PhD Position: Computational Methods for Digital Twins of Embryonic Development

About the role

The Computational Biology Group (Prof Dagmar Iber) at D-BSSE develops digital twins of embryonic development and reproductive health using image-based mechanistic modelling and simulation. The PhD position focuses on building the algorithmic infrastructure behind these digital twins, working with modellers, experimentalists and clinicians, and building on the group's open-source simulation tools. It is a fixed-term position based in Basel.

Key responsibilities

• Develop and benchmark methods for parameter estimation and uncertainty quantification, from classical optimisation and Bayesian inference to physics-informed neural networks and other machine-learning approaches
• Build and extend the simulation environment, focusing on performance, scalability and reproducibility
• Apply the methods to real models and data, from imaging-based tissue-development models to the digital twin of the hormonal cycle and IVF treatment, with the group's collaborators
• Publish results and present them at international conferences
• Contribute to the group's open-source software and to teaching

Required profile

• Master's degree in Computer Science, Computational Science and Engineering, Applied Mathematics, Physics or a related field
• Training in computer science, scientific computing or a related quantitative field, with an interest in applying it to biology and biomedicine
• Interest in biology and biomedicine and willingness to learn the biological background; prior knowledge is not required
• Good written and spoken English

Required skills

• Strong programming skills, e.g. in Python, Julia or C++, with experience writing clean, well-tested code
• Experience in numerical methods, optimisation, statistical inference or machine learning, gained through coursework, a thesis or a project
• An advantage: experience with PDE-based simulations, finite element methods, high-performance computing or deep-learning frameworks such as PyTorch or JAX

What we offer

• A PhD position in an interdisciplinary, international research environment at the interface of mathematics, computing and biology
• Close collaboration with leading experimental groups and clinical partners
• Computing resources at ETH Zurich and support for scientific development, including conference travel and training
• Competitive ETH doctoral salary and conditions

Applications are submitted online through the university's application portal, with a letter of motivation, CV, BSc and MSc diplomas and transcripts, and contact details of two referees. Applications are reviewed on a rolling basis until the position is filled.