Hypermutation as an Evolutionary Mechanism for Achromobacter xylosoxidans in Cystic Fibrosis Lung Infection

Inhibition of Pseudomonas aeruginosa secreted virulence factors reduces lung inflammation in CF mice

(2018) Angela Sandri et al.   Virulence

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Clinical impact of Achromobacter xylosoxidans colonization/infection in patients with cystic fibrosis

(2016) M.C. Firmida et al.   BRAZILIAN JOURNAL OF MEDICAL AND BIOLOGICAL RESEARCH

Links between Transcription, Environmental Adaptation and Gene Variability inEscherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies

(2016) Jean-Paul Feugeas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

Genetic Adaptation of Achromobacter sp. during Persistence in the Lungs of Cystic Fibrosis Patients

(2015) Winnie Ridderberg et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Respiratory bacterial infections in cystic fibrosis

(2013) Oana Ciofu et al.   CURRENT OPINION IN PULMONARY MEDICINE

Achromobacter species in cystic fibrosis: Cross-infection caused by indirect patient-to-patient contact

(2013) C.R. Hansen et al.   Journal of Cystic Fibrosis

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

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Multilocus Sequence Analysis of Isolates of Achromobacter from Patients with Cystic Fibrosis Reveals Infecting Species Other than Achromobacter xylosoxidans

(2012) W. Ridderberg et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Achromobacter xylosoxidans respiratory tract infection in cystic fibrosis patients

(2011) A. Lambiase et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mutators in cystic fibrosis chronic lung infection: Prevalence, mechanisms, and consequences for antimicrobial therapy

(2010) Antonio Oliver   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inflammation in Achromobacter xylosoxidans infected cystic fibrosis patients

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

Genetic Adaptation of Pseudomonas aeruginosa to the Airways of Cystic Fibrosis Patients Is Catalyzed by Hypermutation

(2008) A. Mena et al.   JOURNAL OF BACTERIOLOGY