Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

(2014) Daniele Silvestro et al.   SYSTEMATIC BIOLOGY

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

(2014) Bram Vrancken et al.   PLoS Computational Biology

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Recursive algorithms for phylogenetic tree counting

(2013) Alexandra Gavryushkina et al.   Algorithms for Molecular Biology

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Combining fossil and molecular data to date the diversification of New World Primates

(2013) C. G. Schrago et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Infectious disease transmission as a forensic problem: who infected whom?

(2013) P. Teunis et al.   Journal of the Royal Society Interface

Inferring the Source of Transmission with Phylogenetic Data

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

The reconstructed evolutionary process with the fossil record

(2012) Gilles Didier et al.   JOURNAL OF THEORETICAL BIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Recent progress in paleontological methods for dating the Tree of Life

(2012) Michel Laurin   Frontiers in Genetics

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

Estimating primate divergence times by using conditioned birth-and-death processes

(2009) Richard D. Wilkinson et al.   THEORETICAL POPULATION BIOLOGY