PhD Position in Computational Modelling of Cellular Neighbourhoods in Spatial Multi-Omics
Develop cutting-edge computational methods to analyse spatial multi-omics data for melanoma research within a Horizon Europe MSCA Doctoral Network.
Best for:Best for computational biologists, bioinformaticians, or data scientists with expertise in machine learning, spatial omics, and multi-omics data integration who are passionate about translational biomedical research.
Overview
This fully funded PhD position at Aspect Analytics (Belgium) focuses on advancing computational frameworks to model and interpret multicellular environments using spatial and single-cell multi-omics data. The successful candidate will work on developing novel embedding, clustering, and interpretation methods for spatial biology, with a primary application to melanoma datasets. The role combines industrial research at Aspect Analytics with academic supervision from KU Leuven, including mandatory secondments at the University of Zurich and KU Leuven for specialised training in spatial proteomics, tumour microenvironment analysis, and advanced computational methods. The position offers access to state-of-the-art platforms like Weave®, GPU resources, and a collaborative network (SPACE-MEL) dedicated to spatial multi-omics research in precision medicine.
What you'll do
- Develop computational methods to model and analyse cellular neighbourhoods using integrated spatial and single-cell multi-omics data.
- Expand existing CNs (cellular neighbourhoods) analysis tools with new embedding, clustering, and interpretation techniques for spatial biology data.
- Apply developed methods to melanoma datasets (MuM and ESM) generated within the SPACE-MEL project.
- Work on spatial data integration, CNs modelling, and scalable analysis pipelines using the Weave® platform.
- Conduct research at Aspect Analytics while completing mandatory secondments at the University of Zurich (6 months) and KU Leuven (3 months).
- Collaborate with academic and industrial partners to advance spatial multi-omics research and precision medicine.
- Present research findings at international conferences and contribute to publications, software development, and the doctoral dissertation.
Requirements
Degree required: Master's degree or equivalent in Computer Science, Bioinformatics, Computational Biology, or a related quantitative field
Degree offered: PhD
Language: English; proficiency sufficient for academic research and collaboration
Instruction: English
- Strong programming skills (e.g., Python, R) for bioinformatics and data analysis
- Experience with machine learning and computational modelling techniques
- Familiarity with spatial omics data (e.g., spatial transcriptomics, multiplexed immunofluorescence)
- Knowledge of multi-omics data integration and analysis pipelines
- Ability to work with high-resolution microscopy images and digital pathology data
- Eligible for MSCA Doctoral Networks (EU or associated country nationality or residency requirements apply)
- No prior PhD degree required (applicant must not have been awarded a doctoral degree)
- Mobility rule: applicant must not have resided or carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3 years prior to the recruitment date
Funding & terms
How to apply
Deadline: 2026-11-20 (Europe/Brussels)
Applicants must send their CV, cover letter, and academic transcripts via email to maria.mantas@aspect-analytics.com. The cover letter should outline their motivation, relevant skills, and how they align with the project objectives. Additional documents may be requested during the evaluation process.
- Curriculum Vitae (CV)
- Cover letter
- Academic transcripts (BSc and MSc)
- Proof of English proficiency (if applicable)
Contact
Maria Mantas· Industrial Co-Supervisor
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