T
Timothy G. Vaughan
Researcher at ETH Zurich
Publications - 78
Citations - 9418
Timothy G. Vaughan is an academic researcher from ETH Zurich. The author has contributed to research in topics: Population & Coalescent theory. The author has an hindex of 23, co-authored 72 publications receiving 6834 citations. Previous affiliations of Timothy G. Vaughan include Swinburne University of Technology & Massey University.
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Journal ArticleDOI
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Joseph Heled,Denise Kühnert,Timothy G. Vaughan,Chieh-Hsi Wu,Dong Xie,Marc A. Suchard,Andrew Rambaut,Alexei J. Drummond +8 more
TL;DR: BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform.
Journal ArticleDOI
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Remco R. Bouckaert,Remco R. Bouckaert,Timothy G. Vaughan,Timothy G. Vaughan,Joëlle Barido-Sottani,Joëlle Barido-Sottani,Sebastián Duchêne,Mathieu Fourment,Alexandra Gavryushkina,Joseph Heled,Graham Jones,Denise Kühnert,Nicola De Maio,Michael Matschiner,Fábio K. Mendes,Nicola F. Müller,Nicola F. Müller,Huw A. Ogilvie,Louis du Plessis,Alex Popinga,Andrew Rambaut,David A. Rasmussen,Igor Siveroni,Marc A. Suchard,Chieh-Hsi Wu,Dong Xie,Chi Zhang,Tanja Stadler,Tanja Stadler,Alexei J. Drummond +29 more
TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.
Journal ArticleDOI
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.
Emma B. Hodcroft,Emma B. Hodcroft,Emma B. Hodcroft,Moira Zuber,Sarah Nadeau,Sarah Nadeau,Timothy G. Vaughan,Timothy G. Vaughan,Katharine H.D. Crawford,Katharine H.D. Crawford,Christian L. Althaus,Martina L. Reichmuth,John E. Bowen,Alexandra C. Walls,Davide Corti,Jesse D. Bloom,Jesse D. Bloom,Jesse D. Bloom,David Veesler,David Mateo,Alberto Hernando,Iñaki Comas,Fernando González-Candelas,Tanja Stadler,Tanja Stadler,Richard A. Neher,Richard A. Neher +26 more
TL;DR: A novel SARS-CoV-2 variant, 20E (EU1) that emerged in Spain in early summer, and subsequently spread across Europe is reported in this article.
Posted ContentDOI
BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Timothy G. Vaughan,Joëlle Barido-Sottani,Sebastián Duchêne,Mathieu Fourment,Alexandra Gavryushkina,Joseph Heled,Graham Jones,Denise Kühnert,Nicola De Maio,Michael Matschiner,Fábio K. Mendes,Nicola F. Müller,Huw A. Ogilvie,Louis du Plessis,Alex Popinga,Andrew Rambaut,David A. Rasmussen,Igor Siveroni,Marc A. Suchard,Chieh-Hsi Wu,Dong Xie,Chi Zhang,Tanja Stadler,Alexei J. Drummond +24 more
TL;DR: The full range of new tools and models available on the BEAST 2.5 platform are described, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
Journal ArticleDOI
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
TL;DR: A fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process is presented and can be used to quantify the spread of a pathogen in a structured population.