Essential gene acquisition destabilizes plasmid inheritance

The impact of genetic diversity on gene essentiality within the Escherichia coli species

(2021) François Rousset et al.   Nature Microbiology

Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection

(2021) Rachel Wheatley et al.   Nature Communications

Discovery of multi-operon colinear syntenic blocks in microbial genomes

(2020) Dina Svetlitsky et al.   BIOINFORMATICS

Antibiotics Interfere with the Evolution of Plasmid Stability

(2020) Tanita Wein et al.   CURRENT BIOLOGY

The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification

(2019) Hervé Nicoloff et al.   Nature Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

Cryptic transmission of ST405 Escherichia coli carrying bla NDM-4 in hospital

(2018) Xiaoxia Zhang et al.   Scientific Reports

The Transferable Resistome of Produce

(2018) Khald Blau et al.   mBio

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice

(2017) Bret M. Boyd et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emerging and evolving concepts in gene essentiality

(2017) Giulia Rancati et al.   NATURE REVIEWS GENETICS

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

(2017) Thibault Stalder et al.   Scientific Reports

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Fitness Trade-Offs Determine the Role of the Molecular Chaperonin GroEL in Buffering Mutations

(2015) Beatriz Sabater-Muñoz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

(2015) Mizue Anda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of New Functions De Novo and from Preexisting Genes

(2015) Dan I. Andersson et al.   Cold Spring Harbor Perspectives in Biology

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

(2015) Lukasz Dziewit et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Why There Are No Essential Genes on Plasmids

(2014) Samuel J. Tazzyman et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection of a Multidrug Resistance Plasmid by Sublethal Levels of Antibiotics and Heavy Metals

(2014) E. Gullberg et al.   mBio

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

New quantitative methods for measuring plasmid loss rates reveal unexpected stability

(2013) Billy T.C. Lau et al.   PLASMID

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Cumulative Impact of Chaperone-Mediated Folding on Genome Evolution

(2012) David Bogumil et al.   BIOCHEMISTRY

The tRNAargGene andengAAre Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

(2012) George diCenzo et al.   JOURNAL OF BACTERIOLOGY

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Plasmid-mediated horizontal gene transfer is a coevolutionary process

(2012) Ellie Harrison et al.   TRENDS IN MICROBIOLOGY

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Antibiotic resistance gene spread due to manure application on agricultural fields

(2011) Holger Heuer et al.   CURRENT OPINION IN MICROBIOLOGY

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Complete Sequencing of the blaNDM-1-Positive IncA/C Plasmid from Escherichia coli ST38 Isolate Suggests a Possible Origin from Plant Pathogens

(2011) Tsuyoshi Sekizuka et al.   PLoS One

Gene duplications in prokaryotes can be associated with environmental adaptation

(2010) Marit S Bratlie et al.   BMC GENOMICS

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

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

(2008) T. S. Gunasekera et al.   JOURNAL OF BACTERIOLOGY

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION