Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status

Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations

(2018) David Mayhew et al.   THORAX

Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

The microbiota of the respiratory tract: gatekeeper to respiratory health

(2017) Wing Ho Man et al.   NATURE REVIEWS MICROBIOLOGY

Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions

(2017) Yvonne J. Huang et al.   Translational Research

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

Lung microbiome dynamics in COPD exacerbations

(2016) Zhang Wang et al.   EUROPEAN RESPIRATORY JOURNAL

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males

(2016) Shih-Wei Lee et al.   PLoS One

Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers

(2016) G G Einarsson et al.   THORAX

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype

(2016) Leopoldo N. Segal et al.   Nature Microbiology

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity

(2016) Simon J. S. Cameron et al.   PLoS One

The airway microbiome in patients with severe asthma: Associations with disease features and severity

(2015) Yvonne J. Huang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Functional Metagenomics of the Bronchial Microbiome in COPD

(2015) Laura Millares et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Airway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease

(2014) Y. J. Huang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease

(2014) HeeKuk Park et al.   PLoS One

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

Bronchoalveolar Lavage (BAL) for Research; Obtaining Adequate Sample Yield

(2014) Andrea M. Collins et al.   Jove-Journal of Visualized Experiments

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

(2013) Leopoldo N Segal et al.   Microbiome

The Lung Tissue Microbiome in Chronic Obstructive Pulmonary Disease

(2012) Marc A. Sze et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

(2012) Alexa A. Pragman et al.   PLoS One

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

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

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

Molecular Identification of Bacteria in Tracheal Aspirate Fluid from Mechanically Ventilated Preterm Infants

(2011) Peter M. Mourani et al.   PLoS One

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pseudomonas aeruginosa in patients hospitalised for COPD exacerbation: a prospective study

(2009) C. Garcia-Vidal et al.   EUROPEAN RESPIRATORY JOURNAL

Editorial Commentary:The Many Faces ofPseudomonas aeruginosain Chronic Obstructive Pulmonary Disease

(2008) Timothy F. Murphy   CLINICAL INFECTIOUS DISEASES

ChronicPseudomonas aeruginosaInfection in Chronic Obstructive Pulmonary Disease

(2008) Laura Martínez‐Solano et al.   CLINICAL INFECTIOUS DISEASES

Interleukin-17 in host defence against bacterial, mycobacterial and fungal pathogens

(2008) Meredith M. Curtis et al.   IMMUNOLOGY