Research output per year
Research output per year
Personal profile
Professional profile
His research interests focus on the areas of formal methods, with emphasis on the theoretical of programming languages and program analysis, and scientific and applied computing. In the area of applied computing, his main concern has been the development of methods and software tools for phylodynamic analysis and the study of infectious disease dynamics.
He's the principal developer of PhyDyn, a BEAST2 package that enables the user to simultaneously estimate epidemiological parameters and pathogen phylogenies from genetic data (DNA sequences).
Before joining UTEC, he worked as research fellow and scientific software developer at the Department of Infectious Disease Epidemiology, Imperial College London, where he also formed part of Imperial College's COVID-19 Response Team. He has also worked as a researcher for the University of Reading (Evolution Laboratory), City University London (Department of Computer Science) and the Department of Computing, Imperial College London.
He is a member of the Association of Computer Machinery (ACM) and the Society for Industrial and Applied Mathematics (SIAM).
Education/Academic qualification
PhD, in Computer Science, Northeastern University
Researching Topics
- Formal methods
- scientific and applied computing
- phylodynamic analysis
- the study of the dynamics of infectious diseases
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Collaborations and top research areas from the last five years
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Author Correction: SARS-CoV-2 evolution during treatment of chronic infection (Nature, (2021), 592, 7853, (277-282), 10.1038/s41586-021-03291-y)
The CITIID-NIHR BioResource COVID-19 Collaboration, The COVID-19 Genomics UK (COG-UK) Consortium, Principal investigators, CRF & volunteer research nurses, Sample logistics, Sample processing & data acquisition, Clinical data collection, Royal Papworth Hospital ICU, Addenbrooke’s Hospital ICU, Cambridge & Peterborough Foundation Trust, ANPC & Centre for Molecular Medicine & Innovative Therapeutics, NIHR BioResource, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis and software & analysis tools, Leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, metadata curation, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, leadership & supervision, metadata curation, project administration and samples & logistics, Funding acquisition, leadership & supervision, metadata curation, samples & logistics and sequencing & analysis, Funding acquisition, leadership & supervision, project administration, samples & logistics and sequencing & analysis & Funding acquisition, leadership & supervision, sequencing & analysis, software & analysis tools and visualization & 64 others, , 11 Aug 2022, In: Nature. 608, 7922, p. E23Research output: Contribution to journal › Comment/debate
Open Access3 Scopus citations -
Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (Nature, (2021), 593, 7857, (136-141), 10.1038/s41586-021-03412-7)
Principal investigators, CRF & volunteer research nurses, Sample logistics, Sample processing & data acquisition, Clinical data collection, Royal Papworth Hospital ICU, Addenbrooke’s Hospital ICU, Cambridge & Peterborough Foundation Trust, ANPC & Centre for Molecular Medicine & Innovative Therapeutics, NIHR BioResource, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis and software & analysis tools, Leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, metadata curation, samples & logistics, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, leadership & supervision, metadata curation, project administration and samples & logistics, Funding acquisition, leadership & supervision, metadata curation, samples & logistics and sequencing & analysis, Funding acquisition, leadership & supervision, project administration, samples & logistics and sequencing & analysis, Funding acquisition, leadership & supervision, sequencing & analysis, software & analysis tools and visualization, Funding acquisition, samples & logistics, sequencing & analysis, software & analysis tools and visualization & Leadership & supervision, metadata curation, project administration, samples & logistics and sequencing & analysis & 65 others, , 11 Aug 2022, In: Nature. 608, 7922, p. E24Research output: Contribution to journal › Comment/debate
Open Access1 Scopus citations -
Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
The COVID-19 Genomics UK (COG-UK) Consortium, 1 Dec 2022, In: Nature Communications. 13, 1, 1012.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
The Cambridge Covid-19 testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium & The COVID-19 Genomics UK (COG-UK) Consortium, Dec 2022, In: Nature Communications. 13, 1, 751.Research output: Contribution to journal › Article › peer-review
Open Access27 Scopus citations -
Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study
COVID-19 Genomics UK (COG-UK) Consortium, Jan 2022, In: The Lancet Infectious Diseases. 22, 1, p. 35-42 8 p.Research output: Contribution to journal › Article › peer-review
Open Access560 Scopus citations