Sebastian Duchene Garzon

Development of Phylodynamic Methods for Bacterial Pathogens.

Danielle J Ingle, Benjamin P Howden, Sebastian Duchene

Journal article  |  2021  |  Trends in Microbiology

Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases..

The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic

Anthony Lam, Sebastian Duchene

Journal article  |  2021  |  Viruses

Phylodynamic inference is a pivotal tool in understanding transmission dynamics of viral outbreaks. These analyses are strongly gu..

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Jemma L Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fabio K Mendes, Andrew Sporle, Michael G Baker, David R Murdoch, Nigel French, Colin R Simpson, David Welch, Alexei J Drummond, Edward C Holmes, Sebastian Duchene, et al.

Journal article  |  2020  |  Nature Communications

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide 'lockdown' of all non-e..

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Francesca Di Giallonardo, Sebastian Duchene, Ilaria Puglia, Valentina Curini, Francesca Profeta, Cesare Camma, Maurilia Marcacci, Paolo Calistri, Edward C Holmes, Alessio Lorusso

Journal article  |  2020  |  Viruses

Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2..

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon YW Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele

Journal article  |  2020  |  Molecular Biology and Evolution

Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimati..

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

Sebastian Duchene, Simon YW Ho, Ann G Carmichael, Edward C Holmes, Hendrik Poinar

Journal article  |  2020  |  Current Biology

The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biolog..

Tracking the COVID-19 pandemic in Australia using genomics

Torsten Seemann, Courtney R Lane, Norelle L Sherry, Sebastian Duchene, Anders Goncalves da Silva, Leon Caly, Michelle Sait, Susan A Ballard, Kristy Horan, Mark B Schultz, Tuyet Hoang, Marion Easton, Sally Dougall, Timothy P Stinear, Julian Druce, Mike Catton, Brett Sutton, Annaliese van Diemen, Charles Alpren, Deborah A Williamson, et al.

Journal article  |  2020  |  Nature Communications

Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput gen..

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

David Edwards, Sebastián Duchêne, Bernard Pope, Kathryn Holt

Journal article  |  2020

Homoplasic single nucleotide polymorphisms (SNPs) are considered important signatures of strong (positive) selective pressure, and..

Temporal signal and the phylodynamic threshold of SARS-CoV-2

Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele

Journal article  |  2020  |  Virus Evolution

The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publi..

Dating the emergence of human pathogens

Simon YW Ho, Sebastian Duchene

Journal article  |  2020  |  Science