Research

Current studentships

Transformer-Bio: integrating imaging and omics in large-scale food fermentation

Deadline: 07/01/2026 5:00PM
Studentship code: PHD
Staff name: Professor Claudio Angione
Research centre: Centre for Digital Innovation
Start date: Successful applicants will be expected to start in October 2026.

For integrative tasks in biotechnology, recent advances in deep learning and transformer-based architectures can significantly improve performance, particularly for tasks like joint feature learning and prediction. Recent studies have demonstrated the potential of transformers for tasks like multi-omics and imaging data imputation and integration.

Continuous flow systems of Fusarium venenatum, performed by the leading meat substitute company Quorn, lead to the onset of mutant strains (known as C-variants), which develop altered branching patterns (hyphae). These are extremely challenging to detect in advance, and cause major changes in the texture of the product, which becomes more crumbly, leading to termination of the fermentation, with high costs and emissions.

It is currently unclear why this F. venenatum branching pattern appears. Therefore, a multi-omic characterisation of this fermentation process would be critical for predicting their onset. In this project, we aim to elucidate this by developing a deep learning method that can integrate metabolic modelling, imaging, and omics data. Specifically, using transformers for this task is a promising avenue, due to their ability to integrate time-resolved multi-modal data.

To address this exciting problem, you will be part of a multidisciplinary team of computer scientists, omics, and molecular biologists. The data will be newly collected as part of the project by the wider team, including a lab technician. This interdisciplinary project will combine fermentation, modelling, and deep learning aspects. It will explore the mechanistic characterisation of fungal fermentation, and will aim at addressing a concrete challenge in the food fermentation industry.

By joining this project, you will be part of and supported by the larger interdisciplinary Angione lab, and you will also work with Prof Peter O’Toole (York), Prof Safwan Akram (National Horizons Centre), Prof Annalisa Occhipinti (Teesside), and Dr Nanda Puspita (Quorn).

Funding eligibility

This fully funded PhD Studentship covers tuition fees for the period of a full-time PhD Registration of up to four years and provide an annual tax-free stipend of £20,780 for four years, subject to satisfactory progress.

You must complete your PhD in four years.

Applications are welcome from UK or international students.

Entry requirements

Applicants should hold or expect to obtain a good honours degree (2:1 or above) in any computer science, biological, chemical or physical science or mathematics. A masters level qualification in a relevant discipline is desirable, but not essential, as well as a demonstrable understanding of the research area.

We aim to support the most outstanding applicants from outside the UK and are able to offer a very limited number of bursaries that will enable full studentships to be awarded to international (EU and non-EU) applicants. These full studentships will only be awarded to exceptional quality candidates, due to the highly competitive nature of this scheme.

International students will be subject to the standard entry criteria relating to English language ability, ATAS clearance and, when relevant, UK visa requirements and procedures.

The YBDTP is committed to recruiting extraordinary future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Not all projects will be funded; a limited number of candidates will be appointed via a competitive process.

How to apply

To submit your application, complete the Expression of Interest form below for any of the projects which interest you. You can apply for up to two YBDTP projects (which can be at different universities).

Apply now

Selection process

Shortlisting will take place as soon as possible after the closing date and successful applicants will be notified promptly. If you are shortlisted, you will be invited for an interview on a date to be confirmed in February 2025. You will be notified as soon as possible after the interview dates whether your application has been successful, placed on a reserve list or unsuccessful. If you are successful, you'll be required to confirm your intention to accept the studentship within 10 days.

Successful applicants will progress to an offer of a place, to commence in October 2026.

About Teesside

We are committed to providing a safe, welcoming and inclusive campus and to supporting all members of our University community to thrive whatever their age, gender, disability, sexual orientation, gender identity, race, marital status, nationality or any other characteristic.
More about our Inclusive campus

As a Teesside University research student, you will join a growing and dynamic research community, allowing you to share your experiences, insight and inspiration with fellow researchers. You will benefit from our academic expertise and be supported through a strong programme of research training. You will be offered opportunities and support at each stage of your research degree. Our research is designed to have impact, and to influence policy and practice within our region, the UK and beyond. We work with external organisations to anticipate and respond to research needs, and to put our research into practice in sectors as diverse as the arts, engineering, healthcare and computing.

PhD students are encouraged to work with their supervisors to explore the potential impact of their work.

The successful candidate will be expected to participate fully in research group and centre activities, including training sessions and workshops, and will become a member of the University's wider postgraduate research community. Mentoring and support will be provided for the development of a strong academic and professional CV during the PhD.

Academic enquiries

For academic enquiries, please contact C.Angione@tees.ac.uk.

Key dates

Deadline: 07/01/2026 5:00PM
Interview date: We envisage that interviews will take place in February 2026.
Start date: Successful applicants will be expected to start in October 2026.