Functional Metagenomics of the Bronchial Microbiome in COPD

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Role of Infections

(2014) Kamen Rangelov et al.   CLINICS IN CHEST MEDICINE

Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa

(2014) L. Millares et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Metabolic Alterations to the Mucosal Microbiota in Inflammatory Bowel Disease

(2014) Michael Davenport et al.   INFLAMMATORY BOWEL DISEASES

Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease

(2014) M. Garcia-Nunez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Airway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease

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

The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients

(2014) Shoko Iwai et al.   PLoS One

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

(2014) Rogan Carr et al.   PLoS One

Pseudomonas aeruginosaisolates in severe chronic obstructive pulmonary disease: characterization and risk factors

(2014) Miguel Gallego et al.   BMC Pulmonary Medicine

Lung Microbiota and Bacterial Abundance in Patients with Bronchiectasis when Clinically Stable and during Exacerbation

(2013) Michael M. Tunney et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach

(2013) Xiao Wei et al.   BMC GASTROENTEROLOGY

Oxidative stress and inflammation in the normal airways and blood of patients with lung cancer and COPD

(2013) Esther Barreiro et al.   FREE RADICAL BIOLOGY AND MEDICINE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Incidence, treatment options, and outcomes of lung cancer in patients with chronic obstructive pulmonary disease

(2012) Clara Schroedl et al.   CURRENT OPINION IN PULMONARY MEDICINE

Chronic obstructive pulmonary disease

(2012) Marc Decramer et al.   LANCET

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations

(2012) Anthony A. Fodor et al.   PLoS One

Changes in the Staphylococcus aureus Transcriptome during Early Adaptation to the Lung

(2012) Donald O. Chaffin et al.   PLoS One

The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

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

Decade-long bacterial community dynamics in cystic fibrosis airways

(2012) J. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional predictions from inference and observation in sequence-based inflammatory bowel disease research

(2012) Folker Meyer et al.   GENOME BIOLOGY

Long-term azithromycin therapy in patients with severe COPD and repeated exacerbations

(2011) Xavier Pomares Amigó et al.   International Journal of Chronic Obstructive Pulmonary Disease

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

(2010) Christopher J van der Gast et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations

(2010) Yvonne J. Huang et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Combination of Independent Transcriptional Regulators Shapes Bacterial Virulence Gene Expression during Infection

(2010) Samuel A. Shelburne et al.   PLoS Pathogens

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

(2009) Kati Seidl et al.   BMC MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Infection in the Pathogenesis and Course of Chronic Obstructive Pulmonary Disease

(2008) Sanjay Sethi et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

The role of complex carbohydrate catabolism in the pathogenesis of invasive streptococci

(2008) Samuel A. Shelburne et al.   TRENDS IN MICROBIOLOGY