Doctoral Candidate Position in Spatial Multi-Omics

KU Leuven; Belgique; On-site; EUR 32,000 - 38,000; Full time

Benefits offered by this job

36-month scholarship

Secondments to AtlasXomics

Secondments to Intelligent Biodata

Job summary

KU Leuven's Department of Human Genetics invites applications for a PhD fellowship in spatial single-cell omics. The project is part of SPACE-MEL, a Horizon Europe MSCA Doctoral Network, and will involve hands-on wet-lab and computational training in advanced single-cell technologies.

The doctoral candidate will develop workflows to generate spatial transcriptome, protein and epigenome readouts from the same tissue section, with secondments at AtlasXomics (USA) and Intelligent Biodata (Spain).

Qualifications

• Master’s degree in life sciences (bioengineering, biomedical sciences, genetics, genomics or equivalent). A publication record is a plus.
• Genuine interest and commitment to advancing scientific knowledge and innovation.
• Excellent communication and collaboration skills to work seamlessly across interdisciplinary teams.
• Experience in designing and troubleshooting experiments is a plus.
• Experience with or knowledge of single-cell and/or spatial (multi-)omics methods is a plus.
• Applicants must be doctoral candidates, i.e not already in possession of a doctoral degree.
• 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.

Responsibilities

• Develop a workflow to generate spatial transcriptome, protein and epigenome readouts from the same tissue section.
• Combine single-cell and spatial multi-omics with DBiT-seq-based spatial omics sequencing technology and COMET-based spatial proteomics.
• Collaborate with academia/industry partners during secondments at AtlasXomics and Intelligent Biodata to apply and evaluate workflows.

Skills

Excellent communication

Collaboration across teams

Designing experiments

Interest in single-cell/spatial omics

English proficiency

Education

Master’s degree in life sciences (bioengineering, biomedical sciences, genetics, genomics or equivalent)

Tools

DBiT-seq workflows

COMET-based spatial proteomics

Spatial omics data analysis

Job description

Organisation/Company KU Leuven Department Department of Human Genetics Research Field Technology » Biotechnology Engineering » Biomedical engineering Medical sciences » Cancer research Researcher Profile First Stage Researcher (R1) Positions PhD Positions Application Deadline 7 Dec 2026 - 23:59 (Europe/Brussels) Country Belgium Type of Contract Temporary Job Status Full-time Is the job funded through the EU Research Framework Programme? Horizon Europe - MSCA Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The PhD fellow will be based at KU Leuven under the supervision of Prof. Thierry Voet. Prof. Voet leads the KU Leuven Institute for Single Cell Omics, and his team develops wet-lab and computational methods for single-cell and spatial multi-omics, applying them to human development, ageing and disease. The institute brings together researchers from over 70 groups across KU Leuven, University Hospitals Leuven and VIB, providing a strong interdisciplinary environment for hands-on training in advanced single-cell and spatial technologies.
Co-supervisors of this doctorate will be Dr. Jon Pey, Intelligent Biodata, Spain (Academia); Dr. Jennifer Garbarino, AtlasXomics Inc., United States (Industry)

The PhD will be performed in context of SPACE-MEL, which is an EU-funded MSCA Doctoral Network advancing the next generation of spatial single-cell omics technologies for precision medicine. Bringing together leading European universities, technology providers, clinical partners and innovative companies, the programme will address key experimental and computational challenges currently limiting the clinical translation of spatial biology.

In this doctorate you will develop a workflow to generate spatial transcriptome, protein and epigenome readouts from the same tissue section. The project will combine single-cell and spatial multi-omics with DBiT-seq-based spatial omics sequencing technology and COMET-based spatial proteomics. This project is carried out in strong collaboration with academia/industry partners with visits to their laboratories expected: During a first secondment at AtlasXomics (3 months, United States; co-supervisor Dr. Jennifer Garbarino), the candidate will receive training in spatial epigenomic assay development and DBiT-seq-based workflow optimisation. The resulting workflow will be applied to melanoma samples to characterise tumour and immune cell organisation across multiple molecular layers. During a secondment at Intelligent Biodata (4 months, Spain; co-supervisor Dr. Jon Pey), the candidate will analyse the generated spatial multi-omics data using advanced computational and AI-supported integration approaches. Expected outcomes include optimised AXO DBiT-seq/COMET workflows and high-resolution spatial multi-omics maps of melanoma heterogeneity.

• Master’s degree in life sciences (bioengineering, biomedical sciences, genetics, genomics or equivalent). A publication record is a plus.
• Genuine interest and commitment to advancing scientific knowledge and innovation.
• Excellent communication and collaboration skills to work seamlessly across interdisciplinary teams.
• Experience in designing and troubleshooting experiments is a plus.
• Experience with or knowledge of single-cell and/or spatial (multi-)omics methods is a plus.
• Applicants must be doctoral candidates, i.e not already in possession of a doctoral degree.
• 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.

Specific Requirements

Required skills:

• In-depth knowledge of classical molecular biology techniques and expertise in good laboratory practice.
• Background in cell biology, biochemistry and microfluidics.
• Background in bioinformatics, hands-on expertise with single-cell and/or spatial omics is a plus.
• 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.

Languages ENGLISH Level Excellent

Additional Information

One PhD position is available. The project has a duration of 36-months.

The doctoral candidate (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.

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.