Salary: Funded for 3 years, The indicative gross salary for this position is €50,008 p.a. that includes mobility and family allowances (applicable only to researchers with family obligations) before taxes and social security contributions are deducted.

Applications are invited from individuals interested in enrolling in a PhD research programme as part of ORFeus.

About ORFeus.

ORFeus is a Marie Skłodowska-Curie Actions Doctoral Network (MSCA-DN) under Horizon Europe: 15 academic groups, 13 industry and research partners, and a panel of independent academic advisors, training 15 doctoral candidates across Europe. The network investigates the dark proteome, the proteins and peptides made from overlooked translated regions and what they mean for human disease, combining ribosome profiling and translatomics, proteogenomics, mass-spectrometry proteomics and immunopeptidomics, large-scale genomics, and machine learning to map novel translation products and test their potential as targets for diagnosis, immunotherapy, and drug development in cancer and beyond.

Each doctoral candidate runs an individual project within this shared program, with two academic supervisors, an industry or partner secondment supervisor, and an independent academic advisor, a secondment of around three months with a partner organization, and network-wide schools, workshops, and conferences.

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, and we are committed to equal opportunity and a balanced research workforce.

University College Cork

University College Cork (UCC) is a research-intensive university in Ireland, with strengths in bioinformatics, computational biology, and the biological sciences. UCC hosts a popular suite of data and computational resources for Ribosome Profiling Data Analysis under the umbrella of RiboSeq.Org. Several Schools (e.g. Biochemistry and Pharmacy) have several faculties with strong expertise in RNA Biology and development of RNA therapeutics.

You will join the group of Prof. Pasha Baranov, which develops computational methods for analyzing ribosome profiling data and modeling translation, including the Ribosome Decision Graph (RDG) framework that this project builds on. You will work closely with the group of Prof. Alexander van Oudenaarden at the Hubrecht Institute, who brings complementary expertise in single-cell analysis and translation dynamics. You will enroll as a PhD candidate at University College Cork Biochemistry Programme.

The position

Only a small part of the genome is annotated as protein-coding, yet genetic variants that fall outside these annotated regions can still change how nearby sequences are translated. How such variants alter regulatory translation, including where and how efficiently ribosomes begin translation, remains poorly understood, and interpreting non-coding genetic variation is an open problem at the interface of genetics and dark proteome research.

This project will adapt Ribosome Decision Graphs (RDGs) for genotype specificity, combining public resources (UK Biobank, gnomAD) with publicly available (RiboSeq.Org) and newly generated DepMap ribosome-profiling data to map how genetic variants affect translation initiation, reinitiation, and leaky scanning, and to identify cancer-relevant translation-altering SNPs. It sits within ORFeus Work Package 3, which investigates the roles of the uncharacterised proteome in cancer and immunology.

Methods and platforms: ribosome profiling (Ribo-seq) generation and analysis, including techniques such as TCP-seq, Ribosome Decision Graph (RDG) modeling adapted for genotype specificity; long-read RNA-seq for identifying cancer-specific isoforms; and analysis of human genetic variation using public resources (UK Biobank, gnomAD) and DepMap data, working through the RiboSeq.Org platform.

Secondment: you will spend around three months at Immagina Biotechnology (Trento, Italy), quantifying variant-driven translation changes using the company's translation measurement technologies. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Key duties, responsibilities and abilities (other than those already mentioned above)

• Adapt Ribosome Decision Graphs (RDGs) for genotype specificity, drawing on public data (UK Biobank, gnomAD, RiboSeq.Org) and newly generated DepMap ribosome-profiling data, and integrate isoform-level translation data from the project of another doctoral candidate (DC) in the network, here DC2.
• Map how genetic variants affect translation initiation, reinitiation, and leaky scanning, and work with DC3 to build an integrated map of translation diversity that links variant-triggered and naturally rare translation events.
• Identify a set of cancer-relevant translation-altering SNPs and advance tools for interpreting non-coding variants in patient-derived datasets, sharing DepMap data with DC8 for evolutionary analysis and informing DC13's work on codon substitutions.
• Collaborate across the ORFeus network, contribute datasets and analytical tools to the shared platform, and produce the project's scientific report.

Required qualifications

• A recent postgraduate degree (BSc, MSc) in molecular biology/genetics/evolution, bioinformatics, biotechnology or a related discipline.
• Applicants whose first language is not English must provide an English proficiency certificate. Please check the minimum requirements at: https://www.ucc.ie/en/study/comparison/english/.

• 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 Ireland 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.
• A master's degree (or equivalent) in bioinformatics, computational biology, genetics, computer science, data science, or a related quantitative or life-science field with strong computational skills.
• Strong programming skills (for example Python or R) and hands-on experience working with large genomic or sequencing datasets.
• Desirable: experience with ribosome profiling or RNA-seq data, human genetic variation data (for example variant calling or population-genomics resources such as gnomAD), and an interest in improving fundamental understanding of genomic information.
• Good written and spoken English.
• Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

Funding Details and Further information

A full-time employment contract for 36 months as a salaried researcher, 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 salary has a living allowance and a mobility allowance, plus a family allowance if you have family obligations when you are recruited. The indicative gross salary for this position is €50,008 p.a. It includes mobility allowances and family allowances (applicable only to researchers with family obligations). This is €4,167.34 per month. This is what you are paid before income tax and your own social-security contributions are deducted.

Beyond salary, you will receive:

Supervision by a world-leading, interdisciplinary supervisory team.

A secondment of around three months with an ORFeus industry partner (Immagina Biotechnology).

A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.

Enrollment in a doctoral program leading to a PhD.

The MSCA employment contract covers 36 months of full-time, fully funded employment. In line with the host institution's doctoral policy, the host funds completion of the doctorate beyond the 36-month MSCA contract as continued employment at the standard national doctoral salary scale; terms confirmed at offer stage.

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.