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Dr Matthew Hall

Assistant Professor

United Kingdom

Jump to: Affiliations Research Publications

My research is in pathogen genomic epidemiology and phylogenetics, which a particular focus on the reconstruction of direct transmission and applications of analysis of within-host diversity. I also have an interest in prospective study design.

Affiliations
Department of Clinical Research
Faculty of Infectious and Tropical Diseases

Research
Research Area
Phylogenetics
Genomics
Bioinformatics
Disease and Health Conditions
HIV/AIDS
Syphilis
COVID-19

Selected Publications
Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data
Anker, KM; Evans Pena, R; Kemp, SA; Clarke, J; Zhao, L; Bonsall, D; Grayson, N; Bashton, M; Walker, AS; Golubchik, T; HALL, M; Lythgoe, K; COVID-19 Genomics UK (COG-UK) Consortium,;
2026
Molecular biology and evolution
The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study
HALL, MD; Probert, W; Abeler-Dörner, L; Wymant, C; Di Lauro, F; Xi, X; Sauter, R; Golubchik, T; Bonsall, D; Pickles, M; Cori, A; Bwalya, J; Floyd, S; Bell-Mandla, N; Shanaube, K; Yang, B; Bock, P; Donnell, D; Grabowski, MK; Pillay, D; Rambaut, A; Ratmann, O; Fidler, S; Ayles, H; Hayes, R; ... Fraser, C.
2025
eLife Sciences Publications, Ltd
Data from: Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity
Ferretti, L; Golubchik, T; Di Lauro, F; Ghafari, M; Villabona-Arenas, J; ATKINS, KE; Fraser, C; HALL, M;
2026
Dryad
Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity
Ferretti, L; Golubchik, T; Di Lauro, F; Ghafari, M; Villabona-Arenas, CJ; ATKINS, K; Fraser, C; HALL, M;
2025
bioRxiv
The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study.
HALL, M; Probert, W; Abeler-Dörner, L; Wymant, C; Di Lauro, F; Xi, X; Sauter, R; Golubchik, T; Bonsall, D; Pickles, M; Cori, A; Bwalya, J; Floyd, S; Mandla, N; Shanaube, K; Yang, B; Bock, P; Donnell, D; Grabowski, MK; Pillay, D; Ratmann, O; Fidler, S; Ayles, H; Hayes, R; Fraser, C; ... PANGEA-HIV consortium HPTN 071 (PopART) study team,
2026
medRxiv
Maximum likelihood estimation of phylogenetic branch lengths for a star-like phylogeny
HALL, M; Ferretti, L;
2026
Zenodo
The genetic architecture of HIV-1 virulence.
Blanquart, F; Wymant, C; HALL, M; Power, R; Golubchik, T; Gall, A; De Cesare, M; Macintyre-Cockett, G; Bakker, M; Bezemer, D; Gabrielaite, M; Ong, SH; Kendall, M; Sauter, R; Bannert, N; Fellay, J; Grabowski, MK; Gunsenheimer-Bartmeyer, B; Günthard, HF; Kivelä, P; Kouyos, RD; Laeyendecker, O; Marvig, RL; Meixenberger, K; Meyer, L; ... Fraser, C.
2025
Virus evolution
The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study
HALL, MD; Probert, W; Abeler-Dörner, L; Wymant, C; Di Lauro, F; Xi, X; Sauter, R; Golubchik, T; Bonsall, D; Pickles, M; Cori, A; Bwalya, J; Floyd, S; Bell-Mandla, N; Shanaube, K; Yang, B; Bock, P; Donnell, D; Grabowski, MK; Pillay, D; Rambaut, A; Ratmann, O; Fidler, S; Ayles, H; Hayes, R; ... Fraser, C.
2025
eLife Sciences Publications, Ltd
Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity
Ferretti, L; Golubchik, T; Di Lauro, F; Ghafari, M; Villabona-Arenas, CJ; ATKINS, K; Fraser, C; HALL, M;
2025
bioRxiv
HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.
Golubchik, T; Abeler-Dörner, L; HALL, M; Wymant, C; Bonsall, D; Macintyre-Cockett, G; Thomson, L; Baeten, JM; Celum, CL; Galiwango, RM; Kosloff, B; Limbada, M; Mujugira, A; Mugo, NR; Gall, A; Blanquart, F; Bakker, M; Bezemer, D; Ong, SH; Albert, J; Bannert, N; Fellay, J; Gunsenheimer-Bartmeyer, B; Günthard, HF; Kivelä, P; ... HPTN 071 (PopART) Phylogenetics protocol team, the,
2025
BMC bioinformatics
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Matthew Hall

Contact

United Kingdom