• 2025
  Lopopolo M, Avanzi C, Duchene S, Luisi P, de Flamingh A, Ponce-Soto GY, Tressieres G, Neumeyer S, Lemoine F, Nelson EA, Iraeta-Orbegozo M, Cybulski JS, Mitchell J, Marks VT, Adams LB, Lindo J, DeGiorgio M, Ortiz N, Wiens C, Hiebert J, Bonifaz A, Montes de Oca G, Paredes-Solis V, Franco-Paredes C, Vera-Cabrera L, Pereira Brunelli JG, Jackson M, Spencer JS, Salgado CG, Han XY, Pearce CM, Warren AK, Rosa PS, de Finardi AJ, Belone AFF, Ferreira C, Suffys PN, Fontes ANB, Vasconcellos SEG, Schaub R, Couppié P, Drak Alsibai K, Hernández-Castro R, Silva Miranda M, Estrada-Garcia I, Jurado-Santacruz F, Orlando L, Schroeder H, Quintana-Murci L, Del Papa M, Lahiri R, Malhi RS, Rasmussen S, Rascovan N, Pre-European contact leprosy in the Americas and its current persistence., Science 2025 May; (): eadu7144.
• 2025
  Xie O, Chisholm RH, Featherstone L, Nguyen ANT, Hayes AJ, Jespersen MG, Zachreson C, Tellioglu N, Tonkin-Hill G, Dotel R, Spring S, Liu A, Rofe A, Duchene S, Sherry NL, Baird RW, Krause VL, Holt DC, Coin LJM, Rai NJ, O'Sullivan MVN, Bond K, Corander J, Howden BP, Korman TM, Currie BJ, Tong SYC, Davies MR, Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study., Lancet Microbe 2025 Apr; (): 101053.
• 2025
  Featherstone LA, Ingle DJ, Wirth W, Duchene S, How does date-rounding affect phylodynamic inference for public health?, PLoS Comput Biol 2025 Apr; 21(4): e1012900.
• 2024
  John H Tay, Arthur Kocher, Sebastian Duchene, Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal, PLoS Computational Biology, 2024, 20 (11), pp.e1012371. ⟨10.1371/journal.pcbi.1012371⟩.
• 2024
  Turner AM, Li L, Monk IR, Lee JYH, Ingle DJ, Portelli S, Sherry NL, Isles N, Seemann T, Sharkey LK, Walsh CJ, Reid GE, Nie S, Eijkelkamp BA, Holmes NE, Collis B, Vogrin S, Hiergeist A, Weber D, Gessner A, Holler E, Ascher DB, Duchene S, Scott NE, Stinear TP, Kwong JC, Gorrie CL, Howden BP, Carter GP, Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin., Nature 2024 Nov; 635(8040): 969-977.
• 2024
  Leo Featherstone, Andrew Rambaut, Sebastian Duchene, Wytamma Wirth, Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression, Systematic Biology, 2024, pp.syae003. ⟨10.1093/sysbio/syae003⟩.
• 2023
  Sebastian Duchene, Tracing the origin of virulence, Sciences.
• 2023
  Tay JH, Baele G, Duchene S, Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models., Mol Biol Evol 2023 Oct; 40(10): .
• 2023
  Porter AF, Featherstone L, Lane CR, Sherry NL, Nolan ML, Lister D, Seemann T, Duchene S, Howden BP, The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia., Microb Genom 2023 Aug; 9(8): .
• 2023
  Hannah Frost, Julien Guglielmini, Sebastian Duchêne, Jake Lacey, Martina Sanderson-Smith, Andrew Steer, Mark Walker, Anne Botteaux, Mark Davies, Pierre Smeesters, Promiscuous evolution of Group A Streptococcal M and M-like proteins, Microbiology, 2023, 169 (1), pp.001280. ⟨10.1099/mic.0.001280⟩.
• 2023
  Porter AF, Purcell DFJ, Howden BP, Duchene S, Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink., Virus Evol 2023 ; 9(1): vead002.
• 2022
  Porter AF, Sherry N, Andersson P, Johnson SA, Duchene S, Howden BP, New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia., PLoS Genet 2022 Oct; 18(10): e1010415.
• 2022
  Caly L, Porter AF, Chua J, Collet JP, Druce JD, Catton MG, Duchene S, Lymphocytic Choriomeningitis Virus Infection, Australia., Emerg Infect Dis 2022 Aug; 28(8): 1713-1715.
• 2022
  Tay JH, Porter AF, Wirth W, Duchene S, The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate., Mol Biol Evol 2022 Feb; 39(2): .
• 2020
  Anna Zhukova, Olivier Gascuel, Sebastián Duchene, Daniel Ayres, Philippe Lemey, Guy Baele, Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics, Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.5.3:1--5.3:43, 2020.
• 2016
  Cécile Troupin, Laurent Dacheux, Marion Tanguy, Claude Sabeta, Hervé Blanc, Christiane Bouchier, Marco Vignuzzi, Sebastián Duchene, Edward C Holmes, Hervé Bourhy, Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts., PLoS Pathogens, 2016, 12 (12), pp.e1006041. ⟨10.1371/journal.ppat.1006041.s014⟩.