PhD Studentship: Decoding cellular diversity in the brain: functional annotation of neuronal subtypes across development and disease University of Exeter in United Kingdom

[Funding of fees plus a stipend of £21,805 per annum for 2026/7.]

This is a fully funded PhD studentship at the University of Exeter focused on decoding cellular diversity in the human brain and functionally annotating neuronal subtypes across development and disease.

The project addresses a major challenge in neuroscience: while single-cell RNA sequencing has revealed many excitatory and inhibitory neuronal subtypes, the regulatory mechanisms that establish and maintain these identities are still not well understood, especially for rarer populations. The work will extend existing human post-mortem brain methods and multi-omic regulatory maps to study specific neuronal subtypes in detail.

The PhD student will isolate distinct neuronal populations, including excitatory and inhibitory subtypes and regionally specialised cells such as motor neurons, and compare their regulatory landscapes across brain regions, developmental stages, and ageing. Samples will span cortex, hippocampus, amygdala, hypothalamus, and other disease-relevant regions. The project will combine existing single-cell and multi-omic datasets with fluorescence-activated nuclei sorting, long-read sequencing, ATAC-seq, CUT&Tag profiling of H3K27ac, and direct measurement of DNA hydroxymethylation. Long-read RNA sequencing will be used to define transcript structure and cell-specific isoform usage, with opportunities to explore direct RNA sequencing and epitranscriptomics.

The resulting datasets will provide a functional annotation of neuronal diversity, identifying regulatory elements, transcripts, and epigenetic features that distinguish neuronal populations. These data will also be used to interpret human genetic studies of neurological and psychiatric disease and to develop computational deconvolution methods for estimating the proportions and molecular states of neuronal subtypes in bulk brain datasets. This includes application to in-house DNA methylation datasets from disorders such as Alzheimer’s disease.

The project is highly interdisciplinary, spanning epigenomics, genomics, molecular biology, neuroscience, and computational biology. The student will be based in Exeter and work with collaborators at Imperial College London, King’s College London, the University of Cambridge, and EMBL-EBI. The project is supported by strong resources, including multiomic human brain datasets, post-mortem tissue from multiple brain regions and developmental stages, cell-sorting platforms, sequencing facilities, and high-performance computing.

Funding is provided by the EPSRC Engineering and Physical Sciences Research Council. The studentship covers fees and provides a stipend of £21,805 per annum for 2026/7. The deadline listed is 08 Dec 2026.