Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

Fundamental identifiability limits in molecular epidemiology

(2021) Stilianos Louca et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution

(2021) Ailene MacPherson et al.   SYSTEMATIC BIOLOGY

Extant timetrees are consistent with a myriad of diversification histories

(2020) Stilianos Louca et al.   NATURE

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Sampling through time and phylodynamic inference with coalescent and birth-death models

(2014) E. M. Volz et al.   Journal of the Royal Society Interface

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

(2014) Veronika Boskova et al.   PLoS Computational Biology

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics

(2013) T. G. Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

(2013) T. Stadler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

(2011) Denise Kühnert et al.   INFECTION GENETICS AND EVOLUTION

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

Phylogenetic Inference of Reciprocal Effects between Geographic Range Evolution and Diversification

(2011) Emma E. Goldberg et al.   SYSTEMATIC BIOLOGY

Species Selection Maintains Self-Incompatibility

(2010) E. E. Goldberg et al.   SCIENCE