A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans

Within-Host Evolution of Burkholderia pseudomallei during Chronic Infection of Seven Australasian Cystic Fibrosis Patients

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Rapid adaptation drives invasion of airway donor microbiota by Pseudomonas after lung transplantation

(2017) M. Beaume et al.   Scientific Reports

An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity

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What matters in chronic Burkholderia cenocepacia infection in cystic fibrosis: Insights from comparative genomics

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Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

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Visualizing tumor evolution with the fishplot package for R

(2016) Christopher A. Miller et al.   BMC GENOMICS

Antibiotic resistance in Burkholderia species

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BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Microbial genome-wide association studies: lessons from human GWAS

(2016) Robert A. Power et al.   NATURE REVIEWS GENETICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

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Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection

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Cell Wall Recycling-Linked Coregulation of AmpC and PenB β-Lactamases throughampDMutations in Burkholderia cenocepacia

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The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources

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Clinical and demographic factors associated with post–lung transplantation survival in individuals with cystic fibrosis

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Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms

(2015) Diarmaid Hughes et al.   NATURE REVIEWS GENETICS

Progress and promise in understanding the genetic basis of common diseases

(2015) Alkes L. Price et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung

(2015) Julio Diaz Caballero et al.   mBio

Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis

(2015) Shawn T. Clark et al.   Scientific Reports

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

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Trimmomatic: a flexible trimmer for Illumina sequence data

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

(2014) J. M. Chaston et al.   mBio

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

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The BpeEF-OprC Efflux Pump Is Responsible for Widespread Trimethoprim Resistance in Clinical and Environmental Burkholderia pseudomallei Isolates

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An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome

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P. aeruginosa in the paranasal sinuses and transplanted lungs have similar adaptive mutations as isolates from chronically infected CF lungs

(2013) Oana Ciofu et al.   Journal of Cystic Fibrosis

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

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

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An overview of STRUCTURE: applications, parameter settings, and supporting software

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Mechanisms of antibiotic resistance inBurkholderia pseudomallei: implications for treatment of melioidosis

(2012) Herbert P Schweizer   Future Microbiology

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

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Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective

(2012) Anders Folkesson et al.   NATURE REVIEWS MICROBIOLOGY

Integrase-Mediated Recombination of the veb1 Gene Cassette Encoding an Extended-Spectrum β-Lactamase

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Predicting the Functional Effect of Amino Acid Substitutions and Indels

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Dueling Regulatory Properties of a Transcriptional Activator (MtrA) and Repressor (MtrR) That Control Efflux Pump Gene Expression in Neisseria gonorrhoeae

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BIGSdb: Scalable analysis of bacterial genome variation at the population level

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Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism

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Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Detection of recombination events in bacterial genomes from large population samples

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Genomic Expression Analysis Reveals Strategies of Burkholderia cenocepacia to Adapt to Cystic Fibrosis Patients' Airways and Antimicrobial Therapy

(2011) Nuno P. Mira et al.   PLoS One

Classification and identification of the Burkholderia cepacia complex: Past, present and future

(2011) Peter Vandamme et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Pathogenicity, virulence factors, and strategies to fight against Burkholderia cepacia complex pathogens and related species

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Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence

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The Changing Microbial Epidemiology in Cystic Fibrosis

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Dindel: Accurate indel calls from short-read data

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The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

(2010) S T Kalinowski   HEREDITY

Impact of recombination on bacterial evolution

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Beta-lactam antibiotics: from antibiosis to resistance and bacteriology

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Fast and accurate short read alignment with Burrows-Wheeler transform

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DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

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Circos: An information aesthetic for comparative genomics

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Expanded Multilocus Sequence Typing for Burkholderia Species

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The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

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Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH