Understanding evolutionary dynamics of viral transmission and antiviral evolution

Key Objectives & Core Scope

• Mining the Virtual Fossil Record:
  Using computational biology and high-throughput genetic screening to analyse animal DNA databases.
• Characterizing EVE Diversity and transmission:
  Examining retroviral and non-retroviral elements (such as ancient lineages related to modern viruses such as Hepatitis B, Ebola,, Dengue, and HIV) integrated in host nuclear DNA.
• Virally Derived Immunity (Exaptation):
  Investigating how hosts have repurposed these ancient viral fragments into functional cellular genes that inhibit viral infections.

The project can involve either computation or experimental approaches. Computational methods will involve analysing existing public genomic and transcriptomic datasets, mining thousands of genomes to find viral sequences. Tasks involve running automated bioinformatic workflows using the lab’s custom HI-FEVER Nextflow pipeline, performing large-scale sequence alignments, building phylogenetic trees. They will also involve transcriptomic work to reveal function. You will write code, develop data visualization pipelines, and use statistical modelling to identify patterns of ancient host-switching, working closely with a team of computational biologists.

Experimental approaches will involve cell culture virology, transfection, transduction, FACS, immunity assays and other laboratory techniques.

AK01

This project is part of the DPhil in Biology programme, and is not a funded course at the University of Oxford; as such, students are expected to explore options for funding. However, we anticipate being able to offer around 6 full graduate scholarships to incoming DPhil students in 2027/28.

You will be automatically considered for several Oxford scholarships, which cover fees and stipend, if you fulfil the eligibility criteria and submit your graduate application by 6 January 2026. Scholarships are awarded based on academic achievement and potential to excel as a DPhil student.

For further details about searching for funding as a graduate student visit the graduate study information on our website.

For full entry requirements and eligibility information, please see the main admissions page.