Application deadline: Saturday, October 31, 2026
About the Project
Find hidden peptides on melanoma cells and build a machine learning model that predicts which could be targets for cancer vaccines, at the University of Lausanne.
Why it matters
Cryptic open reading frames outside standard protein catalogs can be translated, and some of their peptides are presented on HLA-I molecules, where they can act as tumor antigens. But translation alone does not guarantee a stable presented peptide. Predicting which cryptic peptides are stably presented is an open problem, and solving it would help choose targets for cancer vaccines and immunotherapy.
The project
You will identify cryptic HLA-I peptides in patient-derived primary melanoma cell lines with advanced immunopeptidomics, measure their stability and turnover with SILAC pulse-chase assays, and build an integrative machine learning model that predicts which cryptic peptides are stably presented. The model draws on ribosome profiling, immunopeptidomics and secreted microprotein data from across the network. The result is a catalog of cryptic melanoma peptides and a tool to prioritize immunogenic targets.
What you will do
- Identify cryptic HLA-I peptides in patient-derived melanoma cell lines
- Measure peptide stability and turnover with SILAC pulse-chase assays
- Build a machine learning model of cryptic peptide presentation
- Integrate ribosome profiling and proteogenomics data from partner projects
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. Michal Bassani-Sternberg at the University of Lausanne, which develops advanced immunopeptidomics and machine learning methods to characterize HLA peptide presentation and identify cancer antigens, including cryptic ORF-derived peptides. You will work closely with the group of Prof. Uwe Ohler at the Max Delbrück Center in Berlin, which brings computational biology and translation modeling expertise.
Who should apply
We welcome applications from immunologists, proteomics and mass spectrometry graduates, and biochemists who want to combine lab work with machine learning. This is a wet-lab project with a substantial computational part.
- A master's degree (or equivalent) in immunology, molecular biology, biochemistry, proteomics, bioinformatics, or a related field
- Hands-on lab experience with mass-spectrometry proteomics, immunopeptidomics or mammalian cell culture
- Good written and spoken English
- Nice to have: HLA peptide analysis, SILAC-based methods, Python, machine learning
Eligibility (MSCA rules)
Living or studying in the UK? You are likely eligible for this position.
You must not have lived or carried out your main activity (work, studies) in Switzerland for more than 12 months in the 36 months before your start date. Compulsory national service, short stays such as holidays, and time spent in a refugee status procedure do not count. 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. Michal Bassani-Sternberg and Prof. Uwe Ohler, with mentoring from partners across academia and industry
- A secondment of around three months with an ORFeus industry partner
- Training with 14 other ORFeus PhD candidates across Europe: network schools, workshops, transferable skills and international conferences
- PhD enrollment at the University of Lausanne
Practical details
Start around March 2027; the exact date depends on the host institution. Reference letters are requested only at the interview stage.
How to apply
You can only apply via https://www.orfeus-dn.eu/apply/.
The application asks for:
- a few eligibility questions
- a short motivation per project (150 to 200 words)
- your experience with the project's key techniques
- your CV
- an overview of your bachelor's and master's grades, in one PDF
- contact details for two referees
- a short motivational video
Funding Notes
Fully funded 36-month employment contract in ORFeus, an MSCA Doctoral Network (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, including applicants living or studying in the UK. Mobility rule: you must not have lived, worked or studied in Switzerland for more than 12 months in the 36 months before your start date. Applicants must not hold a doctoral degree.
