Featherstone LA; Ingle DJ; Wirth W; Duchene S, 2025, 'How does date-rounding affect phylodynamic inference for public health?', Plos Computational Biology, 21, http://dx.doi.org/10.1371/journal.pcbi.1012900
Journal articles | 2025
Taouk ML; Featherstone LA; Taiaroa G; Seemann T; Ingle DJ; Stinear TP; Wick RR, 2025, 'Exploring SNP filtering strategies: the influence of strict vs soft core', Microbial Genomics, 11, http://dx.doi.org/10.1099/mgen.0.001346
Journal articles | 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, 2025, '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, 6, http://dx.doi.org/10.1016/j.lanmic.2024.101053
Journal articles | 2025
Xie O; Featherstone L; Nguyen ANT; Hayes AJ; Pitt ME; Spring S; Liu A; Tonkin-Hill G; Dotel R; Joshi Rai N; Rofe A; Duchêne S; Holt DC; Judd LM; Coin LJM; Krause VL; O'Sullivan MVN; Baird RW; Bond K; Howden BP; Korman TM; Currie BJ; Davies MR; Tong SYC, 2025, 'Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011–23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study', Lancet Microbe, 6, http://dx.doi.org/10.1016/j.lanmic.2025.101182
Journal articles | 2024
Featherstone LA; McGaughran A, 2024, 'The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest', Molecular Genetics and Genomics, 299, http://dx.doi.org/10.1007/s00438-024-02097-7
Journal articles | 2024
Featherstone LA; Rambaut A; Duchene S; Wirth W, 2024, 'Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression', Systematic Biology, 73, pp. 623 - 628, http://dx.doi.org/10.1093/sysbio/syae003
Journal articles | 2024
Featherstone LA; Wirth W, 2024, 'PhyloJS: Bridging phylogenetics and web development with a JavaScript utility library', Ecology and Evolution, 14, http://dx.doi.org/10.1002/ece3.11603
Journal articles | 2023
Eaton K; Featherstone L; Duchene S; Carmichael AG; Varlık N; Golding GB; Holmes EC; Poinar HN, 2023, 'Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis', Communications Biology, 6, http://dx.doi.org/10.1038/s42003-022-04394-6
Journal articles | 2023
Eaton K; Sidhu RK; Klunk J; Gamble JA; Boldsen JL; Carmichael AG; Varlık N; Duchene S; Featherstone L; Grimes V; Golding GB; DeWitte SN; Holmes EC; Poinar HN, 2023, 'Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark', Current Biology, 33, pp. 1147 - 1152.e5, http://dx.doi.org/10.1016/j.cub.2023.01.064
Journal articles | 2023
Featherstone LA; Duchene S; Vaughan TG, 2023, 'Decoding the Fundamental Drivers of Phylodynamic Inference', Molecular Biology and Evolution, 40, http://dx.doi.org/10.1093/molbev/msad132
Journal articles | 2023
Porter AF; Featherstone L; Lane CR; Sherry NL; Nolan ML; Lister D; Seemann T; Duchene S; Howden BP, 2023, 'The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia', Microbial Genomics, 9, http://dx.doi.org/10.1099/mgen.0.001099
Journal articles | 2022
Duchene S; Featherstone L; Freiesleben De Blasio B; Holmes EC; Bohlin J; Pettersson JHO, 2022, 'Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology', Open Forum Infectious Diseases, 9, http://dx.doi.org/10.1093/ofid/ofab665
Journal articles | 2022
Featherstone LA; Zhang JM; Vaughan TG; Duchene S, 2022, 'Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications', Virus Evolution, 8, http://dx.doi.org/10.1093/ve/veac045
Journal articles | 2021
Duchene S; Featherstone L; De Blasio BF; Holmes EC; Bohlin J; Pettersson JHO, 2021, 'The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution', Eurosurveillance, 26, http://dx.doi.org/10.2807/1560-7917.ES.2021.26.44.2001996
Journal articles | 2021
Featherstone LA; Di Giallonardo F; Holmes EC; Vaughan TG; Duchêne S, 2021, 'Infectious disease phylodynamics with occurrence data', Methods in Ecology and Evolution, 12, pp. 1498 - 1507, http://dx.doi.org/10.1111/2041-210X.13620
Journal articles | 2020
Duchene S; Featherstone L; Haritopoulou-Sinanidou M; Rambaut A; Lemey P; Baele G, 2020, 'Temporal signal and the phylodynamic threshold of SARS-CoV-2', Virus Evolution, 6, http://dx.doi.org/10.1093/ve/veaa061
Preprints | 2026
Langevin J; Featherstone LA; Di Giallonardo F; Horsburgh BA; Lloyd A; Rawlinson W; Bull RA; Kelleher A; Coin LJM, 2026, A distributed, privacy-preserving platform for linkage of epidemiological data with pathogen genome sequences, http://dx.doi.org/10.64898/2026.01.18.26344367
Duchene S; Featherstone L; de Blasio BF; Holmes EC; Bohlin J; Pettersson JH-O, 2021, Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology, http://dx.doi.org/10.1101/2021.09.04.21263123
Preprints | 2021
Eaton K; Featherstone L; Duchene S; Carmichael A; Varlık N; Golding B; Holmes E; Poinar H, 2021, Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis, http://dx.doi.org/10.21203/rs.3.rs-1146895/v1
Preprints | 2020
Duchene S; Featherstone L; Haritopoulou-Sinanidou M; Rambaut A; Lemey P; Baele G, 2020, Temporal signal and the phylodynamic threshold of SARS-CoV-2, http://dx.doi.org/10.1101/2020.05.04.077735
Preprints | 2020
Duchene S; Featherstone L; de Blasio BF; Holmes EC; Bohlin J; Pettersson JH-O, 2020, The impact of early public health interventions on SARS-CoV-2 transmission and evolution, http://dx.doi.org/10.1101/2020.11.18.20233767
Preprints | 2020
Taiaroa G; Rawlinson D; Featherstone L; Pitt M; Caly L; Druce J; Purcell D; Harty L; Tran T; Roberts J; Scott N; Catton M; Williamson D; Coin L; Duchene S, 2020, Direct RNA sequencing and early evolution of SARS-CoV-2, http://dx.doi.org/10.1101/2020.03.05.976167
Preprints | 2019
Featherstone LA; Di Giallonardo F; Holmes EC; Vaughan TG; Duchêne S, 2019, Infectious disease phylodynamics with occurrence data, http://dx.doi.org/10.1101/596700
