About the Project
Build deep learning models that find hidden microproteins in the genome, at the University of Southampton. Not open if you spent 12+ months in the UK since March 2024; take a look at the other ORFeus projects!
Why it matters
Many small open reading frames (smORFs) in the genome are translated into microproteins that standard protein catalogs miss. A reliable model that separates real translation from noise would speed up the search for new targets for diagnosis and therapy.
The project
You will build an AI foundation model that predicts which smORFs are translated, and how translation behaves at codon-level resolution. The model combines sequence embeddings with cell-type information and ribosome profiling (Ribo-seq) data. It is trained on experimental data from partner projects across the network and released as open tools.
What you will do
- Develop a deep learning foundation model linking mRNA sequence and cellular context to translation
- Integrate predictions with Ribo-seq, mass-spectrometry and genetic-variant data from partner projects
- Build interactive visualization tools for cross-species and cell-type-specific predictions
- Release models and tools on the shared ORFeome platform and HuggingFace
About ORFeus
This PhD is one of 15 in ORFeus, a Marie Skłodowska-Curie Actions Doctoral Network funded by Horizon Europe. ORFeus brings together 15 research groups in eight European countries, with industry and research partners, to study the dark proteome: the many microproteins made from small open reading frames long dismissed as non-coding. Together, the 15 projects aim to find these proteins, understand what they do, and test their potential in diagnosis, immunotherapy and drug development, with a strong focus on cancer.
Where you will work
You will join the group of Prof. Owen Rackham at the University of Southampton, which develops machine learning and computational methods for genomics, including the prediction of non-canonical translation. You will work closely with the group of Prof. Uwe Ohler at the Max Delbrück Center in Berlin, which brings complementary computational genomics expertise, and with experimental groups across the network.
Who should apply
We welcome applications from bioinformaticians, computer scientists and machine learning graduates with an interest in genomics.
- A master's degree (or equivalent) in bioinformatics, computational biology, computer science, data science, machine learning, or a related field
- Strong programming skills (for example Python) and hands-on machine learning or deep learning experience
- Good written and spoken English
- Nice to have: genomics or sequencing data (Ribo-seq, NGS), sequence models and embeddings including large language models, multi-omics data
Eligibility (MSCA mobility rule)
You are not eligible if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (planned 1 March 2027). This applies whatever your nationality, UK citizens included. For example, a one-year UK master's plus a few more months in the UK already goes over the limit. Compulsory national service, short stays such as holidays, and time spent in a refugee status procedure do not count. Studied or worked in the UK recently? You are likely eligible for our 11 ORFeus positions outside the UK.
You must not hold a doctoral degree. Any nationality may apply.
What we offer
- A 36-month, full-time employment contract with full social security, under MSCA rules
- Supervision by Prof. Owen Rackham and Prof. Uwe Ohler, with mentoring from partners across academia and industry
- A secondment of around three months with an ORFeus industry or research partner
- Training with 14 other ORFeus PhD candidates across Europe: network schools, workshops, transferable skills and international conferences
- Experience in both academic and industry settings, which prepares you for careers in research, biotech or pharma
- PhD enrollment at the University of Southampton
Practical details
Planned start 1 March 2027 (latest 1 May 2027, depending on the host institution). Reference letters are not needed when you apply; we ask for referee details only if you are shortlisted.
How to apply
You can only apply via https://www.orfeus-dn.eu/apply/ - registering your interest is not equivalent to an application. You can apply to up to three of the 15 ORFeus projects and rank them; every project you rank considers you. The application asks for:
- a few eligibility questions
- a short motivation per project (150 to 200 words)
- your grades and your experience with the project's key techniques
- your CV
- a short motivational video
Funding Notes
Fully funded 36-month MSCA Doctoral Network employment contract (Horizon Europe, GA 101309891), with full social security. A salary, not a stipend. Salary details for this position are on the application page. Open to all nationalities. UK mobility rule: you are not eligible for this project if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (planned 1 March 2027), whatever your nationality. Applicants must not hold a doctoral degree. Other ORFeus positions are open to UK residents: orfeus-dn.eu/apply.