Dr Mahan Ghafari
My pronouns are he/him
I am a Principal Investigator and Wellcome Trust Early Career Research Fellow in the Department of Biology at the University of Oxford, where I lead the Ghafari Research Group in the Life and Mind Building. I am also an Independent Investigator affiliated with the Data Analytics and Epidemiology Group at the Pandemic Sciences Institute and Kemp Junior Research Fellow in Medical Sciences at Lincoln College.
Our group studies the molecular evolution of pathogens, particularly those with epidemic or pandemic potential and with broader relevance to human, animal and plant health. We combine phylogenetics, population genetics, evolutionary theory, epidemiological modelling and structural biology to understand how pathogens evolve across hosts and timescales.
A major focus of our work is reconstructing pathogen evolutionary histories. We develop approaches to improve molecular dating, investigate why evolutionary rates vary across biological and temporal scales, and use genomic data to reconstruct pathogen origins and outbreak dynamics. We are particularly interested in situations where genomic or epidemiological data are sparse, and where better evolutionary models can improve what can be inferred early in an outbreak. We are also developing approaches that integrate viral sequence and protein structure, including AI-predicted structures, to investigate evolutionary relationships and functional change across much deeper timescales.
Current Research Themes
- Molecular clocks across timescales: understanding how and why evolutionary rate estimates vary over time, between hosts and across pathogens.
- Reconstructing pathogen origins and outbreaks: developing quantitative tools to infer origin times, host transitions and epidemic dynamics from limited genomic data.
- Structural evolution of viruses: integrating sequence evolution with experimental and AI-predicted protein structures to investigate deep viral ancestry and functional change.
- Evolutionary tools for pandemic preparedness: translating genomic models into practical approaches for analysing emerging outbreaks.
Background
I studied Physics at Sharif University of Technology in Tehran before completing an MSc in Physics at Emory University, where my work increasingly moved towards statistical physics and quantitative evolutionary biology. In 2017, I spent a year as a visiting graduate student in the Department of Genetics at the University of Cambridge, working on influenza transmission and pathogen genomics. I moved to Oxford in 2018 for a DPhil in Interdisciplinary Bioscience, focused on the quantitative analysis of the mode and tempo of viral molecular evolution, which I completed in 2022. I subsequently joined the Big Data Institute as a postdoctoral researcher. In 2025, I was awarded a Wellcome Trust Early Career Award and established an independent research group in the Department of Biology.
Selected News and Features
- From viral histories to protein structures: new directions for understanding virus evolution
- Outbreaks and inequities: tracking the evolution of viruses for a fairer future
- Faster, fairer COVID-19 vaccine roll-out could have saved millions of lives, UN University publication reveals
Joining the Group
I am always happy to hear from motivated researchers interested in joining the group. We host undergraduate and Master’s projects, DPhil students, visiting researchers and postdoctoral researchers working across quantitative pathogen evolution.
For enquiries, please contact mahan.ghafari@biology.ox.ac.uk
Additional affiliations
- Independent Investigator, Data Analytics and Epidemiology Group, Pandemic Sciences Institute
- Kemp Junior Research Fellow in Medical Sciences, Lincoln College
