Sebastian Duchene
Sebastian Duchene
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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
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
Temporal signal and the phylodynamic threshold of SARS-CoV-2
S Duchene, L Featherstone, M Haritopoulou-Sinanidou, A Rambaut, ...
Virus Evolution, 2020
Molecular‐clock methods for estimating evolutionary rates and timescales
SYW Ho, S Duchêne
Molecular ecology 23 (24), 5947-5965, 2014
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
Genome-scale rates of evolutionary change in bacteria
S Duchêne, KE Holt, FX Weill, SL Hello, J Hawkey, DJ Edwards, ...
Microbial Genomics, 2016
17th Century Variola Virus Reveals the Recent History of Smallpox
D Duggan, AT, Perdomo MF, Piombino-Mascali, S Marciniak, D Poinar, ...
Current Biology, 2016
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), 2703, 2018
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
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
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
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
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
Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics
MR Davies, L McIntyre, A Mutreja, JA Lacey, JA Lees, RJ Towers, ...
Nature genetics 51 (6), 1035-1043, 2019
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
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
Bayesian molecular dating: opening up the black box
L Bromham, S Duchêne, X Hua, AM Ritchie, DA Duchêne, SYW Ho
Biological Reviews, 2018
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
JL Geoghegan, X Ren, M Storey, J Hadfield, L Jelley, S Jefferies, ...
Nature Communications, 2020
The molecular clock of Mycobacterium tuberculosis
F Menardo, S Duchene, D Brites, S Gagneux
Plos Pathogens 15 (19), e1008067, 2019
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
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