Phd Position in Multiscale Spatiotemporal Modelling of Microbiome During the First 1000 Days of Life

Phd Position in Multiscale Spatiotemporal Modelling of Microbiome During the First 1000 Days of Life

Published Deadline Location
4 Jun 3 Jul Amsterdam

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Job description

Are you driven by a desire to delve into the convergence of computational modelling, omics research, and exogenous factors as they relate to human health? Specifically, are you excited about utilizing computational science methods to investigate the impact of the human microbiome on health and disease?

The Computational Science Lab (CSL) at the Informatics Institute, together with the Swammerdam Institute for Life Sciences (SILS) at UvA, is seeking a motivated PhD candidate to join our team focused on multiscale spatiotemporal modelling of the human microbiome. The successful candidate will be responsible for constructing, simulating, and validating computational models of the microbiome in oral and gut regions, as part of the MetaHealth consortium project.

The primary aim of this PhD project is to understand how children's microbiome influences their oral and gut health during the first 1000 days of life and beyond. To accomplish this goal, computational models must be developed to account for both endogenous and exogenous factors that impact health. Endogenous factors include internal parameters such as solute levels and species abundance in intestinal tract and dental regions, while exogenous factors encompass external elements such as socio-economic status, culture, diet, and lifestyle. By integrating these factors, you will simulate and explore their complex interactions and effects on the microbiome and innate immune system. Your model simulations will inform personalized interventions targeting metabolic health issues and dental caries. This interdisciplinary project will have access to metagenomics and demographics data from the MetaHealth consortium for use in your research. We welcome applications from candidates who are passionate about harnessing the power of computational science to improve human health.

What are you going to do?
  1. Model Development: Collaborate with an interdisciplinary team of researchers to integrate data from cohort studies, metabolomics analyses and in vitro experiments, to develop computational models relying on spatial modelling techniques such as cellular Potts and reaction-diffusion models that capture the interactions between the macroscopic changes in the host environment and the corresponding physical and biological changes in the microbiome.
  2. Parameter Analysis: Analyse model parameters for interoperability (with other computational models) and interpretability using techniques such as complex network analysis and dimensionality reduction (ordination).
  3. Intervention analysis: Develop qualitative and quantitative mathematical models to simulate the impact of lifestyle factors (e.g., nutrition, physical activity, sleep behaviour, cultural and environmental factors) on oral health and metabolic health outcomes. Use the simulation outcomes to propose intervention strategies.
  4. Individual-Level Microbiome Wellness and Immune Fitness Score: Develop a method to arrive at an individual-level microbiome wellness and immune fitness score using the developed mathematical models.
  5. Collaboration: Collaborate with researchers from various disciplines, including oral health, metabolic health, microbiology, nutrition, computational modelling and epidemiology, to ensure that models are relevant, useful for practical applications and have societal impact.
    For setting up the mathematical models and simulations, most programming will be in Python and/or C++.

What do you have to offer?

Your experience and profile
The ideal candidate will possess a Master's degree or equivalent in computational science, computational biology, computational (bio)physics, applied mathematics, or an allied field. A strong motivation to apply computational modelling to health and disease is essential, and prior research experience in in-silico modelling in the life sciences or medicine domains is highly desirable.

Expertise in programming using Python or C++ is required, and hands-on experience with modelling paradigms such as reaction kinetics and multiomics is considered a plus. The successful candidate will have the opportunity to work in a dynamic and interdisciplinary research team, collaborating with medical professionals, wet lab experts, and other experts in the field.

Excellent English communication skills, both written and spoken, are necessary. A willingness to learn and observe wet-lab techniques, in order to better understand their use cases, limitations and potential for model validation, is highly valued.

Our offer
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

The gross monthly salary, based on 38 hours per week and dependent on relevant experience, ranges between € 2,770 in the first year to € 3,539 in the last year (scale P). UvA additionally offers an extensive package of secondary benefits, including 8% holiday allowance and a year-end bonus of 8.3%. The UFO profile PhD Candidate is applicable. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:
  • 232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
  • Multiple courses to follow from our Teaching and Learning Centre;
  • A complete educational program for PhD students;
  • Multiple courses on topics such as leadership for academic staff;
  • Multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
  • 7 weeks birth leave (partner leave) with 100% salary;
  • Partly paid parental leave;
  • The possibility to set up a workplace at home;
  • A pension at ABP for which UvA pays two third part of the contribution;
  • The possibility to follow courses to learn Dutch;
  • Help with housing for a studio or small apartment when you’re moving from abroad

When applying we ask you to upload your CV and a motivation letter why you apply to this position.

About us
The University of Amsterdam (UvA) is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 42,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.

The Faculty of Science (FNWI) has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

The mission of the Informatics Institute (IvI) is to perform curiosity-driven and use-inspired fundamental research in Computer Science. The main research themes are Artificial Intelligence, Computational Science and Systems and Network Engineering. Our research involves complex information systems at large, with a focus on collaborative, data driven, computational and intelligent systems, all with a strong interactive component.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

Any questions?
Do you have any questions, or do you require additional information? Please contact:

Job application
If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 3 July 2024.

Applications should include the following information (all files apart from your CV should be submitted in one single pdf file):
  • a detailed CV including the months (not just years) when referring to your education and work experience;
  • a letter of motivation;
  • the names and email addresses of two references who can provide letters of recommendation.
  • Your Master thesis (this can be in draft form if not yet finalised)

Please make sure to provide ALL requested documents mentioned above.
You can use the CV field to upload your resume as a separate pdf document. Use the Cover Letter field to upload the other requested documents, including the motivation letter, as one single pdf file.

A knowledge security check may be part of the selection procedure.
(for details: National knowledge security guidelines).

Only complete applications received within the response period via the link below will be considered. Please don’t send any applications by email.

We will invite potential candidates for interviews soon after the expiration of the vacancy.

The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

If you encounter Error GBB451/ GBC451, please try using a VPN connection when outside of the European Union. Please reach out directly to our HR Department directly. They will gladly help you continue your application.

No agencies please.


University of Amsterdam (UvA)


  • PhD
  • max. 38 hours per week
  • €2770—€3539 per month
  • University graduate
  • 13092


University of Amsterdam (UvA)

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Science Park 904, 1098XH, Amsterdam

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