CASE Project: Transformer-Bio: integrating imaging and omics in large-scale food fermentation University of Teesside in United Kingdom

This project will be undertaken in collaboration with Marlow Ingredients (Quorn Foods) and includes a minimum 3-month placement based at the Industry Partner's premises.

Continuous flow systems of Fusarium venenatum, performed by the leading meat substitute company Marlow ingredients (sold as 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 large 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.

For integrative tasks in biotechnology, transformer 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 data imputation and integration, and are therefore promising candidate tools for the proposed integrative task.

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 ( https://sites.google.com/view/angionelab/ ), and you will also work with Prof Peter O’Toole (York), Dr Annalisa Occhipinti (Teesside), Prof Safwan Akram (National Horizons Centre), and Dr Nanda Puspita (Marlow Ingredients, Quorn).

For informal enquiries about the project, please contact Prof Claudio Angione [email protected] .

About YBDTP:

YBDTP brings together world-class bioscience research and innovation, as well as excellence in doctoral supervision, across the region. YBDTP will fund postgraduate researchers at the Universities of Leeds, Sheffield, York, Bradford, Hull, Leeds Beckett, Sheffield Hallam and Teesside forming a strong regional training partnership. In YBDTP you'll benefit from a regional doctoral training programme that has interdisciplinary collaboration at its core. The aim is to enable you to develop a range of research skills in biological, biotechnology and biochemical areas as well as equip you with core data analysis and professional skills that are necessary for bioscience research and related non-academic careers.

https://www.whiterose-mechanisticbiology-dtp.ac.uk/yorkshire-bioscience-dtp/

Funding Notes:

Funding: A tax-free annual stipend at the standard UKRI rate (£19,237 for 2024/25 entry), research costs and tuition fees at UK rate

Academic year: 2025/26

Open to: International (including EU) and UK (home) students

Eligibility:

Open to International (including EU) and UK (home) students.

You can apply if you have, or are expecting to gain, at least an upper second-class honours degree or equivalent. Due to the interdisciplinary nature of this programme, we welcome applications if your background is in any biological, chemical or physical science or mathematics and are interested in using your skills in addressing biological questions. International students should check if they meet the entry requirements for their country .

We aim to support the most outstanding applicants from outside the UK and are able to offer a 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 competitive nature of this scheme.

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.

English language:

If English isn't your first language, you may need to provide evidence of your English language ability.

How to apply:

Application deadline: Monday 6th January 2025

To submit your application, click on the link to the Expression of Interest form in the Funding Notes section of any of your chosen projects. You can apply for up to 3 YBDTP projects (which can be at different universities).

We would advise you to read the questions in the form before submitting your application. Inside the form there is a link to a document for you to see the questions in advance.

If you have any questions about the application process, please email [email protected] .

If you have any questions about the project you are interested in, please email the project supervisor (see project description).

How we allocate:

Shortlisting will take place as soon as possible after the closing date and successful applicants will be notified promptly. If you're shortlisted, you'll be invited for an interview on a date to be confirmed in February 2025. You'll 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.

Terms and conditions:

The studentships are fully funded for four years, and you must complete your PhD in four years.

You'll receive the UKRI minimum doctoral stipend per year for your living costs, which is paid to you in regular instalments. The UK Research and Innovation (UKRI) stipend is tax free and does not need to be paid back.

International students will need to have sufficient funds to cover the costs of their student visa , NHS health surcharge , travel insurance and travel to the UK as these are excluded from UKRI funding.