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Athena's Journey

PhD Position in Generative Modeling of Human Development and Disease

Montreal, QC, Canada
Urban agglomeration of Montreal, QC, Canada

Job type: Full-time
Apply by: Oct 18, 2026
Posting language: English
Posted: Sep 22, 2026

Apply About employer

Applications open in a new tab.

Original job description

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

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

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 (marius.lange.lab@gmail.com).

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

Apply

www.unibas.ch

Apply About employer

More about this job

Responsibilities

Develop generative models for single-cell and spatial genomics data to understand human development, maturation, and disease. Apply these models to biological research, focusing on cell-cell communication, regulatory dynamics, and intervention design.

Requirements

Applicants must hold an MSc in computer science, mathematics, physics, engineering, computational biology, or a related quantitative field. Strong Python programming skills and experience with PyTorch or JAX are required.

Skills

Python
PyTorch
JAX
Computational biology
Single-cell genomics
Spatial genomics
Generative modeling
Statistical modeling
Data integration
Bioinformatics
Machine learning
Scientific programming

Benefits

Internationally competitive salary
Social benefits
International PhD Programme in Biomedicine
Skills training
Career development

Visa sponsorship

Not detected in the job text

Hiring contact

Marius Lange

Hiring contact email

marius.lange.lab@gmail.com

Keywords

Generative modeling
Single-cell genomics
Spatial genomics
Python
PyTorch
JAX
Computational biology
Bioinformatics
Cellular dynamics
Machine learning
Data integration
scVelo
CellRank
moscot
RegVelo
Biomedicine
Genomics
Statistical modeling
Open-source software
PhD position

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