Thank you to all the applicants of the first 2018 Sydney Informatics Hub HPC Publication Incentive round.
Congratulations to the 3 winning papers:
Zoe Patterson Ross et al. The paradox of HBV evolution as revealed from a 16th century mummy
Mang Shi et al. The evolutionary history of vertebrate RNA viruses
Zoe won first prize in the first 2018 SIH Publication Incentive round. Zoe is a PhD candidate studying viral evolution in the School of Life and Environmental Sciences. To study viral evolution, her group gathers nucleotide sequence data for a viral population from a number of samples taken from hosts across the course of a series of infections, compare sampled sequences with those kept in databases such as that maintained by the National Centre for Biotechnology Information in the USA, and then use a variety of computationally intensive statistical methods to infer patterns of change across time. This approach allows them to reconstruct evolutionary histories for viruses, as well as to infer the epidemiological dynamics of those viruses.
In this study, she worked with a team of ancient DNA experts in Canada to recover the complete sequence of a Hepatitis B virus from a 450-year old mummy found in a sacristy in Naples, Italy. Once they had the sequence information, the next stage was to use the SIH’s high performance computing resources to run their analyses. In this case, they ran a series of tests based in probability theory, using Bayesian methods to attempt to discern the most likely scenarios for the history of the virus.
Image courtesy of Zoe Patterson Ross.