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. DuchêneCarlsberg Postdoctoral Fellow, GLOBE Institute, University of CopenhagenVerified email at anu.edu.au
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
Phillip A. MorinResearch Molecular Geneticist, Southwest Fisheries Science CenterVerified email at noaa.gov
Remco BouckaertVerified email at cs.auckland.ac.nz
M Thomas P GilbertUniversity of CopenhagenVerified email at snm.ku.dk
François-Xavier WeillResearch Director, 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
Leo FeatherstoneThe Peter Doherty Institute for Infection and ImmunityVerified email at unimelb.edu.au

Sebastian Duchene

Australian Research Council DECRA fellow, University of Melbourne

Verified email at unimelb.edu.au - Homepage

phylogenetics virus evolution Bayesian statistics phylodynamics


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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	608	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	271	2017
Molecular‐clock methods for estimating evolutionary rates and timescales SYW Ho, S Duchêne Molecular ecology 23 (24), 5947-5965, 2014	241	2014
Genome-scale rates of evolutionary change in bacteria S Duchêne, KE Holt, FX Weill, SL Hello, J Hawkey, DJ Edwards, ... Microbial Genomics, 2016	146	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	143	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	140	2014
17th Century Variola Virus Reveals the Recent History of Smallpox D Duggan, AT, Perdomo MF, Piombino-Mascali, S Marciniak, D Poinar, ... Current Biology, 2016	126	2016
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	118	2011
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	113	2014
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	111	2015
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	90	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	88	2013
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	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	79	2012
Bayesian molecular dating: opening up the black box L Bromham, S Duchêne, X Hua, AM Ritchie, DA Duchêne, SYW Ho Biological Reviews, 2018	73	2018
Temporal signal and the phylodynamic threshold of SARS-CoV-2 S Duchene, L Featherstone, M Haritopoulou-Sinanidou, A Rambaut, ... Virus Evolution, 2020	71	2020
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	70	2019
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages SYW Ho, S Duchêne, D Duchêne Molecular ecology resources 15 (4), 688-696, 2015	67	2015
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	62	2015
Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive para C lineage for millennia Z Zhou, I Lundstrøm, A Tran-Dien, S Duchêne, NF Alikhan, MJ Sergeant, ... Current Biology 28 (15), 2420-2428. e10, 2018	57*	2018

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