The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

(2015) Nobuto Takeuchi et al.   BMC BIOLOGY

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

(2015) Vanessa K Wong et al.   NATURE GENETICS

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

Impermanence of bacterial clones

(2015) Louis-Marie Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Demographic inference using genetic data from a single individual: Separating population size variation from population structure

(2015) Olivier Mazet et al.   THEORETICAL POPULATION BIOLOGY

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

(2015) Lucy A. Weinert et al.   Nature Communications

Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain

(2015) Vegard Eldholm et al.   Nature Communications

Eight challenges in phylodynamic inference

(2015) Simon D.W. Frost et al.   Epidemics

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

(2014) Nicholas J Croucher et al.   BMC BIOLOGY

The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

(2014) Marie Touchon et al.   Genome 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

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

(2014) Aurélien Tellier et al.   MOLECULAR ECOLOGY

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance

(2014) Mark R Davies et al.   NATURE GENETICS

Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates

(2014) Leonor Sánchez-Busó et al.   NATURE GENETICS

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

(2014) Z. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Evolution of European Community-Acquired Methicillin-Resistant Staphylococcus aureus

(2014) M. Stegger et al.   mBio

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

(2014) Taj Azarian et al.   mBio

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination

(2014) M. J. Bart et al.   mBio

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History

(2013) Rasmus Heller et al.   PLoS One

Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study

(2013) Mattia Prosperi et al.   Scientific Reports

Viral Phylodynamics

(2013) Erik M. Volz et al.   PLoS Computational Biology

The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

(2013) Caitlin S. Pepperell et al.   PLoS Pathogens

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans

(2012) Omar E. Cornejo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum

(2012) Nigel F. Delaney et al.   PLoS Genetics

Measuring Selection Coefficients Below 10−3: Method, Questions, and Prospects

(2011) Romain Gallet et al.   GENETICS

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

(2011) Sébastien Wielgoss et al.   G3-Genes Genomes Genetics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study

(2010) Loubna Tazi et al.   BMC INFECTIOUS DISEASES

A Continuous-State Coalescent and the Impact of Weak Selection on the Structure of Gene Genealogies

(2010) B. D. O'Fallon et al.   MOLECULAR BIOLOGY AND EVOLUTION

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational Patterns Cannot Explain Genome Composition: Are There Any Neutral Sites in the Genomes of Bacteria?

(2010) Eduardo P. C. Rocha et al.   PLoS Genetics

A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus

(2010) Ulrich Nübel et al.   PLoS Pathogens

Frequency Spectrum Neutrality Tests: One for All and All for One

(2009) G. Achaz   GENETICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp.

(2008) K. J. Balbi et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of the neisserial DNA uptake sequences on genome evolution and stability

(2008) Todd J Treangen et al.   GENOME BIOLOGY