PhD Position in Generative Modeling of Human Development and Disease

As a joint venture of the University of Basel and the University Hospitals Basel, the Department of Biomedicine (DBM) brings together basic and clinical scientists to advance the understanding of health and disease. We are home to more than 67 research groups and over 800 employees across six locations in the heart of Basel. Our collaborative and international environment fosters innovation, excellence, and impactful research. Join our community and help shape the future of biomedicine. The Computational Cellular Dynamics (CCD) Lab, led by Marius Lange, is a new research group at the Department of Biomedicine and the Basel Research Centre for Child Health (BRCCH). We develop generative models of how human tissues develop, mature and regenerate, and of what goes wrong in disease, with a focus on child health. The group starts in January 2027.

Your position

You will develop generative models on single-cell and spatial genomics data, from sequencing and imaging, and apply them to human developmental and disease biology. Possible research directions include:

• Generative models of cell–cell communication. Move beyond descriptive ligand–receptor analysis to models that predict and help understand how cells react to signaling cues.
• Joint models of regulation and dynamics. Flow- and diffusion-based models of cellular dynamics are expressive enough to map any source to any target state, but they fall short of learning the underlying regulatory principles. We work on regularization, training on time-resolved perturbation and lineage-tracing data, and multi-modal readouts to constrain these models toward biological mechanisms.
• Intervention design and continual learning. Beyond predicting perturbation outcomes: designing interventions that steer cells toward a desired molecular state, and updating trained models as new data arrive, toward a lab-in-the-loop setup.

These directions build on our earlier work on cellular dynamics, regulation and data integration: scVelo, CellRank, CellRank 2, moslin, moscot and RegVelo. In collaboration with partners at the hospitals, universities and institutes in Basel, we generate our own data, on the newest spatial and single-cell platforms.

Your profile

Required:

• MSc in computer science, mathematics, physics, engineering, computational biology or a related quantitative field
• Hands-on experience with biological data
• Strong Python skills and experience with PyTorch or JAX, together with the statistical grounding to reason about the models you use
• A GitHub account with code you have written
• Fluent English

Desirable:

• Experience with single-cell or spatial genomics data
• Contributions to open-source scientific software

Application/Contact

Please upload your application via the online platform. It should include:

• a motivation letter stating your research interests, your fit to the profile and why you are applying (max. one page)
• a short description of a research project you were involved in, e.g. your MSc project, stating its rationale, main outcome and your contribution (max. half a page)
• a CV
• a link to your GitHub account
• a copy of your current MSc transcript of records
• contact details of at least two references (willing to provide recommendation letters upon request), including your relation to them

The position is available from Jan 1, 2027, or later by mutual agreement. Review of applications will begin immediately and continue until the position is filled. For questions, please contact Prof. Dr. Marius Lange ( [email protected] ).

The University of Basel is an equal opportunity and family-friendly employer committed to excellence through diversity.