PhD Position in Generative Modeling of Human Development and Disease

The Department of Biomedicine (DBM) at the University of Basel and the University Hospitals Basel unites basic and clinical researchers to deepen knowledge of health and disease. Within DBM, the Computational Cellular Dynamics (CCD) Lab, led by Prof. Marius Lange, will launch in January 2027 as part of the Basel Research Centre for Child Health (BRCCH). The group focuses on building generative models that describe how human tissues develop, mature, regenerate, and where disease processes diverge, with a special emphasis on paediatric health. In this four‑year PhD position you will create generative models that operate on single‑cell and spatial genomics data obtained from sequencing and imaging platforms. Your work will translate these models into insights on developmental biology and disease mechanisms, covering topics such as predictive cell‑cell communication, joint regulation‑dynamics frameworks, and the design of interventions that steer cellular states. Collaboration with hospital partners and local research institutes will provide you with cutting‑edge data, while you will also extend existing tools like scVelo, CellRank, moslin, moscot and RegVelo. The role requires a Master's degree in a quantitative discipline (computer science, mathematics, physics, engineering, computational biology or a related field) and practical experience handling biological datasets. You must be proficient in Python and familiar with deep‑learning libraries such as PyTorch or JAX, possess a GitHub repository that showcases your code, and communicate fluently in English. These core qualifications ensure you can develop, train, and evaluate the sophisticated models the lab pursues. Additional assets include prior work with single‑cell or spatial genomics data and contributions to open‑source scientific software, both of which are valued but not mandatory. The position offers a fully funded PhD contract (100 % effort), a vibrant, inclusive research culture, and access to a dense life‑science ecosystem in Basel that hosts universities, hospitals, biotech institutes and major pharma companies. You will also join the International PhD Programme in Biomedicine, benefitting from structured courses, skills training and career‑development support. The university guarantees equal‑opportunity employment and a family‑friendly environment. What the role asks for: - MSc in computer science, mathematics, physics, engineering, computational biology or related field - Hands‑on experience with biological data - Strong Python programming skills - Experience with PyTorch or JAX - GitHub account with own code - Fluent English - Experience with single‑cell or spatial genomics data (nice‑to‑have) - Contributions to open‑source scientific software (nice‑to‑have)