Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Genomic Insights into Intrinsic and Acquired Drug Resistance Mechanisms in Achromobacter xylosoxidans

(2014) Yongfei Hu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention

(2014) Thomas H Hampton et al.   Microbiome

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Detection of Achromobacter xylosoxidans in Hospital, Domestic, and Outdoor Environmental Samples and Comparison with Human Clinical Isolates

(2013) Lucie Amoureux et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extended Staphylococcus aureus persistence in cystic fibrosis is associated with bacterial adaptation

(2013) Nina Hirschhausen et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

IslandViewer update: improved genomic island discovery and visualization

(2013) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important Pathogenic Phenotypes

(2013) Tim Holm Jakobsen et al.   PLoS One

The role of the bacterial microbiome in lung disease

(2013) Robert P Dickson et al.   Expert Review of Respiratory Medicine

Innate Aminoglycoside Resistance of Achromobacter xylosoxidans Is Due to AxyXY-OprZ, an RND-Type Multidrug Efflux Pump

(2012) Julien Bador et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Stenotrophomonas maltophilia: an Emerging Global Opportunistic Pathogen

(2012) J. S. Brooke   CLINICAL MICROBIOLOGY REVIEWS

Stenotrophomonas maltophilia

(2012) Christine R. Hansen   CURRENT OPINION IN PULMONARY MEDICINE

Antibiotic resistance of mixed biofilms in cystic fibrosis: impact of emerging microorganisms on treatment of infection

(2012) Susana Patrícia Lopes et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Treatment of lung infection in patients with cystic fibrosis: Current and future strategies

(2012) Gerd Döring et al.   Journal of Cystic Fibrosis

Epidemiology and resistance of Achromobacter xylosoxidans from cystic fibrosis patients in Dijon, Burgundy: First French data

(2012) Lucie Amoureux et al.   Journal of Cystic Fibrosis

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

Cystic Fibrosis: What to Expect now in the Early Adult Years

(2012) Bradley S. Quon et al.   Paediatric Respiratory Reviews

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

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

(2012) Ruibang Luo et al.   GigaScience

First Description of an RND-Type Multidrug Efflux Pump in Achromobacter xylosoxidans, AxyABM

(2011) Julien Bador et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Phenotypic and genotypic characterization of Stenotrophomonas maltophilia isolates from patients with cystic fibrosis: Genome diversity, biofilm formation, and virulence

(2011) Arianna Pompilio et al.   BMC MICROBIOLOGY

Identification of Achromobacter xylosoxidans by detection of the blaOXA-114-like gene intrinsic in this species

(2011) Jane F. Turton et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Stenotrophomonas interspecies differentiation and identification by gyrB sequence analysis

(2011) Liselott A. Svensson-Stadler et al.   FEMS MICROBIOLOGY LETTERS

Haemophilus influenzae in children with cystic fibrosis: Antimicrobial susceptibility, molecular epidemiology, distribution of adhesins and biofilm formation

(2011) Rita Cardines et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Bacteriophages as vehicles of the resistome in cystic fibrosis

(2011) J. M. Rolain et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Clinical Predictive Value (or Lack Thereof) of the Results of In Vitro Antimicrobial Susceptibility Tests

(2011) G. V. Doern et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Chronic pulmonary infection with Stenotrophomonas maltophilia and lung function in patients with cystic fibrosis

(2011) C.S. Dalbøge et al.   Journal of Cystic Fibrosis

Phylogenetic relatedness and diversity of non-typable Haemophilus influenzae in the nasopharynx and middle ear fluid of children with acute otitis media

(2011) R. Kaur et al.   JOURNAL OF MEDICAL MICROBIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Basis of Increased Serum Resistance among Pulmonary Isolates of Non-typeable Haemophilus influenzae

(2011) Shigeki Nakamura et al.   PLoS Pathogens

Stenotrophomonas maltophiliain Cystic Fibrosis

(2010) Valerie Waters et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method

(2010) Hoang Vu-Thien et al.   BMC MICROBIOLOGY

Spectrum of practice in the diagnosis of nosocomial pneumonia in patients requiring mechanical ventilation in European intensive care units

(2010) Despoina Koulenti et al.   CRITICAL CARE MEDICINE

Early adaptive developments ofPseudomonas aeruginosaafter the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts

(2010) Martin Holm Rau et al.   ENVIRONMENTAL MICROBIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Changes in cystic fibrosis sputum microbiology in the United States between 1995 and 2008

(2010) Julia Emerson et al.   PEDIATRIC PULMONOLOGY

Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients

(2010) Michael J. Cox et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Respiratory Microbiology of Patients With Cystic Fibrosis in the United States, 1995 to 2005

(2009) Samiya Razvi et al.   CHEST

Inflammation in Achromobacter xylosoxidans infected cystic fibrosis patients

(2009) C.R. Hansen et al.   Journal of Cystic Fibrosis

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Impact of Pseudomonas and Staphylococcus Infection on Inflammation and Clinical Status in Young Children with Cystic Fibrosis

(2008) Scott D. Sagel et al.   JOURNAL OF PEDIATRICS

Molecular Detection of Multiple Emerging Pathogens in Sputa from Cystic Fibrosis Patients

(2008) Fadi Bittar et al.   PLoS One

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

(2008) Lisa C Crossman et al.   GENOME BIOLOGY