The Computational Cellular Dynamics Lab, a new research group starting in January 2027 at the University of Basel, is interested in building generative models of how human tissues develop, mature and generate. With a particular focus on paediatric health, their models learn from single-cell and spatial genomics and build on open-source tools they developed for cellular dynamics: scVelo, CellRank, CellRank 2, moslin, moscot and RegVelo.
The Group is working on
Cell–cell communication. Models that predict how cells and tissues respond when their signaling environment changes.
Regulation and dynamics. Flow and diffusion models that learn gene regulation, constrained by time-resolved perturbations, lineage tracing and multi-modal data.
Experimental design and continual learning. Choosing the perturbations and measurements that are most informative or that steer cells toward a target state, and updating models as new data come in, with active learning closing the loop between model and experiment.
The group is seeking for people with a strong background in machine learning, mathematics, physics, statistics or computational biology and some exposure to biological data, who want to apply their skills to real biological questions with impact, such as how tissues develop and regenerate, how cells can be reprogrammed and what goes wrong in disease. The applicants should design and train their own models, ideally in PyTorch or JAX, and care about what they assume and where they break.
PhD Position
A four-year fully funded position is available in the research group.
Depending on the applicant’s interests and background, possible research directions include:
Funding for postdoctoral researchers is available within the group. Alternatively, support is available for candidates wishing to apply for independent fellowships. Applications should include a CV, the contact details of two or three referees, a link to the applicant’s GitHub profile, and a brief statement outlining past research and future research interests.
Projects of at least six months’ duration in any of the research areas listed above are available within the group. Applications should include a CV, the contact details of two or three referees, a link to the applicant’s GitHub profile, and a brief statement outlining past research and future research interests.
The Computational Cellular Dynamics Lab, a new research group starting in January 2027 at the University of Basel, is interested in building generative models of how human tissues develop, mature and generate. With a particular focus on paediatric health, their models learn from single-cell and spatial genomics and build on open-source tools they developed for cellular dynamics: scVelo, CellRank, CellRank 2, moslin, moscot and RegVelo.