Project 3: Discovering rare proteins across the smORF landscape (Eivind Valen)

ORFeus doctoral network; Oslo fylke; On-site; NOK 551,000 - 595,000; Full time

Job summary

The ORFeus doctoral network invites applications for a full-time three-year PhD Research Fellow at the University of Oslo. You will join Prof.

Eivind Valen's group to study translation regulation and ribosome profiling, contributing to the RiboSeq.Org platform and ORFeome collaboration. You will spend around three months on secondment at EIRNA Bio in Cork, Ireland, applying non-canonical translation findings to drug discovery and therapeutics, while pursuing interdisciplinary training and

Qualifications

• Master's degree (or equivalent) in bioinformatics, computational biology, computer science, data science or related field with strong computational skills.
• Strong programming skills (preferably in R) and experience analyzing large-scale sequencing/genomics datasets.
• Desirable: experience with ribosome profiling (Ribo-seq) or other NGS data, ML, data aggregation at scale, and interest in translation, microproteins, and the dark proteome.
• Applicants must have good English communication and meet UiO’s English-language requirements for admission to the PhD programme.
• Willingness to travel for secondment and network events.

Responsibilities

• Implement large-scale data aggregation methods to detect rare and non-canonical translation events across 15,000+ ribosome profiling datasets.
• Characterize initiation-site evolution across species and under stress; develop ML approaches to distinguish authentic events from artifacts.
• Experimentally validate rare events by integrating immunopeptidomics and genetic-variant data; build visualization and query tools integrated with RiboSeq.Org and ORFeome.
• Collaborate across the ORFeus network and contribute catalogs/tools to RiboSeq.Org and the ORFeome platform; produce the project’s scientific report.

Skills

Strong programming in R

Large-scale sequencing data analysis

Interest in translation/microproteins

Travel for secondment/network events

Education

Master's degree or equivalent in bioinformatics/computational biology/data science

Tools

R

Job description

The position

Ribosome profiling (Ribo-seq) is a technique that captures a snapshot of every ribosome actively translating messenger RNA in a cell, showing exactly where translation starts and stops. Rare and non-canonical translation events, such as translation from unexpected start sites or under stress, are easy to miss because they are faint and scattered across thousands of separate public experiments that were never analyzed together.

This project aggregates over 15,000 public ribosome profiling libraries through the RiboSeq.Org platform to detect and characterize these rare events at unprecedented scale, turning them into reference resources for the whole consortium. It is a data hub for ORFeus Work Package 1: the aggregated datasets feed the network's AI translation-prediction models, while the cataloged rare events are cross-validated against immunopeptidomics data and genetic-variant data from partner projects. Stress and infection conditions add an important biological dimension and connect the work to partner projects on host-pathogen translation.

Main tasks

• Implement large-scale data aggregation methods that sensitively detect rare and non-canonical translation events across over 15,000 public ribosome profiling datasets, establishing stringent inclusion criteria for coverage, periodicity, and contamination.
• Characterize how translation initiation site selection evolves across species and shifts under stress conditions, including infection studied with other doctoral candidates (DCs) in the network, here DC4, and develop machine-learning approaches that distinguish authentic rare translation events from technical artifacts.
• Experimentally validate rare events by integrating immunopeptidomics data from DC11 and DC15 and genetic-variant data from DC12 to cross-validate cryptic antigens, and build accessible visualization and query tools integrated with the ORFeome platform.
• Collaborate across the ORFeus network, contribute curated translation catalogs and tools to the RiboSeq.Org browser and the ORFeome platform, and produce the project's scientific report.

Methods and platforms: large-scale aggregation and analysis of ribosome profiling (Ribo-seq) data, quality control based on coverage, periodicity, and contamination metrics, machine learning to separate authentic rare translation events from technical artifacts, integration of immunopeptidomics and genetic-variant data, and interactive visualization and query tools, working with public and consortium datasets via the RiboSeq.Org and ORFeome platforms.

Secondment: you will spend around three months at EIRNA Bio (Cork, Ireland), applying findings on non-canonical translation to commercially relevant settings such as drug discovery and therapeutics development. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Your profile

MSCA eligibility

You must meet all of the following on your recruitment date:

• 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 not eligible.
• Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in Norway 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.
• You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at the University of Oslo. Admission to the PhD programme at the Faculty of Mathematics and Natural Sciences (UiO) requires an average grade of C or better in the bachelor’s degree, an average grade of B or better in the master’s degree, and a grade of B or better on the master’s thesis, according to the Norwegian grading scale, or equivalent qualifications.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.
All candidates and projects will have to undergo a check versus national export, sanctions and security regulations. Candidates may be excluded based on these checks. Primary checkpoints are the Export Control regulation, the Sanctions regulation, and the national security regulation.

Project-specific profile

• A master's degree (or equivalent) in bioinformatics, computational biology, computer science, data science, or a related quantitative or life-science field with strong computational skills.
• Strong programming skills (preferably with proficiency in R) and experience analyzing large-scale sequencing or genomics datasets.
• Desirable: experience with ribosome profiling (Ribo-seq) or other next-generation sequencing data, machine learning, data aggregation and curation at scale, and an interest in translation, microproteins, and the dark proteome.
• Applicants must have good oral and written communication skills in English and meet UiO’s English-language requirements for admission to the PhD programme.
• Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

What we offer

A full-time employment contract for 36 months as a salaried PhD Research Fellow, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. This is a paid employment contract, not a stipend or scholarship.

The indicative gross annual salary for this position is NOK 550 800 – 595 000, depending on competence and experience. This includes living and mobility allowances. A family allowance will be added if you have family obligations at the time of recruitment. This is what you will receive before income tax, social-security contributions and a statutory 2% contributions to the Norwegian Public Service Pension Fund are deducted.

Following appointment, the successful candidate may apply for an extension of up to one year, subject to undertaking 25% career-promoting work. Such work may include teaching, supervision and/or research assistance. Any extension will depend on the candidate’s qualifications and the department’s (UiO) needs at the time.

Beyond salary, you will receive:

• Supervision by a world-leading, interdisciplinary supervisory team.
• A secondment of around three months with an ORFeus industry partner (EIRNA Bio).
• A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.
• Enrollment in a doctoral program leading to a PhD.
• A pleasant and stimulating work environment
• Good welfare schemes
• Opportunity of up to 1.5 hours a week of exercise during working hours
• Career development programmes

Working at the University of Oslo

The University of Oslo (UiO) is Norway's oldest and largest university, with a strong research base in the life sciences, bioinformatics, and computational biology. UiO is an open and internationally oriented comprehensive university that strives to be an inclusive and diverse workplace and academic environment. You can read more about UiO’s work on equality, inclusion, and diversity at u io.no.

You will join the group of Prof. Eivind Valen (Department of Bioscience, UiO), which studies the regulation and diversity of translation, including initiation and termination mechanisms and the large-scale analysis of ribosome profiling data. You will work closely with the group of Prof. Pasha Baranov at University College Cork, who brings complementary ribosome profiling and computational biology expertise and co-develops the RiboSeq.Org platform. You will enroll as a PhD candidate at the University of Oslo under the "Regulations for the degree of Philosophiae Doctor (PhD) at the University of Oslo".