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 | 2994 | 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 | 549 | 2017 |
Temporal signal and the phylodynamic threshold of SARS-CoV-2 S Duchene, L Featherstone, M Haritopoulou-Sinanidou, A Rambaut, ... Virus Evolution, 2020 | 399 | 2020 |
Molecular‐clock methods for estimating evolutionary rates and timescales SYW Ho, S Duchêne Molecular ecology 23 (24), 5947-5965, 2014 | 371 | 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 | 276 | 2019 |
Genome-scale rates of evolutionary change in bacteria S Duchêne, KE Holt, FX Weill, SL Hello, J Hawkey, DJ Edwards, ... Microbial Genomics, 2016 | 257 | 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 | 242 | 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 | 236 | 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 | 230 | 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 | 192 | 2014 |
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 | 190 | 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 | 180 | 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 | 180 | 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 | 167 | 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 | 167 | 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 | 154 | 2014 |
Bayesian molecular dating: opening up the black box L Bromham, S Duchêne, X Hua, AM Ritchie, DA Duchêne, SYW Ho Biological Reviews, 2018 | 145 | 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 | 140 | 2020 |
The molecular clock of Mycobacterium tuberculosis F Menardo, S Duchene, D Brites, S Gagneux Plos Pathogens 15 (19), e1008067, 2019 | 132 | 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 | 116 | 2012 |