PhD Position in Computational Modelling of Cellular Neighbourhoods in Spatial Multi-Omics (SPACE-MEL DC11) KU Leuven in Belgium

Doctoral Candidate / PhD Position in the SPACE-MEL MSCA Doctoral Network (DC11)

Aspect Analytics NV is recruiting a fully funded Doctoral Candidate for a 36-month industrial PhD in the Horizon Europe Marie Skłodowska-Curie Doctoral Network SPACE-MEL. The project is based in Belgium and leads to enrolment in a doctoral programme at KU Leuven. The research is centred on computational modelling of cellular neighbourhoods in spatial multi-omics, with melanoma as the main disease context.

The DC11 project will develop new computational frameworks to analyse cellular neighbourhoods, tissue regions, and spatial interactions from integrated spatial and single-cell multi-omics data. The work builds on Aspect Analytics’ existing tools and the Weave® platform, with a strong focus on spatial data integration, scalable pipelines, clustering, embedding, interpretation, and multimodal analysis. The successful candidate will contribute to novel methods for spatial biology while applying them to melanoma datasets generated within SPACE-MEL, including MuM and ESM.

The fellow will be based at Aspect Analytics in Genk, Belgium, a life sciences company specialising in cloud-based software and bioinformatics services for spatial multi-omics. The environment includes access to GPU-based computing, expertise in spatial co-registration and data integration, and support for image analysis, digital pathology annotation, and high-resolution microscopy visualisation. The position offers joint industrial and academic supervision and a personalised career development plan.

Supervision is shared across several experts: Dr Marc Claesen (main supervisor, Aspect Analytics), Prof. Bernd Bodenmiller (academic co-supervisor, University of Zurich), Dr Maria Mantas (industrial co-supervisor, Aspect Analytics), and Dr Alejandro Sifrim (KU Leuven secondment supervisor). Planned secondments include six months at the University of Zurich for training in spatial proteomics, tumour microenvironment analysis, and cross-modal integration, and three months at KU Leuven focusing on multimodal embeddings, cross-modal alignment, and interpretability.

The position is fully funded under SPACE-MEL and includes a full-time 36-month contract, a contractual gross yearly salary of €46,147 for candidates with no qualifying family, a mobility allowance of €2,556 per year, and coverage for eligible research, training, networking, conference, and secondment costs. The applicable MSCA family allowance may also be included where eligible.

Applicants must hold, or expect to hold before the starting date, a relevant master’s degree or equivalent doctoral-entry qualification in a quantitative field such as bioinformatics, computational biology, computer science, data science, artificial intelligence, biostatistics, biomedical engineering, systems biology, or applied mathematics. Strong programming skills, a quantitative background, experience with high-dimensional biological or biomedical data, and good English communication skills are required. Candidates should also be willing to work across computational research, spatial biology, cancer research, and industrial software development, and must be able to complete the planned secondments and network activities.

The MSCA mobility rules apply: applicants must not already hold a doctoral degree and must not have spent more than 12 months in Belgium during the 36 months immediately before recruitment, subject to standard MSCA exceptions. Applications are accepted in English and should include a CV, motivation statement, exam marks, degree certificate, referee contacts, and optional links to publications, repositories, or portfolios.

Deadline: 20 November 2026 at 17:00 (Europe/Brussels).