PhD Cell2Sample: charting cellular communities via spatial omics data

PhD Cell2Sample: charting cellular communities via spatial omics data

Do you want to develop new computational tools to reveal how cells organize and interact?

The project

Spatial transcriptomics combines gene expression data with spatial information, allowing us to see not only which genes are active in cells but also where those cells are located within a tissue. This powerful approach opens up new opportunities to understand how different cell types interact and function together in their native environment.

The Cell2Sample project aims to advance these insights by developing computational methods that explicitly account for spatial context (spatially aware). The project has two main objectives: first, to infer interactions between nearby cells; and second, to link these interactions to intracellular gene regulatory networks. To achieve this, you will develop and adapt machine learning and statistical approaches to model cell-cell communication based on cell-type-specific spatial gene expression, and reconstruct spatially informed gene regulatory networks.

The project offers a balanced focus on method development, implementation, and real-world applications in oncology and neuroscience. You will work with high-quality spatial omics datasets from ...

About your role

Your main role in this PhD position is to develop and implement spatially-aware methods to infer interactions between cells and intra-cellular gene regulatory networks. You will critically apply and test these methods to onco- and neurological data sets in collaboration with biomedical researchers. Results will be published in both methodological and biomedical journals.

Finally, you are expected to play an active role in the ADORE research community, in particular the Biocomputational Focus group. You’ll work in close collaboration with another PhD student in the Cell2Sample project, who will work on multi-omics cell type deconvolution methods.

About you

• You hold an MSc in Bioinformatics, AI, Machine Learning or a closely related discipline;
• You have a strong quantitative background, enabling the development of new computational methods;
• You have a strong interest in biomedical applications and life sciences in general;
• You have strong programming skills, preferably in Python and R;
• You are able to explain complex ideas to non-specialists;
• You have good communication skills in English, both written and spoken;
• You are self-disciplined and have a collaborative mindset.

Our offer

• A flying start to your career in scientific research.
• Plenty of room for your drive to shape tomorrow's healthcare.
• Working on large-scale and in-house research, with motivated colleagues from all over the world.
• You will be employed by Amsterdam UMC Research BV.
• A contract for 12 months, with the intention to extend for a total of 4 years. The Guideline PhD contract applies to this vacancy.
• Salary scale OIO: € 3.017 to € 3.824 gross based on full-time employment (depending on education and experience) and a year-end bonus of 8.3%. From July 1st, 2025, there will be a salary increase of 3%.
• Holiday hours: 190,4 per year for fulltime and a possibility to save additional hours.
• Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
• For >7 km each way, 100% reimbursement for public transport travel costs and, for private transport, €0.18 per km up to a maximum of 40 km each way.
• Do you prefer walking or cycling? Take advantage of our good bike scheme. Moreover, you will receive a reimbursement of €0.18 per km.

About your workplace

At Amsterdam UMC you will join the Bioinformatics Lab of the Department of Epidemiology and Data Science. Our research focuses on integrating single-cell and spatial omics data analysis with computational modelling to better understand complex biological systems. We strongly advocate reproducible research, as demonstrated in our ENCORE project.

You will also be part of the ADORE Biocomputational Focus group, which unites Amsterdam UMC biocomputational researchers who develop and apply computational methods relevant to onco- and neurological applications.

Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided.

Amsterdam UMC has an open culture. This means that we hope that everyone feels welcome in our organization and that we strive to offer equal opportunities to everyone. We therefore cordially invite all interested parties to respond to this vacancy.

We have two PhD positions available within the Cell2Sample project. Please apply for the position you are most interested in, but feel free to apply to both positions if you wish. Suitable candidates may be considered for both roles.

During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely.

If you have any questions about this position, please feel free to contact dr. ir. Perry Moerland, via p.d.moerland@amsterdamumc.nl.

For more information about the application procedure, please contact Chey Edwards, Recruitment advisor, via c.i.edwards@amsterdamumc.nl.

A reference check, screening and hiring test may be part of the procedure. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.