Host laboratory:
The PhD fellow will be based at KU Leuven, in the Single-Cell Spatial Proteomics Unit within the KU Leuven Institute for Single Cell Omics, under the supervision of Prof. Francesca Bosisio. The group combines clinical dermatopathology, melanoma research and spatial omics technology development, with a particular focus on tumour microenvironment organisation, immune-tumour interactions and spatial biomarkers in melanoma. KU Leuven’s LISCO environment brings together more than 65 groups across KU Leuven, University Hospitals Leuven and VIB, providing a strong interdisciplinary setting for single-cell and spatial omics research.
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 LISCO, the candidate will also benefit from platforms for single-cell multi-omics, spatial transcriptomics, sequencing, high-end microscopy and large-scale data processing. This environment provides the experimental, computational and translational framework required to develop robust 3D spatial multi-omics workflows for melanoma precision medicine.
Secondments: This project is carried out in strong collaboration with the following groups, and visits to their laboratories are expected during the project. A willingness to travel and spend time abroad is therefore essential:
4 months at AlpenGlow Biosciences Inc., United States (supervisor: Dr. Alexandra Alvarsson)
3 months at Stellaromics Inc., United States (supervisor: Dr. Ye Fu)
Website unit
Project
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
Supervisor: Prof. Francesca Bosisio, Prof. Asier Antoranz Martinez
Dr. Alexandra Alvarsson, AlpenGlow Biosciences Inc., United States (Industry)
Dr. Ye Fu, Stellaromics Inc., United States (Industry)
PhD project description at KU Leuven:
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 AlpenGlow 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 AlpenGlow 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.
Profile
-
Master’s degree in Bioengineering, Biomedical Sciences, 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.
-
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.
-
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.
-
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.
Offer
One PhD position is available. The project has a duration of 36-months.
The DC will receive a 36-month scholarship to cover her/his living costs. The gross amount of the doctoral scholarship is based on a living allowance that is dependent on a country correction coefficient which takes into account the cost of living in the country of the recruiting institution. For Belgium, the gross amount of the doctoral scholarship (tax-free) will be approximately €3.120,64 per month if the DC is single with no dependent family members. It will be higher if the DC has a registered partner without income and/or dependent child(ren); it will be lower if the DC has a registered partner with income.
The cost of all training activities, including all expenses related to travel and accommodation to attend annual meetings and other network organized events will be paid by the network through the Horizon Europe MSCA-DN grant. DCs will have access to a dedicated workspace and to research facilities. Bench/consumables costs to execute the research project will be covered by the institutions.
Interested?
Interested candidates should apply by submitting the required documents via the KU Leuven platform. Please note that only applications submitted through this online system will be considered. Applications submitted via email will not be taken in consideration. Ensure that all requested documents are included, as incomplete applications will not be reviewed.
All applications will have to be written in English and will be checked for eligibility. Incomplete applications will not be considered.
Applications must be submitted by before 23rd August at 17:00 Central European time. All data provided by the applicants are processed according to GDPR regulations and will be used solely for the purpose of the selection of the doctoral candidates.
-
Detailed curriculum vitae, including personal information, studies, list of publications, participation in research projects, extracurricular training, mobility, other qualifications or relevant skills.
-
Certified copies of official Academic Transcripts relating to all academic courses taken to earn every degree (bachelor/master or equivalent), translated into English, and correspondent grade point average.
-
English Proficiency Certificate (minimum scores: TOEFL 79, IELTS overall 6.5, Cambridge English CAE or CPE, ITACE C1 or ITACE C2). Applicants who have obtained a degree in a programme taught in English in Australia, English-speaking Canada, Ireland, New Zealand, the United Kingdom, or the United States of America are exempt from this requirement. If the certificate is not available at the time of application, it may be submitted later; however, it will be required from the selected candidate.
SPACE-MEL will adopt the Charter for Researchers and Code of Conduct promoting an inclusive, merit-based, transparent and unbiased recruitment and attractive working and employment conditions. A two-step procedure for applicants’ selection will be followed:
1. After an eligibility check, an initial selection will be made based on the submitted documents and the abovementioned criteria.
2. Afterwards, promising candidates will be contacted by email after the deadline for application has been closed. It is the intention that the selected DC starts in October 2026.
KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace diversity among individuals and groups as an asset. Open dialogue and differences in perspective are essential for an ambitious research and educational environment. In our commitment to equal opportunity, we recognize the consequences of historical inequalities. We do not accept any form of discrimination based on, but not limited to, gender identity and expression, sexual orientation, age, ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence, employment disability, health, or socioeconomic status. For questions about accessibility or support offered, we are happy to assist you at [email protected]
For more information please contact Mrs. Nancy De Sutter, mail: [email protected].
KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace diversity among individuals and groups as an asset. Open dialogue and differences in perspective are essential for an ambitious research and educational environment. In our commitment to equal opportunity, we recognize the consequences of historical inequalities. We do not accept any form of discrimination based on, but not limited to, gender identity and expression, sexual orientation, age, ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence, employment disability, health, or socioeconomic status. For questions about accessibility or support offered, we are happy to assist you at this email address.
