PhD Fellowship in Biology

VU University of Amsterdam

Are you interested in a comprehensive, interactive and international research programme? Do you want your research to cover the broader aspects and interface between biology, bioinformatics, statistics, systems biology, predictive microbiology and artificial intelligence? Then, please apply for this PhD fellowship at Vrije Universiteit Amsterdam (VU).

FTE: 1.0

Job description

In this project, we will develop tools and methods to integrate dynamic multi-level omics data with genome-scale mechanistic models in the context of microbial communities. With partners in the E-MUSE Network (KUL, UNIBO, USZ, CHRH) we will explore: (1) The use of machine-learning approaches for feature selection, for example SVM, Random forest, Ensemble techniques, etc., for model development and prioritization. (2) Conversely the use of the mechanistic models and Individual-based Model as prior knowledge to constrain the search space in data-driven approaches. We will integrate the data into dynamic constraint-based ecosystem models, and apply the tools and methods to the biological study cases, i.e. the cheese ripening case and the growth physiology of associated microbial species.

Expected results:

We expect to deliver tools (open source software) and methods (algorithms, modelling strategies) to use multi-omics data to generate insight in the relevant interactions inside and between microorganisms in complex dynamic ecosystems. We will provide insight in the usefulness of combining machine-learning and mechanistic modelling approaches. Finally, we will provide, in collaboration with the network partners, specific models and predictions that will lead to a better understanding of the biological use cases.

Planned secondment(s):

In total, 2 months will be spent at the Agencia estatal consejo superior de investigaciones cientificas in Spain (dynamic optimisation technologies), 2 months at the Katholieke Universiteit Leuven in Belgium (modelling aspects) and 3 months at the Institut national de recherche pour l’agriculture, l’alimentation et l’environnement in France and at the Chr. Hansen A/S in Denmark (biological data)

Enrolment in Doctoral degree: Vrije Universiteit Amsterdam (VU) (

Website for additional job details:


  • Master’s degree in systems biology, bioinformatics, (bio)physics, engineering or biology with a strong theoretical/computational component              
  • Independence, curiosity, open mindedness, ability to (learn to) communicate with different disciplines (experimental, computational, theoretical) and will to understand complex systems       
  • Educational background and previous research experience relevant for the chosen position
  • Networking and communication skills in a multicultural and multidisciplinary environment
  • Willingness to travel abroad for the purpose of research, training and dissemination

Specific Requirements - Eligibility Criteria

  • Candidate of any foreign nationality is welcome
  • Early Stage Researcher (ESR)
  • The applicant needs to be in the first four years of her/his research career at the date of recruitment by the host organisation, and has not been awarded a doctoral degree. The first four years are measured from the date of applicant’s degree either in the country in which the degree was obtained or in the country in which the researcher is recruited, irrespective of whether doctorate was ever envisaged.
  • Mobility Rule
  • The ESR must have not resided or carried out main activity (work, studies, etc.) in the country of their host organisation ≤ 12 months* in the 3 years prior to their recruitment. Exceptions: The ESR must not have spent more than 12 months in the 3 years prior to the date of selection in the same appointing international organisation.
    *EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the Geneva Convention
  • Language: Applicants must show fluent reading, writing and speaking abilities in English.

What are we offering?

  • A comprehensive, interactive and international training programme covering the broader aspects and interface between biology, bioinformatics, statistics, systems biology, predictive microbiology and artificial intelligence as well as transferable skills
  • An enthusiastic team of professionals to co-operate with
  • Personal Career development plan (PCDP) to prepare young researchers for their future careers
  • Each ESR will undergo individual training at individual institutes according to the PCDP description
  • Remuneration according to Dutch PhD regulations minimal €2395 gross salary/month first year to €3061 in third year. Plus € 600 gross mobility allowance/month and €500 gross family allowance/month (if applicable).  Taxation and social contribution deductions based on national and company regulations will apply
  • Duration of recruitment: 36 months

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 2 years.
Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:

  • a maximum of 41 days of annual leave based on full-time employment
  • 8% holiday allowance and 8.3% end-of-year bonus
  • a wide range of sports facilities which staff may use at a modest charge
  • discounts on collective insurances (healthcare- and car insurance);

About Vrije Universiteit Amsterdam

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavour – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.

Vrije Universiteit Amsterdam is home to more than 26,000 students. We employ over 4,600 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.


We are an inclusive university community. Diversity is one of our most important values. We believe that engaging in international activities and welcoming students and staff from a wide variety of backgrounds enhances the quality of our education and research. We are always looking for people who can enrich our world with their own unique perspectives and experiences.

The Faculty of Science

The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.

Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.

About the department

The lab of VUA, in which the proposed work will be carried out, studies the molecular networks inside cells that give rise to cell behavior and fitness, in isolation and in interaction with other cells and their environment. The team focuses on the principles and general understanding of how those networks adapt in response to environmental and genetic changes and combine mathematical modelling, theory, and experiments. The approach is to apply the fundamental insights and methods in a biotechnological and biomedical setting.
The lead supervisor is prof. dr. B. Teusink (VU), the head of the Systems Bioinformatics group, which he runs together with prof. dr. F. Bruggeman (VU) who is also one of the co-supervisors. B. Teusink’s group currently houses 12 PhD students and 2 postdocs. Of previous students, 2 PhD and 3 PDs now have a faculty position at Dutch Universities; 2 PhDs and 5 PDs moved to R&D jobs in industry, 3 PhDs are currently postdocs elsewhere, and 3 PhDs work as data analysts for bank and insurance companies.The co-supervisors for this role are also dr D. Molenaar (VU) – member of  prof. Teusink group who is specialist in microbiology, bioinformatics and data analysis and J. Van Impe (KUL) – the Division Head and founder of BioTeC (Chemical and Biochemical Process Technology and Control) research group at KU Leuven.


Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until 15/04/2021, 23:59.

Applications received by e-mail will not be processed.

Vacancy questions
If you have any questions regarding this vacancy, you may contact:

Name: Prof.dr. B. Teusink
Position: group leader

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