Project Reference: ICS27-SCI-ST2
Project title: From genetic variation to immune cell function: combining cell-type-specific deep learning with experimental validation
Project outline
A fundamental goal of functional genetics is to understand how non-coding genetic variation controls gene regulation in a cell-type and state specific way. Immune cells are an ideal system for addressing this question as population-scale studies have discovered thousands of regulatory variants influencing immune traits. Interpreting these signals has proven difficult, as most are non-coding and act in highly specific cellular contexts. Deep learning models can predict functional consequences of genetic variation, but remain limited in their ability to capture this cell-type and state-specificity, leaving an important gap in linking genome sequence with gene regulation and cellular function.
This project aims to bridge the gap by building a deep learning model that predicts cell-type-specific effects of regulatory variants, and by experimentally validating its predictions. Within the project, the PhD candidate can choose a computational or an experimental emphasis. The computational aims are to 1) fine-tune a pre-existing foundation model for improved cell-type-specific predictions by integrating multiple large-scale single-cell sequencing datasets from immune cells, and 2) benchmark the fine-tuned model against existing models and experimental data across various contexts, including variant classes and cell types. The experimental aims are to 1) identify regulatory mechanisms of immune-associated variants by assessing them with the fine-tuned model, and 2) validate the predicted regulatory mechanisms using perturbation models, and confirm associated changes in cell composition and state using flow cytometry and immunohistochemistry.
The Teichmann lab is ideal for this project as it is at the forefront of single-cell analytics and has done pioneering work in unravelling immune cell function and regulation. It has collected massive single-cell datasets, has strong expertise in deep learning modelling, and offers extensive experimental and computational resources.
Principal Supervisor
Professor Sarah Teichmann
Email address: sat1003@cam.ac.uk
Department / Partner Institute: Cambridge Stem Cell Institute
Website: http://www.teichlab.org/
Industrial Partner
OtoImmune Ltd
BBSRC strategic theme
Understanding the rules of life
Funding and international applicants (How to apply page)
Deadline: Tuesday 8 December 2026
This is a fully funded programme supported by the BBSRC Doctoral Landscape Awards. An offer of a place includes full funding for your stipend (currently £21,805 for the 2026–27 academic year), as well as payment of the University tuition fees. Applicants are not required to apply to any additional funds (i.e. GATES). For the 2027 intake, approximately 25 studentships will be available across the Targeted and iCASE route.
Read more about the Targeted & iCASE studentships, including programme structure, Professional Internships, training and networking.
Important information for applicants
Academic qualifications and supporting documents
International applicants
A limited number of studentships up to 30% of the cohort can be offered to international candidates, including those from the EU and outside the EU. For example, for a cohort of 25 students, up to 7 studentships may be awarded to international candidates. The Cambridge Biosciences DTP will cover the costs of student visas and health surcharge for any international BBSRC DTP students recruited and will also provide funding to cover both fees and a stipend to support living costs.
Before you apply
Before applying, please check the University of Cambridge's entry requirements .
Applicants should normally hold, or be expected to achieve, a high upper second-class honours degree (High 2:1) or its equivalent.
A pass in a UK-equivalent Master's degree in a relevant subject will exceed the University's minimum academic entry requirement.
If you obtained your qualifications outside the UK, please check the University's International Qualifications guidance to confirm the equivalent qualification for your country.