PhD Position in Mathematical Modelling of Microbial Evolution

PhD Position in Mathematical Modelling of Microbial Evolution

Published Deadline Location
22 Dec 15 Feb Amsterdam

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Job description

Many current challenges are related to the evolution of species: the spread of pandemics, extinction of species through climate change, and the rise of antibiotic resistance affecting treatment outcomes. Therefore, predicting evolutionary dynamics is highly relevant. Current approaches, such as fitness landscapes, often focus on a single organism, but the environment and communities that micro-organisms live in are highly relevant. As an example we can take antibiotic resistance evolution, which can emerge through the evolution of enzymes that degrade antibiotics. Those enzymes clear the environment of antibiotics and therefore alter the selection on its own population and that of cohabiting populations.

The group of dr. Meike Wortel focusses on developing mathematical and computational techniques to include the environment, including other species, in the analysis of evolutionary trajectories and apply this to antibiotic resistance evolution and the evolution of microbial communities. To achieve this, the group combines evolutionary approaches with systems biology, that links the intricate networks that make up cells to their overserved behavior at the cell level.

The group is embedded in the Microbiology Theme at the Swammerdam Institute for Life Sciences, one of the largest research institutes of the Faculty of Sciences at the University of Amsterdam, and affiliated with interdisciplinary collaborations in Systems Biology and research on Origin and Evolution of Life and Emergence. The group uses ongoing collaborations to link theory directly to experimental systems, together with the group of prof. de Visser in Wageningen for antibiotic resistance and the groups in the Amsterdam Microbiome Initiative for (gut) microbiome communities.

To contribute to our research we are looking for an enthusiastic and intrinsically motivated PhD candidate. If you are interested in studying living systems with mathematical models, then this is the position for you!

What are you going to do?
You are expected to create and analyse mathematical models of antibiotic resistance evolution and evolution in microbial communities. You are expected to combine existing methods and design new approaches, when necessary. You will start by using data from the ongoing collaboration on antibiotic resistance evolution in laboratory communities and develop models and methods for that system. Then you can apply these methods and techniques in various settings.

Tasks and responsibilities:
  • complete and defend a PhD thesis within the official appointment duration of four years;
  • plan and perform scientific data analysis and experiments in an independent manner;
  • critically analyze and interpret results;
  • take a leading role in writing manuscripts;
  • present your results (inter)national scientific meetings;
  • collaborate with international and local researchers;
  • participate in the Faculty of Science PhD training programme;
  • assist in teaching undergraduates and Master’s students;
  • co-supervise MSc/BSc students.


University of Amsterdam (UvA)


You are passionate about science with a particular interest to study living systems with mathematical models. You should be able and motivated to acquire new knowledge, both biological and mathematical/computational. You should enjoy interdisciplinary collaborations, particularly with experimental microbiologists and evolutionary biologists.

Your experience and profile:
You have/are:
  • a Master degree, preferably in a highly quantitative discipline (Physics/Mathematics/Computational/Systems Biology or a related field);
  • affinity with interdisciplinary research;
  • highly motivated;
  • good programming skills;
  • good analytical, writing and presenting skills;
  • are proficient in English, both spoken and written.

Conditions of employment

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). 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 salary, depending on relevant experience before the beginning of the employment contract, will be € 2,770 in the first year to € 3,539 in the last year (scale P) gross per month, based on a fulltime contract (38 hours a week). This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Take a look here.


Faculty of Science

The Faculty of Science has a student body of around 7,000, as well as 1,600 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 Swammerdam Institute for Life Sciences is one of eight institutes in the Faculty of Science (FNWI). SILS is a multidisciplinary research institute with a systems biology approach to the life sciences. The institute brings together approximately 240 researchers in 18 research groups.

Do you recognize yourself in the job profile? Then we look forward to receiving your application by 15 February 2024. You can apply online by using the link below.

Applications in .pdf should include:
  • a motivation letter and CV,
  • a copy of your Master’s thesis (when available). If not yet available, please include a copy of your Bachelor’s thesis.
  • a list of all university courses taken, including a transcript of grades;
  • the name and contact details (including email address) of two referees who can provide details about your profile

(one of whom should be the main supervisor of your Master thesis).

Please mention the months (not just years) in your CV when referring to your education and work experience.

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


  • PhD
  • Natural sciences
  • max. 38 hours per week
  • University graduate
  • 12471


University of Amsterdam (UvA)

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Science Park 904, 1098XH, Amsterdam

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