PhD Positions

A large number of small open reading frames (smORFs), long treated as non-coding, turn out to be translated into microproteins. These microproteins take part in cellular regulation, disease, and immune recognition, yet most of them have never been characterized, and many are missed by standard annotation and proteomics. ORFeus brings together 15 research groups in eight European countries, together with industry and research partners, to find these proteins, understand what they do, and test their potential in diagnosis, immunotherapy, and drug development, with a strong focus on cancer.

The network combines ribosome profiling and translatomics, long-read and single-cell sequencing, mass-spectrometry proteomics and immunopeptidomics, evolutionary and comparative genomics, protein design, and machine learning.

The 15 projects

Each position is a separate project at its own host institution. Full project descriptions, supervisor details, and the application forms are at orfeus-dn.eu/apply.

Work Package 1: Uncovering the dark genome and proteome

• DC1: AI-driven model for cross-species smORF prediction and classification. University of Southampton, United Kingdom (Prof. Owen Rackham)
• DC2: Uncovering smORF and microprotein diversity using single-molecule translation mapping. Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany (Prof. Uwe Ohler). PhD awarded by Humboldt-Universität zu Berlin
• DC3: Discovering rare proteins across the smORF landscape. University of Oslo, Norway (Prof. Eivind Valen)
• DC4: Profiling microprotein interactions in bacterial pathogen infections. The Institute of Cancer Research (ICR), London, United Kingdom (Prof. Jyoti Choudhary). PhD awarded by the University of London
• DC5: Capturing secreted and diffusible microproteins using bioorthogonal tagging and XL-MS. University of Freiburg, Germany (Prof. Simon Elsässer)

Work Package 2: Understanding smORF and dark proteome functions

• DC6: Computational design of microprotein binders for functional modulation. Hubrecht Institute (KNAW), Utrecht, the Netherlands (Dr. Danny Sahtoe). PhD awarded by Utrecht University
• DC7: Dissecting mechanisms regulating smORF translation from lncRNAs. University of Leeds, United Kingdom (Prof. Julie Aspden)
• DC8: Predicting microprotein functionality through evolutionary analysis. Hospital del Mar Research Institute, Barcelona, Spain (Prof. Mar Albà). PhD awarded by Universitat Pompeu Fabra
• DC9: Single-cell translation dynamics following targeted smORF base editing. Hubrecht Institute (KNAW), Utrecht, the Netherlands (Prof. Alexander van Oudenaarden). PhD awarded by Utrecht University
• DC10: Mining the functional microproteome landscape using thermal proteome profiling. Ghent University, Belgium (Prof. Petra Van Damme)

Work Package 3: Investigating dark proteome roles in cancer and immunology

• DC11: Non-canonical translation from smORFs in HPV-driven cancer. University of Dundee, United Kingdom (Prof. Nicola Ternette)
• DC12: Impact of genetic variation in smORFs on protein expression. University College Cork, Ireland (Prof. Pasha Baranov)
• DC13: The dark proteome in cancer. Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (Dr. Sebastiaan van Heesch). PhD awarded by Utrecht University
• DC14: CRISPR-based discovery of regulators in cancer-linked smORF antigen presentation. Netherlands Cancer Institute (NKI-AVL), Amsterdam, the Netherlands (Prof. Reuven Agami). PhD awarded by Erasmus University Rotterdam
• DC15: Biogenesis and HLA presentation of cryptic ORF-derived peptides. University of Lausanne, Switzerland (Prof. Michal Bassani-Sternberg)

What the positions involve

Each doctoral candidate carries out an individual research project at the host institution and enrolls in a doctoral program leading to a PhD. Every candidate is supervised by a main supervisor and a co-supervisor from another ORFeus group, and is further supported by an industry supervisor and an independent academic advisor.

Every project includes a secondment of around three months with one of the network's industry or research partners, where the candidate applies their work in a company or large-scale research setting. Candidates also take part in a shared training program with the other 14 doctoral candidates: network schools and workshops, training in transferable skills such as research integrity, intellectual property, and science communication, and presentation of their work at international conferences.

Who we are looking for

We are looking for candidates with a master's degree (or equivalent, depending on requirements of the host institute, see individual vacancies) in molecular biology, biochemistry, biomedical sciences, bioinformatics, computational biology, computer science, immunology, or a related field, with a genuine interest in one or more of the ORFeus research areas. The projects range from mostly wet-lab to fully computational, and the specific skills required differ per project. These are listed in each project description at orfeus-dn.eu/apply. Good written and spoken English is required for all positions.

You can apply to up to three projects. See "How to apply" under Additional information.

Where to apply

Website: https://www.orfeus-dn.eu/apply/

Requirements

Research Field: Biological sciences » Biology

Education Level: Master Degree or equivalent

Skills/Qualifications

A master's degree (or equivalent) in a relevant field, completed by the start date, that gives access to a doctoral program in the host country. Hands-on experience in at least one area relevant to the project(s) you apply to, for example ribosome profiling or sequencing, mass-spectrometry proteomics or immunopeptidomics, molecular and cell biology, or programming and data analysis. The required and desirable skills for each project are listed in its project description at orfeus-dn.eu/apply.

Specific Requirements

Candidates must meet the MSCA Doctoral Network eligibility rules (see "Eligibility criteria"). The positions involve relocating to the host country, a secondment of around three months with a partner organization, and travel to network events.

Additional Information

Benefits

All positions are full-time employment contracts for 36 months, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. These are salaried positions, not stipends or scholarships.

The salary follows the MSCA Doctoral Network rules for the 2025 call. Amounts are the total cost to the employer and include the employer's social-security contributions. Your gross salary (before income tax and your own social-security contributions) is therefore lower than the sum of the allowances. The exact gross salary depends on the host country and is stated in project descriptions.

In addition you will receive:

• supervision by two academic supervisors from different ORFeus groups, an industry supervisor, and an independent academic advisor;
• a secondment of around three months with an ORFeus industry or research partner;
• a network-wide training program of schools, workshops, and transferable-skills training, and participation in international conferences;
• enrollment in a doctoral program leading to a PhD degree;
• the employment conditions of the host institution, such as paid leave and pension arrangements.

Eligibility criteria

You must meet all of the following conditions on your recruitment date (the start of your employment contract):

• You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are also not eligible.
• Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in the country of the host institution for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months. Because the host country differs per project, this is checked separately for each project you apply to.
• You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctoral program at the degree-awarding university of the project.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not hold a doctorate. You will be asked to provide proof of eligibility before the employment contract is signed.

Selection process

How to apply

Go to orfeus-dn.eu/apply, read the project descriptions, and apply through the application form of each project you are interested in. You can apply to up to three projects; each is a separate application, and you rank them as first, second, and third choice. Every project you rank will consider you, not only your first choice.

Each application asks for:

• a few short eligibility questions;
• your motivation for that specific project (150 to 200 words);
• a rating and short description of your experience with the key techniques of the project;
• your CV, which should clearly list your academic record, research experience (projects, methods, and results), and any publications and awards;
• an overview of your bachelor's and master's grades, in one PDF;
• optionally, a short video (up to about 90 seconds). Leaving it out does not count against you.

Reference letters are not needed when you apply. We ask for your referees' details only if you progress to the later stages of selection.

Assessment

Applications are assessed by the supervisors of each project against four weighted criteria: academic excellence (40%), research potential and motivation (30%), communication skills (20%), and international experience (10%). Shortlisted candidates are invited for a short introductory call, followed by a formal interview with both academic supervisors. The ORFeus Steering Committee oversees the process across the network to make sure the criteria are applied consistently.

Timeline

• 1 October 2026: applications open
• 22 October 2026, 23:59 CET: applications close
• November 2026: assessment, shortlisting, and introductory calls
• December 2026: interviews and selection
• 1 March 2027: planned start (latest 1 May 2027, depending on the host institution)

The process takes several weeks, so a period without news is not a negative sign. Every applicant is informed of the outcome.

Equal opportunities

ORFeus and its partners recruit in an open, transparent, and merit-based way, in line with the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers. We welcome applications from all qualified candidates regardless of gender, age, ethnic or national origin, religion or belief, disability, sexual orientation, or any other characteristic. We aim for a gender-balanced cohort. If you need an adjustment to take part in the selection process, let us know and we will make reasonable arrangements.

Additional comments

Questions about the positions or the procedure: please check orfeus-dn.eu first, as it answers most questions. For anything else, contact Simon Venneman, ORFeus program manager, at info@orfeus-dn.eu.

This position is funded by the European Union under the Marie Skłodowska-Curie Actions Doctoral Networks, Horizon Europe (Grant Agreement No. 101309891). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Work Location(s)

• University of Southampton — Southampton, United Kingdom (1 offer)
• Max Delbrück Center for Molecular Medicine (MDC) — Berlin, Germany (1 offer)
• University of Oslo — Oslo, Norway (1 offer)
• The Institute of Cancer Research (ICR) — London, United Kingdom (1 offer)
• University of Freiburg — Freiburg, Germany (1 offer)
• Hubrecht Institute (KNAW) — Utrecht, Netherlands (2 offers)
• University of Leeds — Leeds, United Kingdom (1 offer)
• Hospital del Mar Research Institute — Barcelona, Spain (1 offer)
• Ghent University — Ghent, Belgium (1 offer)
• University of Dundee — Dundee, United Kingdom (1 offer)
• University College Cork — Cork, Ireland (1 offer)
• Princess Máxima Center for Pediatric Oncology — Utrecht, Netherlands (1 offer)
• Netherlands Cancer Institute (NKI-AVL) — Amsterdam, Netherlands (1 offer)
• University of Lausanne — Lausanne, Switzerland (1 offer)