Horizon Europe MSCA Doctoral Network PhD scholarship in Computational Proteomics and Machine Learning - DTU Biosustain

Jobbeskrivelse

If you are curious and proactive scientist with expertise and interest in computational biology and data science, and you are looking to make a difference working on projects that will have impact on world level challenges, this PhD position is for you! The project is supervised by Alberto Santos Delgado at the Technical University of Denmark part (DTU) and co-supervised by Prof. Julios Saez-Rodriguez at the European Bioinformatics Institute (EBI) as part of ProtAIomics, a Horizon Europe MSCA Doctoral Network. In this project, we will design a federated knowledge graph framework that facilitates the querying, consolidation, analysis, and interpretation of distributed proteomics-focused clinical knowledge graphs. To achieve this, we will employ machine learning techniques to develop local graph representation models, which will be aggregated globally to enhance their predictive power and translational relevance, all while maintaining strict data privacy standards.

Responsibilities and qualifications

As a PhD student embarking on a three-year journey in proteomics-focused data science and machine learning, you will learn leadership, project management, mentoring, and scientific communication. Here's a snapshot of the key responsibilities you will hold:

• Research Project Management: Strategically drive the project from conception through to publication, ensuring adherence to scientific and funding objectives.
• Student Supervision: Guide and support students' research, promoting their academic growth and contributions to the project's success.
• Scientific Dissemination: Actively publish and present research findings, enhancing the project's visibility and impact in the scientific community.

Requirements

• You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.
• Proven ability to bridge computational methods (e.g., machine learning) with biological/biomedical domains (e.g., biomarker discovery).
• Experience developing knowledge graphs or integrating heterogeneous omics data.
• Familiarity with ontology-based modelling for integrating heterogeneous data.
• Knowledge of Graph Neural Networks (GNNs) and graph embedding techniques (e.g., using PyTorch Geometric).
• Experience working with MS-based proteomics data and/or other omics data types.
• Familiarity with data preprocessing pipelines for high-throughput omics data (e.g., Nextflow).
• Strong programming skills in Python (Data and Machine Learning stacks).
• Experience with version control and cloud/HPC computing platforms.
• Familiarity with containerization (Docker).
• Ability to collaborate with multidisciplinary teams (e.g., biologists, clinicians, software engineers) and to communicate complex technical concepts to non-experts.
• Previous experience with federated machine learning is highly valuable, though not strictly required.

We offer

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms

The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. Furthermore, the PhD salary will be based on the Marie S. Curie compensation scheme conditions and according to the grant agreement. The period of employment is 3 years. Based on seniority the candidate will receive a minimum of DKK 29.701,83 (base salary) and 1551,00 (PhD supplement). In addition, DTU will also pay pension consisting of 18,07%. Finally, it is possible to apply for family allowance.

Application procedure

Your complete online application must be submitted no later than 30 November 2025 (23:59 Danish time) through the DTU system. Additionally, to be eligible, you must also submit your application via the ProtAIomics portal, following the application instructions provided. Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Research Experience (~ 500 words)
• Scientific Interests (~ 500 words)
• Contact details of 2 referees

You may apply prior to obtaining your master's degree but cannot begin before having received it. Applications received after the deadline will not be considered.