Mahan Ghafari is a post-doctoral research scientist at Big Data Institute, Nuffield Department of Medicine, University of Oxford. Address: Old Road Campus, Headington, Oxford, OX3 7XP, United Kingdom Email: mahan.ghafari@biodtp.ox.ac.uk LinkedIn: mahanghafari Twitter: @Mahan_Ghafari ORCiD: 0000-0002-4123-3287 Publications: Google Scholar

Scientific interests

Pathogen dynamics and evolution

Molecular evolution

Population genetics

Education

DPhil, Interdisciplinary Bioscience, University College, University of Oxford, 2022.Thesis: ‘‘Quantitative analysis of the mode and tempo of virus molecular evolution’’.
Supervisors: Aris Katzourakis and Oliver Pybus

MSc, Physics, Emory University, 2018. Thesis: ‘‘Quantitative analysis of adaptive evolution’’.
Advisor: Daniel Weissman

BSc, Physics, Sharif University of Technology, 2015.

Research

Mahan's DPhil research focuses on developing quantitative methods to understand biological mechanisms that can alter the molecular evolutionary rate of viruses over time and investigate the implications of having a time-dependent rate of evolution for reconstructing the phylogenetic history of viruses. He also explores alternative methods to estimating the time of origin and reconstructing the evolutionary trajectory of viruses using mobility data, national vital statistics, and serology surveys.

Prior to joining Oxford, Mahan spent one year as a visiting graduate student in Cambridge working with Chris Illingworth on within-host genetic diversity and transmission events in influenza A viruses where they developed a novel haplotype reconstruction method to estimate transmission bottleneck sizes from short-read data (the software package is available online on github). During his Master's, he worked with Daniel Weissman on the evolution of ‘irreducible complexity’ and how fast sexual populations can acquire complex adaptations.

Publications

For the full list of publications, please visit Mahan's Google Scholar

Talks

On the role of purifying selection in creating time-dependent evolutionary rates in SARS-CoV-2 and pH1N1, Virus Genomics and Evolution conference (virtual), Wellcome Connecting Science Conference, UK, Sep 2021.

Time-dependent rate phenomenon in viruses, 5th Uppsala Transposon Symposium (virtual), Sweden, Oct 2020.

Covid-19 epidemic in Iran. Population Biology, Ecology and Evolution Graduate Program journal club (virtual), Emory University, US, Jun 2020.

Covid-19 modelling and forecast in Iran. Contemporary Iran Forum, The Program in Iranian Studies at the MacMillan Center (virtual), Yale University, US, May 2020.

Can we predict the future? - mathematical modelling of the covid-19 pandemic and future pandemics (virtual), IBC, University of Oxford, May 2020.

Luria-Delbruck revisited: The classic experiment does not rule out Lamarckian evolution, Q-bio conference, July 2016.

Complex adaptation through individually neutral mutations, Q-bio summer school, June 2016.

Passenger vs. driver mutations in Acute Myeloid Leukemia Q-bio summer school symposium, June 2016.

Poster Presentations

Detailed reconstruction of the COVID-19 transmission dynamics in Iran, 8th International Conference on Infectious Disease Dynamics, Nov 2021.

Cross-immunity controls the duration and re-emergence of influenza, Nordita workshop on Molecular Basis to Predictability and Control of Evolution, July 2019.

How fast can sexual populations cross a fitness plateau?, ICMS Edinburgh workshop on Stochastic Models of Evolving Populations from Bacteria to Cancer, June 2018.

Inferring transmission bottleneck size from pathogen short-read sequencing data, Sanger Institute conference on Virus Genomics and Evolution, Cambridge, UK, April 2018.

Rate of complex adaptation in sexual populations, University of Cambridge Evolutionary Genetics and Genomics Symposium, March 2018.

Awards

Accelerating Impact Award, Interdisciplinary Bioscience DTP, University of Oxford, May 2022

Doctoral Training Programme Impact Award, jointly awarded by the BBSRC and Oxford University Innovation, University of Oxford, November 2021

ESEB Travel Award, Fantastic Forces workshop, University of St. Andrews, June 2019

Oxford-Radcliffe Scholarship, University College, University of Oxford, 2018-2022

Laney Graduate School Scholarships, Emory University, 2015-2018

Communicate Your Science Award, Genetics Society, April 2018

Marie Skłodowska-Curie actions research fellowship (Declined), 2018-2022

Industrial Strategy EPSRC-IDS scholarship, Imperial College London (Declined), 2018-2021

NSF-sponsored travel award for the 10th q-bio conference, Nashville, TN, USA, June 2016

NSF-sponsored q-bio summer school award, Fort Collins, CO, USA, June 2016

Emory University professional development travel award, June 2016