Bio
James received his DPhil from Oxford University in Statistics under Gesine Reinert and Charlotte Deane. His work covered analysis of brain and protein networks, and network metadata. James worked briefly at University College London under Richard Rosch and Karl Friston on epilepsy networks. James is now a Postdoctoral Research Associate at the Turing and associate researcher at the Earlham Institute for life sciences and cellular genomics. He works as part of the ATI-CELLGEN (Cellular Genomics) partnership with Sebastian Ahnert.
Research interests
James' interests include dynamic and static networks in neuroscience and biological cellular systems, with a particular interest in the study of consciousness and multi-scale biological systems from single-cell gene regulation to functional brain connectivity.
His work includes finding methods to explore the link between morphology (cell shape), development and chromosomal composition in an immunologically important line of bone marrow cells using a combination of single cell sequencing and imaging flow cytometry data. These projects will utilise both semi-supervised and unsupervised generative approaches to create a map of the bone marrow transcriptomic and gene regulatory space. The project will focus particularly on understanding how gene variant (splice variant) diversity in these and other cells (such as in the brain's neocortex) contribute to the functional repertoire of cells using protein structure prediction.
James is particularly interested in understanding the relationship between metadata encoded in so-called ontologies (a set of descriptions and rules for annotating genes, cells and other systems) and domain-specific biomedical knowledge. James is using Large Language Models (LLMs) and in-context learning techniques to understand this link and establish new measures for understanding biological annotations.