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
-
Journal article
Gonçalves BP. et al, (2022), eLife, 11
-
Journal article
ISARIC Clinical Characterisation Group. Electronic address: james.lee@ndm.ox.ac.uk None., (2021), The Lancet. Infectious diseases
-
Journal article
ISARIC Clinical Characterisation Group None., (2021), Infection, 49, 889 - 905
-
Journal article
Hinch R. et al, (2021), PLoS computational biology, 17
-
Journal article
Villabona-Arenas CJ. et al, (2021)