Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis

(2018) Lisa A. Carmody et al.   PLoS One

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Stress and stability: applying the Anna Karenina principle to animal microbiomes

(2017) Jesse R. Zaneveld et al.   Nature Microbiology

The Microbiome and the Respiratory Tract

(2016) Robert P. Dickson et al.   Annual Review of Physiology

The role of anaerobic bacteria in the cystic fibrosis airway

(2016) Laura J. Sherrard et al.   CURRENT OPINION IN PULMONARY MEDICINE

How stable is the human gut microbiota? And why this question matters

(2016) Harald Brüssow   ENVIRONMENTAL MICROBIOLOGY

The fermentation product 2,3-butanediol alters P. aeruginosa clearance, cytokine response and the lung microbiome

(2016) Mytien Nguyen et al.   ISME Journal

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling

(2016) William H. DePas et al.   mBio

Ecological networking of cystic fibrosis lung infections

(2016) Robert A Quinn et al.   npj Biofilms and Microbiomes

The Role of Short-Chain Fatty Acids, Produced by Anaerobic Bacteria, in the Cystic Fibrosis Airway

(2015) Bojana Mirković et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Short-chain fatty acids affect cystic fibrosis airway inflammation and bacterial growth

(2015) Peyman Ghorbani et al.   EUROPEAN RESPIRATORY JOURNAL

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

(2015) Leah Cuthbertson et al.   ISME Journal

Clinical implications and characterization of Group A Streptoccoccus infections in adults with cystic fibrosis

(2015) Kate Skolnik et al.   BMC Pulmonary Medicine

The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

(2015) Lisa A Carmody et al.   Microbiome

qgraph: Network Visualizations of Relationships in Psychometric Data

(2015) Sacha Epskamp et al.   Journal of Statistical Software

Changes in Cystic Fibrosis Airway Microbial Community Associated with a Severe Decline in Lung Function

(2015) Patrizia Paganin et al.   PLoS One

Reduced Bacterial Colony Count of Anaerobic Bacteria Is Associated with a Worsening in Lung Clearance Index and Inflammation in Cystic Fibrosis

(2015) Katherine O’Neill et al.   PLoS One

Lung microbiota across age and disease stage in cystic fibrosis

(2015) Bryan Coburn et al.   Scientific Reports

Metabolite transfer with the fermentation product 2,3-butanediol enhances virulence by Pseudomonas aeruginosa

(2014) Arvind Venkataraman et al.   ISME Journal

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

(2014) Robert A Quinn et al.   ISME Journal

Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation

(2014) Katrine L Whiteson et al.   ISME Journal

Sets and intersections

(2014) Alexander Lex et al.   NATURE METHODS

Biogeochemical Forces Shape the Composition and Physiology of Polymicrobial Communities in the Cystic Fibrosis Lung

(2014) R. A. Quinn et al.   mBio

Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories

(2014) E. Kathryn Morris et al.   Ecology and Evolution

Anaerobic Bacterial Infection in Patients with Cystic Fibrosis

(2013) Andrew Tai et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Cystic Fibrosis Therapy: A Community Ecology Perspective

(2013) Douglas Conrad et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

(2013) Y. W. Lim et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Inflammation and Airway Microbiota during Cystic Fibrosis Pulmonary Exacerbations

(2013) Edith T. Zemanick et al.   PLoS One

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

The cystic fibrosis airway microbiome

(2012) Harvey R. Rabin et al.   CURRENT OPINION IN PULMONARY MEDICINE

Optimal Detection of Changepoints With a Linear Computational Cost

(2012) R. Killick et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone 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

Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing of Bacterial 16S rRNA Hypervariable Regions

(2012) Heather Maughan 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

Effect of pulmonary exacerbations on long-term lung function decline in cystic fibrosis

(2011) Valerie Waters et al.   EUROPEAN RESPIRATORY JOURNAL

Pulmonary exacerbation: Towards a definition for use in clinical trials. Report from the EuroCareCF Working Group on outcome parameters in clinical trials

(2011) D. Bilton et al.   Journal of Cystic Fibrosis

Anaerobic bacteria in cystic fibrosis: pathogens or harmless commensals?

(2011) A. M. Jones   THORAX

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Antibiotic-resistant obligate anaerobes during exacerbations of cystic fibrosis patients

(2009) D. Worlitzsch et al.   CLINICAL MICROBIOLOGY AND INFECTION

Detection of Anaerobic Bacteria in High Numbers in Sputum from Patients with Cystic Fibrosis

(2008) Michael M. Tunney et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE