Timothy G Vaughan

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Alexei J. DrummondProfessor of Computational Biology, University of AucklandVerified email at cs.auckland.ac.nz
Tanja StadlerETH ZurichVerified email at env.ethz.ch
Denise KühnertMax Planck Institute for the Science of Human HistoryVerified email at shh.mpg.de
Joëlle Barido-SottaniIBENS, ENS PSLVerified email at bio.ens.psl.eu
Chieh-Hsi WuLecturer in Statistics, University of SouthamptonVerified email at soton.ac.uk
David A RasmussenNorth Carolina State UniversityVerified email at ncsu.edu
Peter D. DrummondProfessor of Theoretical Physics, Swinburne University of TechnologyVerified email at swin.edu.au
Sebastian DucheneAustralian Research Council Future fellow and NHMRC EL2 fellow, University of MelbourneVerified email at unimelb.edu.au
Joseph HeledAuckland UniversityVerified email at cs.auckland.ac.nz
Remco BouckaertVerified email at cs.auckland.ac.nz
Andrew RambautProfessor of Molecular Evolution, University of EdinburghVerified email at ed.ac.uk
Dong (Walter) XieDepartment of Computer Science, University of AucklandVerified email at cs.auckland.ac.nz
Marc A. SuchardProfessor, University of California, Los AngelesVerified email at ucla.edu
Nicola Felix MüllerPostdoctoral Researcher at the Fred Hutchinson Cancer Research Center, SeattleVerified email at fredhutch.org
Huw Alexander OgilvieRice UniversityVerified email at rice.edu
Sarah NadeauPhD Student, ETH ZurichVerified email at bsse.ethz.ch
Chi ZhangInstitute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesVerified email at ivpp.ac.cn
Louis du PlessisUniversity of OxfordVerified email at zoo.ox.ac.uk
Fábio Kuriki MendesPostdoctoral fellow, Washington University in St. LouisVerified email at wustl.edu
Alexandra "Sasha" GavryushkinaPostdoctoral fellow at Canterbury UniversityVerified email at canterbury.ac.nz

Timothy G Vaughan

Department of Biosystems Science and Engineering, ETH Zürich, Switzerland

Verified email at bsse.ethz.ch

Phylogenetics Phylodynamics Bayesian Statistics Computational Biology


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BEAST 2: a software platform for Bayesian evolutionary analysis R Bouckaert, J Heled, D Kühnert, T Vaughan, CH Wu, D Xie, MA Suchard, ... PLoS computational biology 10 (4), e1003537, 2014	5697	2014
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis R Bouckaert, TG Vaughan, J Barido-Sottani, S Duchêne, M Fourment, ... PLoS computational biology 15 (4), e1006650, 2019	2138	2019
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 EB Hodcroft, M Zuber, S Nadeau, TG Vaughan, KHD Crawford, ... Nature 595 (7869), 707-712, 2021	490	2021
Phylodynamics with migration: a computational framework to quantify population structure from genomic data D Kühnert, T Stadler, TG Vaughan, AJ Drummond Molecular biology and evolution 33 (8), 2102-2116, 2016	132	2016
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model D Kühnert, T Stadler, TG Vaughan, AJ Drummond Journal of the Royal Society Interface 11 (94), 20131106, 2014	126	2014
Efficient Bayesian inference under the structured coalescent TG Vaughan, D Kühnert, A Popinga, D Welch, AJ Drummond Bioinformatics 30 (16), 2272-2279, 2014	124	2014
A Bayesian model predicts the response of axons to molecular gradients D Mortimer, J Feldner, T Vaughan, I Vetter, Z Pujic, WJ Rosoff, K Burrage, ... Proceedings of the National Academy of Sciences 106 (25), 10296-10301, 2009	113	2009
Einstein-Podolsky-Rosen entanglement strategies in two-well Bose-Einstein condensates QY He, MD Reid, TG Vaughan, C Gross, M Oberthaler, PD Drummond Physical review letters 106 (12), 120405, 2011	101	2011
Taming the BEAST—A community teaching material resource for BEAST 2 J Barido-Sottani, V Bošková, LD Plessis, D Kühnert, C Magnus, V Mitov, ... Systematic biology 67 (1), 170-174, 2018	92	2018
The origin and early spread of SARS-CoV-2 in Europe SA Nadeau, TG Vaughan, J Scire, JS Huisman, T Stadler Proceedings of the National Academy of Sciences 118 (9), e2012008118, 2021	88	2021
IcyTree: rapid browser-based visualization for phylogenetic trees and networks TG Vaughan Bioinformatics 33 (15), 2392-2394, 2017	85	2017
Axon guidance by growth-rate modulation D Mortimer, Z Pujic, T Vaughan, AW Thompson, J Feldner, I Vetter, ... Proceedings of the National Academy of Sciences 107 (11), 5202-5207, 2010	79	2010
Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft J Scire, SA Nadeau, T Vaughan, B Gavin, S Fuchs, J Sommer, KN Koch, ... Swiss medical weekly 150 (19-20), w20271, 2020	71	2020
A stochastic simulator of birth–death master equations with application to phylodynamics TG Vaughan, AJ Drummond Molecular biology and evolution 30 (6), 1480-1493, 2013	63	2013
Estimating epidemic incidence and prevalence from genomic data TG Vaughan, GE Leventhal, DA Rasmussen, AJ Drummond, D Welch, ... Molecular Biology and Evolution, msz106, 2019	45	2019
Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial C Pacioni, H Hunt, ME Allentoft, TG Vaughan, AF Wayne, A Baynes, ... Molecular Ecology 24 (23), 5813-5828, 2015	43	2015
A multitype birth–death model for Bayesian inference of lineage-specific birth and death rates J Barido-Sottani, TG Vaughan, T Stadler Systematic biology 69 (5), 973-986, 2020	41	2020
Inferring ancestral recombination graphs from bacterial genomic data TG Vaughan, D Welch, AJ Drummond, PJ Biggs, T George, NP French Genetics 205 (2), 857-870, 2017	40	2017
How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? T Stadler, TG Vaughan, A Gavryushkin, S Guindon, D Kühnert, ... Proceedings of the Royal Society B: Biological Sciences 282 (1806), 20150420, 2015	37	2015
Entanglement, number fluctuations and optimized interferometric phase measurement QY He, TG Vaughan, PD Drummond, MD Reid New Journal of Physics 14 (9), 093012, 2012	36	2012

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