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

Organisation/Company KU LEUVEN Research Field Medical sciences » Medicine Biological sciences » Biology Computer science » 3 D modelling Computer science » Informatics Computer science » Programming Researcher Profile First Stage Researcher (R1) Final date to receive applications 23 Aug 2026 - 23:59 (UTC) Country Belgium Type of Contract Temporary Job Status Full-time Offer Starting Date 1 Oct 2026 Is the job funded through the EU Research Framework Programme?

Horizon Europe - MSCA Reference Number BAP
- Marie Curie Grant Agreement Number  Is the Job related to staff position within a Research Infrastructure? No

Host institution:
Katholieke Universiteit Leuven (KUL
-a ) , Department of Imaging and Pathology , and Spatial Proteomics Unit within the KU Leuven Institute for Single Cell Omics , Leuven, Belgium

DC1 will develop 3D spatial multi-omics workflows to translate established 2D melanoma findings into three-dimensional tissue structures. Building on a proof-of-concept 3D multiplexed protein/RNA experiment from KU Leuven and Alpen G low Biosciences, the project pursues three integrated objectives: i ) optimise 3D multiplex immunohistochemistry and RNA-based spatial profiling in thick tissue samples; ii) develop disease-specific 3D RNA/protein panels with expanded marker coverage;

iii) establish an automated pipeline for integrated 2D-to-3D analysis.

At KU Leuven, the candidate will adapt 2D multiplex immunohistochemistry workflows to 3D tissues by addressing antibody penetration, signal stripping, optical aberrations and out-of-focus signals. The project will implement cleavable antibody tags based on disulfide-linked fluorophores and combine them with RNA-scope probes for simultaneous protein and transcriptional target detection. During secondments at Alpen G low Biosciences and Stellaromics , the candidate will receive training in advanced 3D tissue imaging, spatial transcriptomics and translatomics , and benchmark the newly developed workflow against state-of-the‑art industrial technologies.

Expected outcomes include an optimised 3D spatial multi-omics protocol, an analytical pipeline for 3D datasets, and validated translation of 2D melanoma insights into 3D tissue structures.

Eligibility conditions:

Master’s degree in Bioengineering , Biomedical Science s, Bioinformatics or related fields. Both wet and dry lab skills are required . The candidate should be able to program and perform computational analyses and able or willing to learn to carry out experiments in the wet lab .

Candidates are doctoral candidates (DCs) ( i.e not already in possession of a doctoral degree at the date of the recruitment. Researchers who have successfully defended their PhD thesis but not yet received their degree are not considered eligible.

DCs can be of any nationality

Mobility rule: researchers must not have resided or carried out their main activity in the country of the recruiting beneficiary for more than 12 months in the 36 months immediately before their recruitment date . Compulsory national service, short stays such as holidays and time spent by the researcher as part of a procedure for obtaining refugee status under the Geneva Convention are not considered.

Required skills:

Hands‑on expertise in wet lab , organoids, live tissue, imaging/ microscopy and bioinformatics analyses including molecular and/or single‑cell and/or spatial‑omics analyses.

Experience using Python programming language. Experience with the scverse tools is a plus.

Interest in research on spatial omics , data analysis, pathology and melanoma/oncology

Hands‑on expertise in (spatial) lipidomics , spatial multi‑omics and data analysis tools is a plus

Good command of spoken and written English

Ambitious, hard‑working and accurate

Above average motivation, teamwork and in dependency

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…