEMICAL TRANSACTIONS

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES