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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution

(2014) Lizhi Ian Gong et al.   PLoS Genetics

Trends of Etiology and Drug Resistance in Enteric Fever in the Last Two Decades in Nepal: A Systematic Review and Meta-analysis

(2013) Surendra Karki et al.   CLINICAL INFECTIOUS DISEASES

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

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

(2013) Iñaki Comas et al.   NATURE GENETICS

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Tracking the establishment of local endemic populations of an emergent enteric pathogen

(2013) K. E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

(2013) Zhemin Zhou et al.   PLoS Genetics

Convergent Molecular Evolution of Genomic Cores in Salmonella enterica and Escherichia coli

(2012) Sujay Chattopadhyay et al.   JOURNAL OF BACTERIOLOGY

Global Phylogeny of Shigella sonnei Strains from Limited Single Nucleotide Polymorphisms (SNPs) and Development of a Rapid and Cost-Effective SNP-Typing Scheme for Strain Identification by High-Resolution Melting Analysis: Fig 1

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Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond 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

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

(2012) M. Achtman   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pan-Genomic Analysis Provides Insights into the Genomic Variation and Evolution of Salmonella Paratyphi A

(2012) Weili Liang et al.   PLoS One

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

(2012) Y. Cui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

(2012) J. R. Meyer et al.   SCIENCE

Age of the Association between Helicobacter pylori and Man

(2012) Yoshan Moodley et al.   PLoS Pathogens

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

High-throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children

(2010) Kathryn E Holt et al.   BMC INFECTIOUS DISEASES

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

(2009) Kathryn E Holt et al.   BMC GENOMICS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

Laboratory‐Based Surveillance of Paratyphoid Fever in the United States: Travel and Antimicrobial Resistance

(2008) Sundeep K. Gupta et al.   CLINICAL INFECTIOUS DISEASES

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis

(2008) C. O. Buckee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA