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

About this position

Title: Computational modelling of cellular neighbourhoods in spatial multi-omics

Aspect Analytics is recruiting a Doctoral Candidate for a fully funded, 36-month industrial PhD within SPACE-MEL, a Horizon Europe Marie Sklodowska-Curie Doctoral Network. The candidate will develop computational methods to model and interpret multicellular environments in spatial and single-cell multi-omics data, using melanoma as the principal disease context.

Supervision

Main supervisor: Dr Marc Claesen, Co-founder and Chief Technology Officer, Aspect Analytics, Belgium

Academic co-supervisor: Prof. Bernd Bodenmiller, University of Zurich, Switzerland

Industrial co-supervisor: Dr Maria Mantas, Aspect Analytics, Belgium

KU Leuven secondment supervisor: Dr Alejandro Sifrim, KU Leuven, Belgium

Degree-awarding institution: KU Leuven, Belgium

Research project

DC11 will develop a framework to analyse cellular neighbourhoods (CNs) using integrated spatial and single-cell multi-omics data. The project will build on Aspect Analytics’ existing CNs analysis tools and expand them with new embedding, clustering and interpretation methods for spatial biology data. It pursues two integrated objectives: i) develop computational methods to model cellular neighbourhoods, tissue regions and spatial interactions; ii) apply these methods to melanoma datasets generated within SPACE-MEL, including MuM and ESM.

At Aspect Analytics, the candidate will work on spatial data integration, CNs modelling and scalable analysis pipelines using the Weave® platform. During a first secondment in Dr. Bernd Bodenmiller’s lab at the University of Zurich, the candidate will receive training in spatial proteomics and tumour microenvironment analysis. A second secondment with Dr. Alejandro Sifrim at KU Leuven will focus on multimodal embeddings, cross-modal alignment and interpretability.

Expected outcomes include: (1) novel CN analysis methods; and (2) application of these methods to MuM and ESM melanoma datasets.

About Aspect Analytics and the research environment

The PhD fellow will be based at Aspect Analytics in Belgium, under the supervision of Dr. Marc Claesen. Aspect Analytics is a Belgian life sciences solutions provider specialising in cloud-based software and bioinformatics services for spatial multi-omics. The company has strong expertise in spatial co-registration, data integration and analysis across modalities including spatial transcriptomics, multiplexed immunofluorescence, mass spectrometry imaging and histology.

The host offers access to the Weave® platform for spatial omics data integration, image co-registration, metadata management, digital pathology annotation and visualisation of high-resolution microscopy images. The candidate will also benefit from dedicated GPU-based computing resources and expertise in developing machine-learning tools and end-to-end pipelines for spatial biology and translational biomedical research.

Planned secondments

University of Zurich, Switzerland - six months: Training with Prof. Bernd Bodenmiller in spatial and single-cell technologies, tumour heterogeneity, cross-modal integration and biological interpretation of spatial multi-omics data.

KU Leuven, Belgium - three months: Training with Dr Alejandro Sifrim in advanced computational methods, including deep learning and multimodal data-fusion approaches relevant to cellular-neighbourhood modelling.

Timing will be agreed through the career development plan. Applicants must be able to complete both secondments and travel for network activities.

About SPACE-MEL

SPACE-MEL - SPAtial single-CEll omics research training for MELanoma precision medicine - brings together academic institutions, clinical researchers, technology providers, bioinformatics and software companies. The network aims to advance three-dimensional spatial tissue analysis, integrate multiple omics technologies and develop the computational expertise required to interpret complex spatial datasets, using melanoma as its shared disease context. Further information: https://space-mel.eu/ .

What Aspect Analytics and SPACE-MEL offer

• A full-time, 36-month Aspect Analytics contract and enrolment in a doctoral programme at KU Leuven.
• Joint industrial and academic supervision with a personalised career development plan.
• Advanced scientific training in spatial biology, computational biology, multi-omics integration and machine learning.
• International research experience through secondments at the University of Zurich and KU Leuven.
• Participation in SPACE-MEL workshops, summer schools, network meetings and transferable-skills training.
• Opportunities to present internationally and contribute to publications, software and the doctoral dissertation.