Project 1: AI-driven model for cross-species smORF prediction and classification (Owen Rackham)

ORFeus doctoral network; Southampton; On-site; GBP 44,000 - 47,000; Full time

Benefits offered by this job

High-level supervision

Secondment at EMBL-EBI

Structured training

PhD candidature

Comprehensive benefits

Job summary

ORFeus doctoral network at the University of Southampton seeks a PhD candidate to build an AI foundation model predicting smORF translation and codon-level translation behavior. The project combines sequence embeddings with multi-omics data and includes a three-month secondment at EMBL-EBI, with access to a supported doctoral program and training.

Applicants should have strong computational skills and interest in dark proteome research.

Qualifications

• Relevant degree in bioinformatics/computational biology or a related field.
• Strong programming skills (Python) with ML/DL experience.
• Interest in dark proteome, microproteins and cross-disciplinary research.

Responsibilities

• Develop foundation model for translation prediction at codon-level using sequence embeddings.
• Integrate multi-omics data with embeddings and codon-substitution data.
• Collaborate across the ORFeus network and contribute to shared platforms (ORFeome/HuggingFace).
• Publish scientific reports and participate in secondments across partner organisations.

Skills

Python

Machine learning

Deep learning

Communication

Education

Bioinformatics or related degree

Tools

HuggingFace

Ribo-seq analysis

Mass spectrometry

Job description

The position

Only a fraction of the genome codes for the proteins in standard reference catalogues. Many small open reading frames (smORFs) scattered across the genome are, in fact, translated into microproteins that those catalogues miss, and distinguishing a genuinely translated smORF from background noise using sequence and experimental data remains an open computational problem at the heart of dark proteome research.

This project will build an AI foundation model that predicts which smORFs are translated and how translation behaves at the codon level, combining state-of-the-art sequence embeddings with cell-type information and ribosome-profiling data. It is the computational backbone of ORFeus Work Package 1 and a hub for the whole network: the model is trained and validated on experimental data from partner projects across the consortium and released as open tools. The work connects closely to partner projects on rare translation events, genetic variation, codon substitutions, isoform-level translation, and evolutionary analysis.

Main tasks

• Develop a foundation model that captures how mRNA sequence and cellular context determine translation at codon-level resolution, drawing on state-of-the-art sequence-embedding architectures.
• Integrate sequence-based predictions with multi-omics evidence from ribosome profiling and mass spectrometry, including genetic-variant data from the projects of other doctoral candidates (DCs) in the network, here DC3 and DC12, and codon-substitution data from DC13, and refine the model iteratively using isoform-level translation data from DC2.
• Deploy interactive visualisation tools for cross-species and cell-type-specific translation predictions, refined by experimental validation feedback from across the network.
• Collaborate across the ORFeus network, contribute models and tools to the shared ORFeome platform and to HuggingFace (or similar), and produce the project's scientific report.

Methods and platforms: machine learning and deep learning for genomics (sequence-embedding and foundation-model architectures), ribosome profiling (Ribo-seq) data analysis, integration of mass-spectrometry proteomics and other multi-omics data, and interactive data visualisation, working with public and consortium datasets via the ORFeome platform and HuggingFace.

Secondment: you will spend around three months at EMBL-EBI (Hinxton, near Cambridge, UK), integrating large-scale mass-spectrometry datasets for cross-species applications of the model. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the experimental validation of the model.

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 the United Kingdom 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 enrol in a doctorate, and you can enrol in the doctoral program at the University of Southampton.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

Project-specific profile

• A relevant degree in bioinformatics, computational biology, computer science, data science, machine learning, or a related quantitative or life-science field with strong computational skills.
• Strong programming skills (for example Python) and hands-on experience with machine learning or deep learning.
• Desirable: experience with genomics or sequencing data (for example ribosome profiling or next-generation sequencing), sequence models and embeddings (including large language models), mass spectrometry or multi-omics data, and an interest in microproteins and the dark proteome.
• Good written and spoken English.
• 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 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 at the time of recruitment. The indicative gross salary for this position is £43,994.09 per year (including a mobility allowance), increasing to £47,279.86 per year (including a family allowance, if eligible). This is what you are paid before income tax, and your own social security contributions are deducted. This figure is subject to regular review, as this post is funded in Euros and uses a forecast exchange rate.

Beyond salary, you will receive:

• Supervision by a world-leading, interdisciplinary supervisory team.
• A secondment of around three months with an ORFeus partner organisation (EMBL-EBI).
• A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.
• Enrolment in a doctoral program leading to a PhD.
• A competitive set of benefits according defined by University policy

The MSCA employment contract covers 36 months of full-time, fully funded employment.

Working at the University of Southampton

The University of Southampton is a research-intensive university in the United Kingdom, with strong programs in computational biology, artificial intelligence, and biomedical data science. The University provides a collaborative, interdisciplinary research environment, supported by advanced computing facilities and specialist expertise across computational biology, artificial intelligence, and biomedical data science. Its attractive, self-contained campus offers a welcoming and vibrant setting for study and research, with excellent facilities, green spaces, and a strong academic community.

You will join the group of Prof. Owen Rackham, which develops machine-learning and computational methods for ‘omic data, including the prediction of non-canonical translation and the dark proteome. You will work closely with the group of Prof. Uwe Ohler at the Max Delbrück Centre (MDC) in Berlin, which brings complementary computational genomics expertise. You will enrol as a PhD candidate at the University of Southampton with the Faculty of Environment and Life Sciences