PhD Position in Multiscale Mechanistic Modelling of Animal Development

Join the Tsingos group to model how subcellular protein interactions regulate organ-scale morphology in animal development.

Job

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!

Profile

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.

Benefits

embedding in a great team of top Computational Biologists and Life Sciences Researchers;
a position for 18 months, with an extension to a total of four years upon successful assessment;
a working week of 38 hours and a gross monthly salary between €2,901 and €3,707 (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 has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Company profile

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

Working at the Faculty of Science means bringing together inspiring people across disciplines and with a variety of perspectives and backgrounds. The Faculty has six departments: Biology, Pharmaceutical Sciences, Information & Computing Sciences, Physics, Chemistry and Mathematics. Together, we work on excellent research and inspiring education. We do so, driven by curiosity and supported by outstanding infrastructure. Visit us on LinkedIn and discover how you can become part of our community.

The Theoretical Biology & Bioinformatics division is part of the Department of Biology. Research in this division makes use of a wide range of different data analysis and modelling strategies to decipher the mechanisms underlying biological processes. Research subjects range from plant development and adaptation, to the functioning of the immune system, and the evolution of complexity.