Sebastian Duchene

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Simon HoProfessor of Molecular Evolution, University of SydneyVerified email at sydney.edu.au
Edward C HolmesUniversity of SydneyVerified email at sydney.edu.au
David A. DuchêneMarie Skłodowska-Curie Postdoctoral Fellow, GLOBE Institute, University of CopenhagenVerified email at sund.ku.dk
Kathryn HoltMonash University & LSHTMVerified email at lshtm.ac.uk
Jemma L GeogheganUniversity of Otago; ESR; Rutherford Discovery FellowVerified email at otago.ac.nz
Tanja StadlerETH ZurichVerified email at env.ethz.ch
Remco BouckaertVerified email at cs.auckland.ac.nz
Phillip A. MorinResearch Molecular Geneticist, Southwest Fisheries Science CenterVerified email at noaa.gov
M Thomas P GilbertUniversity of CopenhagenVerified email at snm.ku.dk
Leo FeatherstoneThe Peter Doherty Institute for Infection and ImmunityVerified email at unimelb.edu.au
François-Xavier WeillProfessor, Institut Pasteur, Paris, FranceVerified email at pasteur.fr
Francesca Di GiallonardoPostdoctoral Research Fellow, University of New South WalesVerified email at kirby.unsw.edu.au
John-Sebastian EdenSenior Research Fellow; The Westmead Institute & University of SydneyVerified email at sydney.edu.au
Robert LanfearAustralian National UniversityVerified email at anu.edu.au
Guy BaeleAssistant Professor, KU LeuvenVerified email at kuleuven.be
Philippe LemeyAssociate Professor, KU LeuvenVerified email at kuleuven.be
Kelly L. WyresMonash UniversityVerified email at monash.edu
Margaret LamDepartment of Infectious Diseases, Central Clinical School, Monash UniversityVerified email at monash.edu
Jane HawkeyMonash University, Department of Infectious DiseasesVerified email at monash.edu
David EdwardsDepartment of Infectious Disease, Monash University (Alfred Hospital)Verified email at monash.edu

Sebastian Duchene

Australian Research Council DECRA fellow, University of Melbourne

Verified email at unimelb.edu.au - Homepage

phylogenetics virus evolution computational biology


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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	948	2019
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus LS Weyrich, S Duchene, J Soubrier, L Arriola, B Llamas, J Breen, ... Nature 544 (7650), 357-361, 2017	318	2017
Molecular‐clock methods for estimating evolutionary rates and timescales SYW Ho, S Duchêne Molecular ecology 23 (24), 5947-5965, 2014	265	2014
Genome-scale rates of evolutionary change in bacteria S Duchêne, KE Holt, FX Weill, SL Hello, J Hawkey, DJ Edwards, ... Microbial Genomics, 2016	165	2016
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families JL Geoghegan, S Duchêne, EC Holmes PLoS pathogens 13 (2), e1006215, 2017	156	2017
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates S Duchêne, EC Holmes, SYW Ho Proceedings of the Royal Society B: Biological Sciences 281 (1786), 20140732, 2014	155	2014
Temporal signal and the phylodynamic threshold of SARS-CoV-2 S Duchene, L Featherstone, M Haritopoulou-Sinanidou, A Rambaut, ... Virus Evolution, 2020	145	2020
17th Century Variola Virus Reveals the Recent History of Smallpox D Duggan, AT, Perdomo MF, Piombino-Mascali, S Marciniak, D Poinar, ... Current Biology, 2016	143	2016
The impact of calibration and clock-model choice on molecular estimates of divergence times S Duchêne, R Lanfear, SYW Ho Molecular phylogenetics and evolution 78, 277-289, 2014	124	2014
Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation S Duchêne, FI Archer, J Vilstrup, S Caballero, PA Morin PloS one 6 (11), e27138, 2011	124	2011
The performance of the date-randomization test in phylogenetic analyses of time-structured virus data S Duchêne, D Duchêne, EC Holmes, SYW Ho Molecular Biology and Evolution 32 (7), 1895-1906, 2015	121	2015
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae KL Wyres, RR Wick, LM Judd, R Froumine, A Tokolyi, CL Gorrie, ... PLoS genetics 15 (4), e1008114, 2019	105	2019
Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination MMC Lam, KL Wyres, S Duchêne, RR Wick, LM Judd, YH Gan, CH Hoh, ... Nature communications 9 (1), 1-10, 2018	105	2018
Tracking the COVID-19 pandemic in Australia using genomics T Seemann, C Lane, N Sherry, S Duchene, AG da Silva, L Caly, M Sait, ... Nature Communications 11, 4376, 2020	104	2020
Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts C Troupin, L Dacheux, M Tanguy, C Sabeta, H Blanc, C Bouchier, ... PLOS Pathogens, 2016	102	2016
Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago HD Nguyen, Y Tomitaka, SYW Ho, S Duchêne, HJ Vetten, D Lesemann, ... PloS one 8 (2), e55336, 2013	93	2013
Bayesian molecular dating: opening up the black box L Bromham, S Duchêne, X Hua, AM Ritchie, DA Duchêne, SYW Ho Biological Reviews, 2018	87	2018
Marine turtle mitogenome phylogenetics and evolution S Duchene, A Frey, A Alfaro-Núñez, PH Dutton, MTP Gilbert, PA Morin Molecular phylogenetics and evolution 65 (1), 241-250, 2012	84	2012
Comment on “Phylogenomics resolves the timing and pattern of insect evolution” KJ Tong, S Duchêne, SYW Ho, N Lo Science 349 (6247), 487-487, 2015	71	2015
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages SYW Ho, S Duchêne, D Duchêne Molecular ecology resources 15 (4), 688-696, 2015	71	2015

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