PhD Position in Generative Modeling of Human Development and Disease

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 

We offer you

● A fully funded four-year PhD position (100 %) in a new research group with generous resources for both computation and data generation 
● A collaborative and supportive research environment, with access to pediatric and adult clinical samples through hospital collaborations in Basel. We promote a dynamic and supportive team culture that values diversity and inclusion 
● Internationally competitive salary and social benefits according to the rules of the University of Basel; enrolment in the International PhD Programme in Biomedicine, with courses, skills training and career development 
● One of Europe's densest life-science ecosystems: alongside the University and its hospitals, Basel hosts ETH Zurich's D-BSSE, the Botnar Institute of Immune Engineering (BIIE), the Friedrich Miescher Institute (FMI), the Institute of Molecular and Clinical Ophthalmology Basel (IOB), the BRCCH where this lab sits, and two global pharma companies, all within a few kilometres, in an international city at the border of France and Germany with a high quality of life