Phylogenetic methods for genome surveillance of microbial pathogens
Grant number: DE190100805 | Funding period: 2019 - 2022
This project aims to develop phylogenetic approaches to harness the potential evolution of bacterial and virus pathogens data and to improve early detection of infectious outbreaks. Genome surveillance programs consist in routine sequencing of particular organisms to track their evolution over time. Such programs currently exist for important bacterial and virus pathogens. This project expects to develop computational methods to improve our understanding of pathogen outbreak emergence and infectious spread using genome data. This project will expand our knowledge base and research capability in the evolution and epidemiology of infectious agents, and aid in the prevention and control strateg..View full description
Related publications (8)
Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,,12:i:- in Australia
Danielle J Ingle, Rebecca L Ambrose, Sarah L Baines, Sebastian Duchene, Anders Goncalves da Silva, Darren YJ Lee, Miriam Jones, Mary Valcanis, George Taiaroa, Susan A Ballard, Martyn D Kirk, Benjamin P Howden, Jaclyn S Pearson, Deborah A Williamson
Salmonella enterica serovar 4,,12:i:- (Salmonella 4,,12:i:-) is a monophasic variant of Salmonella Typhimurium that has emer..
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
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimati..
Temporal signal and the phylodynamic threshold of SARS-CoV-2
Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele
The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publi..
Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
David A Duchene, K Jun Tong, Charles SP Foster, Sebastian Duchene, Robert Lanfear, Simon YW Ho
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees ..