About the Project
Mine more than 15,000 public ribosome profiling datasets for rare hidden proteins that no single experiment can detect, at the University of Oslo.
Why it matters
Ribosome profiling (Ribo-seq) shows exactly where ribosomes translate RNA in a cell. Rare and non-canonical translation events, such as translation from unexpected start sites or under stress, are easy to miss: they are faint and scattered across thousands of public experiments that were never analyzed together. Combining them reveals hidden proteins that no single experiment can detect.
The project
You will aggregate over 15,000 public Ribo-seq libraries, building on the ORFik framework and the RiboSeq.Org platform to detect and characterize rare translation events at scale. Your catalogs become reference resources for the whole network, feeding its AI prediction models and cross-validated against immunopeptidomics and genetic-variant data.
What you will do
- Build large-scale aggregation methods with stringent quality criteria (coverage, periodicity, contamination)
- Study how translation start site selection evolves across species and shifts under stress and infection
- Develop machine learning to separate genuine rare translation events from technical artifacts
- Build visualization and query tools for RiboSeq.Org and the ORFeome platform
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. Eivind Valen at the University of Oslo, which studies how translation is regulated, including initiation and termination, and analyzes Ribo-seq data at large scale. You will work closely with the group of Prof. Pasha Baranov at University College Cork, which co-develops the RiboSeq.Org platform.
Who should apply
We welcome applications from bioinformaticians, computational biologists and data scientists who enjoy working with large sequencing datasets. This is a computational project built on the RiboSeq.Org platform.
- A master's degree (or equivalent) in bioinformatics, computational biology, computer science, data science, or a related field
- Strong programming skills (for example Python) and experience with large-scale sequencing or genomics data
- Good written and spoken English
- Nice to have: Ribo-seq or other NGS data, machine learning, data curation at scale
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 Norway 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. Eivind Valen and Prof. Pasha Baranov, with mentoring from partners across academia and industry
- A secondment of around three months at EIRNA Bio (Cork, Ireland)
- Training with 14 other ORFeus PhD candidates across Europe: network schools, workshops, transferable skills and international conferences
- PhD enrollment at the University of Oslo
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/. 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 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 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, including applicants living or studying in the UK. Mobility rule: you must not have lived, worked or studied in Norway for more than 12 months in the 36 months before your start date. Applicants must not hold a doctoral degree.