Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways

An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer

(2018) Jonas S. Madsen et al.   ISME Journal

The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa

(2017) João Botelho et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

(2017) Wesley Loftie-Eaton et al.   Nature Ecology & Evolution

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

(2017) James P. J. Hall et al.   Nature Ecology & Evolution

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

(2017) Thibault Stalder et al.   Scientific Reports

Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

(2016) Andreas Porse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

(2015) Magdalena A. Machnicka et al.   BMC BIOINFORMATICS

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

(2015) James P.J. Hall et al.   ENVIRONMENTAL MICROBIOLOGY

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes

(2015) Alejandra Rodríguez-Verdugo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

(2015) Alvaro San Millan et al.   Nature Communications

Role of small colony variants in persistence of Pseudomonas aeruginosa infections in cystic fibrosis lungs

(2015) Jacob Malone   Infection and Drug Resistance

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Antibiotic resistance correlates with transmission in plasmid evolution

(2014) Paul E. Turner et al.   EVOLUTION

Linking System-Wide Impacts of RNA Polymerase Mutations to the Fitness Cost of Rifampin Resistance in Pseudomonas aeruginosa

(2014) Qin Qi et al.   mBio

Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

(2013) Jianhui Xiong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Gac regulon ofPseudomonas fluorescens SBW25

(2013) Xu Cheng et al.   Environmental Microbiology Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

High Expression Hampers Horizontal Gene Transfer

(2012) Chungoo Park et al.   Genome Biology and Evolution

The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

(2012) J. M. Hughes et al.   mBio

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

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

(2010) A. McKenna et al.   GENOME RESEARCH

Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein

(2010) Masahiro Sota et al.   ISME Journal

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Conjugative plasmids: vessels of the communal gene pool

(2009) A. Norman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Secondary metabolite production facilitates establishment of rhizobacteria by reducing both protozoan predation and the competitive effects of indigenous bacteria

(2008) A. Jousset et al.   FUNCTIONAL ECOLOGY

Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid

(2008) L. De Gelder et al.   GENETICS