PhD position in Computational Developmental Biology – Multiscale Mechanistic Modelling of C. elegans intestinal development

What?

4-year PhD position on modelling how subcellular protein interactions regulate organ-scale morphology

Where?

Computational Animal Development group at Utrecht University in the Netherlands

Scientific background

How do cells shape tissues? How are cells themselves shaped by the proteins within them? How do all these different levels of regulation interact to create functional organs? These questions are fundamental in developmental biology and also have applications in regenerative biomedicine. Understanding the multiscale regulatory feedbacks between genes, proteins, cell behaviours, and tissue-scale mechanics is a major challenge.

You will tackle this challenge by developing mechanistic computational models. You will apply these models to recapitulate key aspects of intestinal development in the nematode Caenorhabditis elegans, which is an excellent model system to study multiscale regulation, as mutations in proteins involved in cell shaping lead to cascading impacts on organ-level morphogenesis and lumen formation.

The project will consist of creating models at various levels (subcellular, cell-level, organ-level). At the subcellular level, you will develop models of protein interactions using ordinary differential equations. In a second step, these can be integrated with cell based models to investigate feedbacks between subcellular networks and cell shape regulation. One potential direction of the project is to then investigate how the virtual cells interact to shape an entire simulated organ.

To calibrate and parametrize the models, you will have access to data from experimental collaborators (Boxem Lab). In turn, your models will help our experimental collaborators design targeted experiments to test model predictions.

Come be part of the vibrant Computational Biology community at Utrecht University!

Your qualities

You are a curious and collaborative colleague, with the following qualifications:

• a Master’s degree in Computational Biology, Applied Mathematics, Physics, Computer Science, or a related field;
• enthusiasm for learning the biological background and working closely with collaborators;
• familiarity with or a keen interest in developing mechanistic models of dynamical biological systems (differential equation-based modelling, agent-based modelling, cellular Potts modelling);
• familiarity with or a keen interest in working with code and programming;
• fluency in English, both spoken and written.

How to apply?

For more information and application, use the “Apply Now” button on the webform: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-position-in-multiscale-mechanistic-modelling-of-animal-development