The effect of genetic structure on molecular dating and tests for temporal signal

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

(2015) Gavin K. Paterson et al.   Nature Communications

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

(2014) David Duchêne et al.   Molecular Ecology Resources

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story

(2013) Israel Pagán et al.   PLoS One

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

(2012) L. A. Weinert et al.   Biology Letters

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

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

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus

(2012) P. R. McAdam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

(2012) Xavier Didelot et al.   GENOME BIOLOGY

Measuring the temporal structure in serially sampled phylogenies

(2011) Rebecca R. Gray et al.   Methods in Ecology and Evolution

Evaluating the evidence for virus/host co-evolution

(2011) Paul M Sharp et al.   Current Opinion in Virology

Rapid Genetic Diversification and High Fitness Penalties Associated with Pathogenicity Evolution in a Plant Virus

(2010) A. Fraile et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

(2010) C. Firth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Combining contemporary and ancient DNA in population genetic and phylogeographical studies

(2010) MIGUEL NAVASCUÉS et al.   Molecular Ecology Resources

Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

(2009) S. Duffy et al.   JOURNAL OF GENERAL VIROLOGY

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

(2009) MIGUEL NAVASCUÉS et al.   MOLECULAR ECOLOGY

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Evolutionary History and Phylogeography of Human Viruses

(2008) Edward C. Holmes   Annual Review of Microbiology

Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression

(2008) Ha Youn Lee et al.   PLoS Computational Biology

Utility of DNA viruses for studying human host history: Case study of JC virus

(2007) Andrew Kitchen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION