Matthew Hall
SENIOR RESEARCHER, NUFFIELD DEPARTMENT OF MEDICINE
I am a researcher in pathogen phylodynamics, with a particular interest in inference of who infected who. I am also interested in investigating the effects of sampling bias in molecular epidemiological studies. I obtained my PhD in 2015 at the University of Edinburgh under Professor Mark Woolhouse and Professor Andrew Rambaut. I currently work at the BDI with Professor Christophe Fraser on the PANGEA HIV project, focussing on the reconstruction of transmission patterns within a very large and rich dataset of next-generation HIV sequences.
Software in which I have a hand:
Phyloscanner (construction of phylogenies and investigation of transmission in large genetic datasets)
BEASTLIER (simultaneous phylogeny and transmission tree reconstruction within BEAST)
STraTUS (an R package for enumeration and uniform sampling of transmission trees for a fixed phylogeny)
Recent publications
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An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.
Journal article
Gonçalves BP. et al, (2022), eLife, 11
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The value of open-source clinical science in pandemic response: lessons from ISARIC
Journal article
Abbas A. et al, (2021), The Lancet Infectious Diseases, 21, 1623 - 1624
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COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study
Journal article
Abdukahil SA. et al, (2021), Infection, 49, 889 - 905
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OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing
Journal article
Hinch R. et al, (2021), PLOS Computational Biology, 17, e1009146 - e1009146
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USING PHYLOGENETICS TO INFER HIV-1 TRANSMISSION DIRECTION BETWEEN KNOWN TRANSMISSION PAIRS
Journal article
Villabona-Arenas CJ. et al, (2021)