Baseline T cell infiltration and the spatial distribution of T cells within a tumour has been found to be a significant indicator of patient outcomes. This observation, coupled with the increasing availability of spatially-resolved imaging data of individual cells within the tumour tissue, motivates the development of mathematical models which capture the spatial dynamics of T cells. Agent-based models allow the simulation of complex biological systems with detailed spatial resolution, and generate rich spatio-temporal datasets. In order to fully leverage the information contained within these simulated datasets, spatial statistics provide methods of analysis and insight into the biological system modelled, by quantifying inherent spatial heterogeneity within the system. We present a cellular automaton model of interactions between tumour cells and cytotoxic T cells, and an analysis of the model dynamics, considering both the temporal and spatial evolution of the system. We use the model to investigate some of the standard assumptions made in these models, to assess the suitability of the models to accurately describe tumour-immune dynamics.

The overall goal of the Sherwood lab is to advance genomic and precision medicine applications through high-throughput, multi-disciplinary science. In a shortened talk this past autumn, I described our recent efforts using combined analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening to improve the identification of genes, coding variants, and non-coding variants whose alteration impacts serum LDL cholesterol (LDL-C) levels.

In this talk, I will discuss our emerging efforts to optimize and employ precision CRISPR techniques such as base editing and prime editing to better understand the impacts of coding and non-coding variation on serum LDL-C levels and coronary artery disease risk. This work involves the development of novel high-throughput screening platforms and computational analysis approaches that have wide applicability in dissecting complex human disease genetics.

The term cancer covers a multitude of bodily diseases, broadly categorised by having cells which do not behave normally. Cancer cells can arise from any type of cell in the body; cancers can grow in or around any tissue or organ making the disease highly complex. My research is focused on understanding the specific mechanisms that occur in the tumour microenvironment via mathematical and computational modelling. In this talk I shall present a 3D individual-based force-based model for tumour growth and development in which we simulate the behaviour of, and spatio-temporal interactions between, cells, extracellular matrix fibres and blood vessels. Each agent is fully realised, for example, cells are described as viscoelastic sphere with radius and centre given within the off-lattice model. Interactions are primarily governed by mechanical forces between elements. However, as well as he mechanical interactions we also consider chemical interactions, by coupling the code to a finite element solver to model the diffusion of oxygen from blood vessels to cells, as well as intercellular aspects such as cell phenotypes. 

Nanopore sequencing is a method to infer the sequence of nucleotides in DNA or RNA molecules from small variations in ionic current during transit through a nanoscale pore. We will give an introduction to nanopore sequencing and some of its applications and then explore simple models of the signal generation process. These can provide insight to guide optimisation of the system and inform the design of more flexible neural network models, capable of extracting the rich contextual information required for accurate sequence inference.

The Turing pattern is a key concept in the modern study of reaction-diffusion systems, with Turing patterns proposed a possible explanation for the spatial structure observed in myriad physical, chemical, and biological systems. Real-world systems are not always so clean as idealized Turing systems, and in this talk we will take up the case of more messy reaction-diffusion systems involving explicit space or time dependence in diffusion or reaction terms. Turing systems of this nature arise in several applications, such as when a Turing system is studied on a growing substrate, is subjected to a temperature gradient, or is immersed within a fluid flow. The analysis of these messy Turing systems is not as straightforward as in the idealized case, with the explicit space or time dependence greatly complicating or even preventing most standard routes of analysis. Motivated by patterning in phenomena involving explicit space or time dependence, and by the interesting mathematical challenges inherent in the study of such systems, in this talk we consider the following questions:

* Is it possible to obtain generalizations of the Turing instability conditions for non-autonomous, spatially heterogeneous reaction-diffusion systems?
* What can one say about predicting nascent patterns in these systems?
* What role does explicit space or time dependence play in selecting fully developed patterns in these systems?
* Is it possible to exploit this space or time dependence in order to manipulate the form of emergent patterns?

We will also highlight some of the applications opened up by the analysis of heterogeneous Turing systems.