PhD Position in Computational Modelling of Fungal Evolution

Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. As a creative, computationally skilled PhD candidate you help us develop and analyse spatial, individual-based models of horizontal gene transfer in multicellular fungi. Your mission: understanding how Starships reshape the frequency, threat, and persistence of disease in both nature and agriculture.

Your job
You are a passionate computational biologist with an interest in ecology and evolutionary dynamics. During this project, you will be the first to work with large-scale computational models of eco-evolutionary dynamics of fungal pathogens.

During ASTRAfun, you will develop and analyse cutting-edge multi-level computational models that integrate:

• Fungal growth & network morphology – How do hyphal structures influence gene flow?
• Genome architecture – Why do some genes stay put while others hitch rides on Starships?
• Agricultural practices – How do crop rotation, ploughing, and diversity shape fungal evolution? How does that compare to natural populations where plant diversity is high?

This PhD will grant you an appreciation and understanding of complex biological systems and biodiversity. You will get the opportunity to learn about both simple and complex biological models, computer programming, data visualisation, and bioinformatic methods to cross-compare insights from your simulations with real-world data. Additionally, the position will provide opportunities to pick up on additional skills such as teaching and science communication, and enables you to build a strong scientific network. You will be embedded in a great team of world-class scientists, where English is the main working language and receive academic training within the Graduate School of Life Sciences. Finally, our goal is to help you pursue scientific ambitions while also maintaining a healthy work-life balance.

We are looking for a passionate colleague with a drive to understand the hidden lives of soil-borne fungal plant pathogens. To apply to this PhD position, you need:

• A completed (or nearly completed) Master’s degree in biology or a related discipline.
• A proven affinity with computational modelling.
• An interest in the ecology and evolution of microbial ecosystems.
• Proficiency in English, both spoken and written.

It is considered a plus if you have:

• A background in fungal biology, fungal ecology, and/or fungal genome evolution.
• Experience with analytical (mathematical) models.

Note: women, ethnic minorities, and people from any other minority group are especially encouraged to apply. Please do not feel demotivated when you feel like you do not meet all the listed criteria. When in doubt, please reach out to us.

• a position for 18 months, with an extension to a total of four years upon successful assessment in the first 18 months;
• a gross monthly salary starting at € 3,059 in the first year and increasing annually up to €3,881 in the fourth year, based on full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU));
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University also offers a range of its own schemes for employees. This includes arrangements for professional development, various types of leave, and options for sports and cultural activities. You can also tailor your employment conditions through our Terms of Employment Options Model. In this way, we encourage you to keep investing in your personal and professional development. For more information, please visit Working at Utrecht University.

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The research will be performed at the research group headed by Dr. Bram van Dijk at Utrecht University since September 2023. The team specialises on building multi-scale simulations of microbial ecosystems (“virtual laboratories”) and use these to unpack fundamental rules that govern microbial life. Current interests are geared towards understanding why various vehicles of gene transfer (MGEs like phages, plasmids, transposons, and of course Starships!) have different impacts on microbial evolution, for example by driving the horizontal transfer of different types of genes. However, many other interesting topics are ongoing, including:

• The evolution of environmentally transmitted microbiomes.
• The evolution of transposable elements and their copy numbers.
• Black queen dynamics in bacterial communities.
• Gamification of plant-pathogen evolution in agriculture (outreach project within ASTRAfun).

The team is embedded in the Theoretical Biology and Bioinformatics group (department of Biology), which uses computational biology, bioinformatics, modelling, and big data to address both fundamental and applied questions in the life sciences. A selection of ongoing research lines includes the evolution of genomes, protein complexes, systems genetics, metagenomics, host-microbe interactions, and the basic principles of ecology and evolution. Together with more than 35 research groups distributed over five research and educational institutes, we form the Utrecht Bioinformatics Centre that combines world-class bioinformatics research and coordinates bioinformatics education at all levels at the Utrecht Science Park.

For more information, please contact Dr. Bram van Dijk at b.vandijk@uu.nl.

Do you have a question about the application procedure? Please send an email to science.recruitment@uu.nl.

Candidates for this vacancy will be recruited by Utrecht University.