Doctoral Candidate position HORIZON-MSCA-DoctoralNetwork SPACE-MEL 3D multiomics

Doctoral Candidate Position HORIZON-MSCA-DoctoralNetwork SPACE-MEL 3D multiomics

KU Leuven, an autonomous university founded in 1425, hosts the PhD fellow in the Single‑Cell Spatial Proteomics Unit within the KU Leuven Institute for Single Cell Omics, under the supervision of Prof. Francesca Bosisio. The laboratory specializes in clinical dermatopathology, melanoma research, and spatial omics technology development, with a focus on tumour microenvironment organisation and spatial biomarkers in melanoma.

The host laboratory offers access to advanced pathology and spatial biology infrastructure, including BondRx, Zeiss Axioscan, AKOYA PhenoCycler, Lunaphore COMET, and DISSCOvery software for high‑throughput image analysis. Through the LISCO environment, the candidate also benefits from platforms for single‑cell multi‑omics, spatial transcriptomics, sequencing, high‑end microscopy, and large‑scale data processing.

Project

Develop 3D spatial multi‑omics workflows to translate established 2D melanoma findings into three‑dimensional tissue structures. The objectives are:

• Optimize 3D multiplex immunohistochemistry and RNA‑based spatial profiling in thick tissue samples.
• Develop disease‑specific 3D RNA/protein panels with expanded marker coverage.
• Establish an automated pipeline for integrated 2D‑to‑3D analysis.

Key tasks include adapting 2D workflows to 3D tissues, addressing antibody penetration and optical issues, implementing cleavable antibody tags, and integrating RNA‑scope probes for simultaneous protein and transcriptional target detection.

Secondments: 4 months at AlpenGlow Biosciences Inc., United States (supervisor: Dr. Alexandra Alvarsson) and 3 months at Stellaromics Inc., United States (supervisor: Dr. Ye Fu). These visits provide training in advanced 3D tissue imaging, spatial transcriptomics, and translatomics.

Responsibilities

As a doctoral candidate, you will:

• Design and optimize 3D spatial multi‑omics protocols for melanoma tissues.
• Perform wet‑lab experiments involving organoids, live tissue, imaging, and microscopy.
• Analyze data using Python and bioinformatics pipelines; familiarity with scverse tools is a plus.
• Collaborate with industry partners during secondments and benchmark developed workflows against commercial technologies.
• Document findings and contribute to the automated analytical pipeline for 3D datasets.

Qualifications

• Master’s degree in Bioengineering, Biomedical Sciences, Bioinformatics, or related fields.
• Hands‑on expertise in wet‑lab techniques, organoids, live tissue, imaging/microscopy, and bioinformatics analyses.
• Experience with Python programming; knowledge of scverse tools is a plus.
• Interest in spatial omics, data analysis, pathology, and melanoma/oncology.
• Proficiency in spoken and written English; an English proficiency certificate may be required.
• Ambitious, hard‑working, accurate, and able to work autonomously within a team.

Benefits

The position offers a 36‑month scholarship covering living costs. For Belgium, the scholarship is approximately €3,120.64 per month (tax‑free) for single candidates with no dependents. The amount adjusts for partners. All training activities, including travel and accommodation to attend network‑organized events, are covered. Dedicated workspace and access to research facilities are provided, and bench/consumables costs are covered by the institution.

Equal Opportunity Statement

KU Leuven strives for an inclusive, respectful, and socially safe environment. We embrace diversity among individuals and groups as an asset. We promote equal opportunity and do not accept discrimination on the basis of gender identity, sexual orientation, age, ethnicity, religion, neurodivergence, disability, or socioeconomic status.

Contact

For more information, please contact Mrs. Nancy De Sutter at nancy.desutter@kuleuven.be.