Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

(2020) A. Amir Hassan et al.   Frontiers in Microbiology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

(2019) Heike Sichtig et al.   Nature Communications

In vitro susceptibility of Burkholderia cepacia complex isolated from cystic fibrosis patients to ceftazidime-avibactam and ceftolozane-tazobactam

(2018) A Van Dalem et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Julio Diaz Caballero et al.   PLoS Pathogens

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

(2017) Alyse A. Larkin et al.   Environmental Microbiology Reports

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

(2017) Jaroslav Nunvar et al.   PLoS Pathogens

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

(2017) Charlotte Peeters et al.   PLoS One

Extensive cultivation of soil and water samples yields various pathogens in patients with cystic fibrosis but not Burkholderia multivorans

(2016) Charlotte Peeters et al.   Journal of Cystic Fibrosis

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

(2016) Emily V. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Inês N. Silva et al.   mSystems

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

(2014) Birgit De Smet et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Factors Influencing Acquisition of Burkholderia cepacia Complex Organisms in Patients with Cystic Fibrosis

(2013) K. A. Ramsay et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere

(2013) Charlotte Peeters et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

Clinical Significance of Microbial Infection and Adaptation in Cystic Fibrosis

(2011) A. R. Hauser et al.   CLINICAL MICROBIOLOGY REVIEWS

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

(2010) Karlene H Lynch et al.   BMC GENOMICS

The Changing Microbial Epidemiology in Cystic Fibrosis

(2010) J. J. LiPuma   CLINICAL MICROBIOLOGY REVIEWS

Unusual Distribution of Burkholderia cepacia Complex Species in Danish Cystic Fibrosis Clinics May Stem from Restricted Transmission between Patients

(2010) N. Norskov-Lauritsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Species distribution of Burkholderia cepacia complex isolates in cystic fibrosis and non-cystic fibrosis patients in New Zealand

(2010) Christopher E. Pope et al.   Journal of Cystic Fibrosis

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Expanded Multilocus Sequence Typing for Burkholderia Species

(2009) T. Spilker et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

(2008) M. T. G. Holden et al.   JOURNAL OF BACTERIOLOGY

The changing epidemiology of Burkholderia species infection at an adult cystic fibrosis centre

(2008) Megan W. France et al.   Journal of Cystic Fibrosis