Postdoctoral researcher in single-cell phylodynamics

 The Computational Evolution Group, led by Prof. Dr. Tanja Stadler, in the Department of Biosystems Science and Engineering (D-BSSE) works at the interface of mathematics, computer science and evolutionary biology. We develop phylogenetic and phylodynamic methods to understand evolutionary, ecological, epidemiological and developmental processes on different scales based on genetic data. 

Our research group is located in BaselSwitzerland’s oldest university city and a European hot-spot for biomedical research. Our department is in close proximity to several other academic research institutes as well as major pharmaceutical and biotech companies. We are also part of the Swiss Institute of Bioinformatics, a major developer and provider of bioinformatics services and resources.

Applications are invited for the position of postdoctoral researcher with Prof. Dr. Tanja Stadler. The position is fixed-term for 2 years with possibility of extension.

Project background

How does a single fertilised egg develop into a functioning organism?

The answer to this question depends on the underlying population dynamic process, i.e. the division and change of individual cells. Within the EU-funded PhyCogy project, one of our goals is to introduce phylodynamics into developmental biology, by formulating and characterizing models describing the division and change of individual cells. With the resulting so-called phylodynamic modelling framework, we will move from a qualitative description of developmental processes to a quantification of developmental processes.  

Job description

The open position is in the emerging field of single-cell phylodynamics. You will work closely with Prof. Dr. Tanja Stadler and other team members in the Computational Evolution group. Basel's excellent research environment will allow you to interact directly with single-cell genomics experts Barbara Treutlein and Alex Schier.

The ultimate goal of the project is to quantify important developmental processes from single-cell data that have so far only been qualitatively described. You will quantify the rates of cell division (i.e., replication), cell apoptosis (i.e., death), and cell differentiation (i.e., transition) based on single-cell phylogenies that are estimated from single-cell lineage tracing (e.g., GESTALTiTracer) and single-cell transcriptomic data. We recently developed and implemented a conceptual framework for such quantification. You are envisioned to contribute your ideas on biological questions as well as computational method extensions such that single-cell lineage and transcriptomic data can deepen our understanding of development.

Your profile

  • We are looking for a highly motivated early career researcher with strong quantitative skills.
  • You will have completed a PhD in biology, computational biology, biostatistics or a related discipline prior to starting the position.
  • Familiarity with single-cell analysis or developmental biology is a requirement for the position.
  • Experience with single-cell lineage tracing is a big plus. 
  • Extensive knowledge of phylogenetics or phylodynamics is not required, but a strong interest in learning to handle and understand these tools will be essential.
  • You will engage in interdisciplinary research as part of a team, so clear and effective communication skills are a priority.
  • We value an open and inclusive group culture.
  • As a member of the Computational Evolution group, you will be expected to help us maintain a positive team dynamic and a welcoming work environment.
  • Our working language in the group is English and no knowledge of German is required.
  • In line with our commitment to an open and inclusive group culture we welcome applications from individuals of all demographic groups and personal backgrounds. 

We look forward to receiving your online application with the following documents by March 13th 2023:

  • Curriculum Vitae including your educational history and a full list of publications.
  • Letter of motivation of max. 2 pages covering your past research experiences and future research interests, goals and how they would relate to and fit in with the PhyCogy project and the Computational Evolution group’s research domain and activities.
  • Names, e-mail addresses, and phone numbers of at least two references, mentioning for each the professional relationship you have with them.

Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered. Applications should be written in English. The selection committee will review all applications within 3-4 weeks after the application deadline.

For further information please visit our lab website for further information. Questions regarding the position (no applications) should be directed to Dr Louis du Plessis (

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