Matthew Hall
Contact information
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
ISARIC Clinical Characterisation Group. Electronic address: james.lee@ndm.ox.ac.uk None., (2021), The Lancet. Infectious diseases
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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
ISARIC Clinical Characterisation Group None., (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
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USING PHYLOGENETICS TO ACCURATELY INFER HIV-1 TRANSMISSION DIRECTION
Journal article
Villabona-Arenas CJ. et al, (2021)