Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections

Pseudomonas aeruginosa Phenotypes Associated With Eradication Failure in Children With Cystic Fibrosis

(2014) Nicole Mayer-Hamblett et al.   CLINICAL INFECTIOUS DISEASES

Comparative Genomics of Isolates of a Pseudomonas aeruginosa Epidemic Strain Associated with Chronic Lung Infections of Cystic Fibrosis Patients

(2014) Julie Jeukens et al.   PLoS One

Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa

(2014) T. Markussen et al.   mBio

Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections

(2014) Sofía Feliziani et al.   PLoS Genetics

Extensive diversification is a common feature of Pseudomonas aeruginosa populations during respiratory infections in cystic fibrosis

(2013) Abdul Ashish et al.   Journal of Cystic Fibrosis

Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK

(2013) K. Martin et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Phenotypic Heterogeneity of Pseudomonas aeruginosa Populations in a Cystic Fibrosis Patient

(2013) Matthew L. Workentine et al.   PLoS One

Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts

(2013) S. Damkiaer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators

(2013) Rasmus Lykke Marvig et al.   PLoS Genetics

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal Medicine

Transmissible strains ofPseudomonas aeruginosain cystic fibrosis lung infections

(2012) Joanne L. Fothergill et al.   EUROPEAN RESPIRATORY JOURNAL

Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

(2012) Jade C. S. Chung et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Pseudomonas aeruginosa Exhibits Frequent Recombination, but Only a Limited Association between Genotype and Ecological Setting

(2012) Timothy J. Kidd et al.   PLoS One

Pseudomonas aeruginosaPopulation Diversity and Turnover in Cystic Fibrosis Chronic Infections

(2011) Eilidh Mowat et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Increasing resistance of the Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa (Psa) to antibiotics in cystic fibrosis (CF)—A cause for concern?

(2011) Abdul Ashish et al.   Journal of Cystic Fibrosis

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Clonal epidemiology of Pseudomonas aeruginosa in cystic fibrosis

(2010) Nina Cramer et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Infection With Transmissible Strains of Pseudomonas aeruginosa and Clinical Outcomes in Adults With Cystic Fibrosis

(2010) Shawn D. Aaron et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Nutrient Availability as a Mechanism for Selection of Antibiotic Tolerant Pseudomonas aeruginosa within the CF Airway

(2010) Lucas R. Hoffman et al.   PLoS Pathogens

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Instantaneous Within-Patient Diversity of Pseudomonas aeruginosa Quorum-Sensing Populations from Cystic Fibrosis Lung Infections

(2009) C. N. Wilder et al.   INFECTION AND IMMUNITY

Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants

(2009) O. Ciofu et al.   MICROBIOLOGY-SGM

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

(2008) C. Winstanley et al.   GENOME RESEARCH

Fitness of Isogenic Colony Morphology Variants of Pseudomonas aeruginosa in Murine Airway Infection

(2008) Elza Rakhimova et al.   PLoS One

Testing regions with nonsmooth boundaries via multiscale bootstrap

(2007) Hidetoshi Shimodaira   JOURNAL OF STATISTICAL PLANNING AND INFERENCE