PhD Work

Analysis of the T Cell Receptor Repertoire

The Decombinator pipeline is a toolkit for rapid identification and analysis of TCR sequences in next-generation sequencing datasets.

Decombinator has been used to process a range of sample types, such as blood and bulk tumour tissue, in order to profile and contrast the TCR repertoires of patients with disease against those of healthy volunteers.

Computational Docking for TCR-pMHC Modelling

Understanding the nature of the TCR-pMHC recognition process on a molecular level is essential for TCR-based therapeutics and vaccine design.

Accurate computational modelling of protein structures and structural complexes offers an efficient alternative to traditional crystallography.

I have compared the performance of four popular docking platforms in the context of TCR-pMHC modelling.

Structural Optimisation for TCR Design

Improvements in the accuracy of protein modelling tools provide an opportunity to speculate about how structural modelling may be integrated with other approaches for automated protein design.

I have built a prototype computational framework that aims to enhance desirable properties in TCR structures by artificially evolving them over successive generations using a genetic algorithm optimisation routine.

Other Work

Self-Assembling Collagen Architectures

Collagen molecules are the most abundant proteins found in humans and self-assemble into complex hierarchies that provide important structural support and function for a wide range of biological components.

Molecular dynamics simulations were built to explore the relationship between the electrostatic and hydrophobic interactions between collagen monomers as a driver for self-assembly.

Wnt Signalling Pathways in Prostate Cancer

A number of Wnt family ligands are known to activate the release of free Ca2+ within PC3 cancer cell lines. There is the potential that repurposing certain drugs to target these pathways may provide novel cancer therapy.

Automatic image analysis techniques were applied to model intra- and inter-cellular calcium wave dynamics in the context of prostate cancer.