Computational modelling of cellular neighbourhoods in spatial multi-omics

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. Where to apply E-mail: maria.mantas@aspect-analytics.com Requirements Research Field: Biological sciences » Other Education Level: Master Degree or equivalent Research Field: Computer science » Programming Education Level: Master Degree or equivalent Skills/Qualifications Essential qualifications A master's degree, or equivalent qualification granting doctoral access, in bioinformatics, computational biology, computer science, data science, artificial intelligence, biostatistics, biomedical engineering, systems biology, applied mathematics or a related quantitative field. Candidates completing the degree before the starting date may apply. A strong quantitative, computational or bioinformatics foundation and programming experience in Python or a comparable scientific language. Experience analysing high-dimensional biological or biomedical data and an understanding of statistics, machine learning or data-analysis methodology. Ability to formulate research questions and develop reproducible, well-documented computational solutions. Proficiency in the English language is required, as well as good communication skills, both oral and written. Successful candidates will need to provide an English test (e.g. IELTS, TOEFL, Cambridge English). You may be exempt if you are a national of a majority native-English speaking country, or have qualifications / degree that has been taught and assessed in English. The supervisor may also confirm that a candidate has the required level of English. Motivation to work at the intersection of computational research, spatial biology, cancer research and industrial software development. Ability to work independently and collaboratively and to participate in international secondments and network activities. Desirable experience Spatial or single-cell omics and multimodal data integration. Image analysis, digital pathology, multiplex tissue imaging or spatial statistics. Representation learning, clustering, graph-based methods, deep learning or interpretable machine learning. High-performance and distributed computing and/or technologies like Docker. Cancer biology, tumour immunology or melanoma research. Version control, software engineering or interactive visualisation. Additional Information Benefits Employment conditions Aspect Analytics will employ the successful candidate under a full-time, 36-month contract governed by Belgian employment, taxation and social-security legislation. Eligible research, training, networking, conference and secondment costs will be supported under SPACE-MEL and organisational rules. Contractual gross yearly salary: €46.147 (for candidates with no qualifying family) Mobility allowance treatment: €2.556 per year Additional Aspect Analytics benefits: Meal vouchers Group insurance Health insurance Net salary will depend on Belgian taxation, social-security contributions and personal circumstances. The applicable MSCA family allowance may be included where eligibility conditions are met. Eligibility criteria MSCA eligibility requirements Applicants must meet the applicable Marie Sklodowska-Curie Doctoral Network requirements on the recruitment date: They must not hold a doctoral degree. Candidates who have defended a doctoral thesis but have not yet formally received the degree are not eligible. They must not have resided or carried out their main activity in Belgium for more than 12 months during the 36 months immediately before recruitment. Applicable MSCA exceptions include compulsory national service, holidays and time spent seeking refugee status under the Geneva Convention. Applicants of any nationality may apply, but the selected candidate must be eligible for admission to KU Leuven's doctoral programme and have sufficient English proficiency for research and doctoral training. The candidate must work primarily in Genk and be available for the planned secondments and network activities. Required documents Curriculum vitae covering education, relevant experience, computational skills and applicable research outputs. A motivation statement of approximately one page explaining the applicant's interest in DC11, relevant experience and motivation for an industrial, international doctorate. A certificate of University examinations taken (with marks). A final degree certificate translated into English. If, at the time of application, candidates should not be yet in possession of a degree certificate, they can submit it at the time of the examination. However, if successful, the candidate will be required to provide a translated and legalised certificate as proof of eligibility for doctoral admission. Contact information of up to two contact persons for reference letters. Optional links to publications, software repositories, a thesis or project portfolio. Do not submit confidential information or proprietary source code. Selection process How to apply Applications must be submitted in English through the designated recruitment route by the stated deadline. Application link or email: maria.mantas@aspect-analytics.com Application deadline: November 20, 2026 at 5PM CET Selection process Applications will be checked for completeness, doctoral-programme eligibility and compliance with the MSCA doctoral-degree and mobility rules. Eligible candidates will be assessed on academic preparation, computational experience, research potential, motivation and alignment with DC11. Shortlisted candidates will be invited to an online or in-person interview. Appointment will be conditional on verification of qualifications, mobility history, MSCA eligibility, KU Leuven admission and Aspect Analytics' standard employment procedures. Equal opportunities and data protection Aspect Analytics and SPACE-MEL are committed to equal opportunity, inclusion and fair recruitment. Applications are welcomed from qualified candidates regardless of characteristics protected by applicable law. Application data will be processed only for recruitment, eligibility assessment and related administration, in accordance with applicable data-protection law and Aspect Analytics' privacy policy. Additional comments Enquiries For general information about SPACE-MEL, visit the project website ( https://space-mel.eu/ ). For additional information on this project, please contact Dr. Maria Mantas ( maria.mantas@aspect-analytics.com ). Website for additional job details: https://www.aspect-analytics.com/ Work Location(s) Number of offers available: 1 Company/Institute: Aspect Analytics NV Country: Belgium City: Genk Postal Code: 3600 Street: C-mine 12 Contact State/Province: Genk City: Genk Website: https://www.aspect-analytics.com/ Street: C-mine 12 Postal Code: 3600