Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague

KlebSeq, a Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae

(2016) Jolene R. Bowers et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

(2015) Simon Rasmussen et al.   CELL

Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007

(2015) Julia M. Riehm et al.   PLoS Neglected Tropical Diseases

Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing

(2015) Rebecca E. Colman et al.   PLoS One

New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis

(2014) M. S. Wright et al.   mBio

Evolution of a Pathogen: A Comparative Genomics Analysis Identifies a Genetic Pathway to Pathogenesis in Acinetobacter

(2013) Jason W. Sahl et al.   PLoS One

A Decade of Plague in Mahajanga, Madagascar: Insights into the Global Maritime Spread of Pandemic Plague

(2013) A. J. Vogler et al.   mBio

Understanding the Persistence of Plague Foci in Madagascar

(2013) Voahangy Andrianaivoarimanana et al.   PLoS Neglected Tropical Diseases

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

(2013) Carine Brouat et al.   PLoS Neglected Tropical Diseases

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar

(2011) Amy J. Vogler et al.   PLoS Neglected Tropical Diseases

Assessing Human Risk of Exposure to Plague Bacteria in Northwestern Uganda Based on Remotely Sensed Predictors

(2010) Rebecca J. Eisen et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

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

(2010) A. McKenna et al.   GENOME RESEARCH

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Study on the Movement of Rattus rattus and Evaluation of the Plague Dispersion in Madagascar

(2010) Soanandrasana Rahelinirina et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic understanding of clonal populations in an era of whole genome sequencing

(2009) Talima Pearson et al.   INFECTION GENETICS AND EVOLUTION

Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases

(2009) Paul S. Keim et al.   NATURE REVIEWS MICROBIOLOGY

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION