About the Project
Use machine learning and Oxford Nanopore long-read data to map which hidden microproteins cells make from each RNA isoform, at the Max Delbrück Center in Berlin.
Application deadline: Saturday, October 31, 2026
Why it matters
Many small open reading frames (smORFs) are translated into microproteins that standard protein catalogs miss. Which ORF a ribosome reads can depend on the exact RNA isoform, but conventional methods cannot tell which isoform a translation event came from. Solving this tells us which hidden proteins a cell actually makes, and from which transcript.
The project
You will build computational models that map translated ORFs onto individual RNA isoforms, using single-molecule translation data from RiboSTAMP and Oxford Nanopore long-read direct RNA sequencing. You will also study how RNA structure and modifications such as m6A shape translation. Your isoform-level maps feed the prediction models and experimental projects across the network.
What you will do
- Develop computational and machine learning methods for single-molecule, long-read translation data
- Link translation events to specific RNA isoforms and integrate them with Ribo-seq and proteomics evidence
- Model how RNA structure and m6A modification influence which ORFs are translated
- Spend around three months at Oxford Nanopore Technologies working on nanopore-based workflows
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. Uwe Ohler at the Max Delbrück Center for Molecular Medicine (MDC) in Berlin, which develops computational approaches to RNA regulation and translation, including Ribo-seq analysis and the detection of non-canonical ORFs. You will work closely with the group of Prof. Eivind Valen at the University of Oslo, which specializes in large-scale analysis of translation across public Ribo-seq data.
Who should apply
We welcome applications from bioinformaticians, computational biologists and machine learning researchers with an interest in RNA and translation. This is a mainly computational project.
- A master's degree (or equivalent) in bioinformatics, computational biology, computer science, machine learning, or a related quantitative or life-science field
- Strong programming skills (for example Python or R) and experience analyzing sequencing data
- Good written and spoken English
- Nice to have: machine learning, long-read sequencing (nanopore or PacBio), genomics or NGS, mass-spectrometry proteomics data, post-transcriptional gene regulation
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 Germany 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. Uwe Ohler and Prof. Eivind Valen, with mentoring from partners across academia and industry
- A secondment of around three months at Oxford Nanopore Technologies
- 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 Humboldt-Universität zu Berlin
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, including applicants living or studying in the UK. Mobility rule: you must not have lived, worked or studied in Germany for more than 12 months in the 36 months before your start date. Applicants must not hold a doctoral degree.