PhD Candidate in AI-driven 3D spheroid modelling for lymphoma research

Shape the future of cancer research with AI-Driven 3D spheroid model simulations!

We are seeking a motivated PhD candidate to join our interdisciplinary team bridging experimental in vitro work clinical data and AI-driven modelling for cancer research!

In this role you will bridge the gap between machine learning computational biology and haematological oncology. You do not need to arrive as an expert in modelling: what matters most is your passion for human physiology your curiosity about cancer cells behaviour and your willingness to develop new computational skills along the way.

This position is genuinely interdisciplinary: you will collaborate daily with experimental biologists and clinicians at Amsterdam UMC and computational biologist/AI experts at the University of Amsterdam (UvA). The heart of this project is to understand how tumor cells interact with their microenvironment how drugs disrupt those interactions and answering those questions by developing computational tools.

Develop AI-driven mechanistic computational models of Non-Hodgkin lymphomas such as mantle cell lymphoma (MCL) diffuse large B-cell lymphoma (DLBCL) and Richter syndrome.

You will develop and apply an innovative AI-driven 3D spheroid model to recreate the tumour microenvironment (TME) observed in vitro to enable more physiologically realistic drug testing and therapy prediction. As a PhD candidate you are expected to bring your own creativity to the challenge: How can image-based AI analysis reveal drug effects How can mechanistic computational models develo on spheroid morphology predict which treatment will work for which patient

You will be supported by experimental and clinical data using cutting-edge infrastructure including IncuCyte live-cell imaging single-cell RNAseq flow cytometry and an access to the Dutch National Supercomputing facility Snellius to perform all the computational work.

Your tasks and responsibilities include:

• Developing optimising and computationally characterising 3D primary spheroid models for MCL DLBCL and Richter syndrome using patient samples from in-house biobanks.
• Implementing and fine-tuning state-of-the-art AI image segmentation models for automated analysis of spheroid morphology and drug-induced structural changes.
• Building and refining the computational analysis pipeline: from image preprocessing and feature extraction (spheroid size cell cluster count area distribution inter-cluster distance) to cellular Potts model (CPM) simulations of spheroid growth and drug responses.
• Integrating multi-modal data streams such as live-cell imaging bulk and single-cell RNAseq and flow cytometry into a unified predictive framework.
• Mechanistically connect in vitro drug response profiles with clinical patient characteristics to develop and validate a patient-specific treatment outcome prediction models.
• Presenting your findings at national and international conferences and publishing in peer-reviewed journals.
• Contributing to teaching and the broader scientific activities of both research groups.
• Co-supervising Bachelor Master students and teaching assistance where appropriate.

We are looking for someone who is genuinely excited about computational biology and not afraid of challenges. When the data or model outputs do not make any sense you dig deeper! You communicate openly and thrive in a collaborative environment across different disciplines.

Your experience and profile(below are examples you dont need to use them):

• MSc degree in computational science (bio)medical sciences biomedical engineering or a related field with strong biological content.
• Interest in cancer biology and/or haematology.
• Affinity for quantitative data analysis. Programming experience in Python is an advantage but not a prerequisite. You are expected to develop these skills during the PhD.
• Excellent written and spoken English.
• Ability to work independently and as part of an interdisciplinary team.
• Willingness to engage across disciplinary boundaries from experimental work to segmentation algorithms with computer scientists.

It is a preference if you additionally have experience in performing interdisciplinary research together with another scientific specialty or prior experience in machine learning/image analysis in a biological context.

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years).The preferred starting date is 01 September should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

The gross monthly salary based on 38 hours per week and dependent on relevant experience ranges between 3059 to 3881 (scale P). This does not include 8% holiday allowance and 83% year-end allowance. The UFO profile PhD Candidate is applicable. A favourable tax agreement the 30% ruling may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Curious about our extensive secondary benefits package You can read more about it here.

At the University of Amsterdam (Computational Science Lab Informatic Institute) you will work under the supervision of Dr. Vivek Sheraton M and Dr. Alfons Hoekstra to develop AI imaging analysis pipelines and simulation models. You will also be embedded in an exciting collaboration with Amsterdam UMC with Dr. Eric Eldering and Dr. Marco Haselager who bring deep expertise in CLL biology cell death mechanisms tumour microenvironment interactions and therapeutic vulnerabilities. Their close ties with clinical haematologists ensure that research questions stay anchored to real patient needs.

TheFaculty of Science has a student body of around 8000 as well as 1800 members of staff working in education research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works be it elementary particles the birth of the universe or the functioning of the brain.

Want to know more about our organisation Read more aboutworking at the University of Amsterdam.

If you feel the profile fits you and you are interested in the job we look forward to receiving your application. You can apply online via the button. We accept applications until and including 30/07/2026.

Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• a list of publications;
• the names and email addresses of two references who can provide letters of recommendation.

If you have any questions or do you require additional information Please contact:

• Dr. Vivek Sheraton M Assitant Professor .