The Francis Crick Institute Limited is hiring: Bauer Lab | Molecular mechanisms

A 2026 Crick PhD project with David LV Bauer.

Project background and description

An enormous amount of diversity in biology arises not from the gradual accumulation of mutation, but from the exchange and rearrangement of large genomic regions. Underpinned by processes such as recombination and transposition, these events drive step-changes in evolution and the emergence of new species across all domains of life.

RNA viruses, which store their genomes as RNA instead of DNA, accomplish the same rearrangements, but with different molecular mechanisms. In positive-strand RNA viruses such as picornaviruses or coronaviruses, recombination can lead to events with sudden and drastic consequences for their host, such as a change in tissue tropism, horizontal acquisition of a gene that helps replication, or the ability to infect an entirely new host. Similarly, in segmented negative-strand RNA viruses such as influenza, reassortment of genome segments between two viruses that circulate in different hosts can lead to an such as escape from host immunity (“antigenic shift”).

We know these processes occur because of the ‘successes’ of these viruses but we know little of their ‘failures’ — critical information if we want to understand the mechanisms with a view towards risk-assessing the likelihood of a new strain emerging or designing new classes of antiviral drugs to counteract viral evolution.

In this project, we will use a combination of sequencing-based approaches and imaging techniques such as super-resolution microscopy in cell-based in vitro models to study recombination and reassortment of RNA viruses. We will take advantage of our existing toolbox of sequencing-based methods[1] and conventional molecular virology approaches[2], and apply them to established coronavirus or influenza virus models (or a combination) available in our lab, with the aim of determining ‘When?’, ‘Where?’, and ‘How?’ recombination and reassortment occurs during infection.

This project would suit a candidate with a strong background in molecular virology, or molecular biology with an interest in virology.

References

• Dadonaite, B., Gilbertson, B., Knight, M.L., Trifkovic, S., Rockman, S., Laederach, A., . . Bauer, D.L.V. (2019) The structure of the influenza A virus genome. Nature Microbiology 4: 1781-1789. PubMed abstract
• Mears, H.V., Young, G.R., Sanderson, T., Harvey, R., Barrett-Rodger, J., Penn, R., . . Bauer, D.L.V. (2025) Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion. PLOS Biology 23: e3002982. PubMed abstract