PhD position in spatiotemporal diversity of phages

July 9, 2024
Location Wageningen
End date Mon 26 August 2024
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Your job

Do you want to pursue a PhD in computational biology? Are you interested in the genome diversity of bacteriophages across space and time? Do you want to combine bioinformatics and mathematical modelling to study the evolutionary factors that impact bacteriophage diversity? Then we are looking for you! 

Viruses that infect bacteria – bacteriophages – are the most abundant biological entities on Earth. They contribute significantly to bacterial ecology and evolution and hence impact the function of all ecosystems. Due to their parasitic lifestyle, phages are constantly under selection, resulting in an enormous phage genome diversity. Metagenomics, i.e., bulk sequencing the genetic content of environmental samples, has recently revealed a surprising amount of phage diversity. Particularly, the within-species diversity of phages varies to a large extent in natural populations, and little is known about the distribution of phage diversity across space and time, and which factors drive this diversity. 

In this project, you will combine bioinformatics and modelling to untangle the drivers of phage diversity across space and time. Potential factors influencing phage diversity are host diversity, presence of other phages, and environmental factors like spatial structure. You will compare phage diversity in different types of environments, such as marine and soil environments. Particularly, you will develop bioinformatics pipelines to analyze public phage genome and metagenome data with the aim to estimate phage diversity. Additionally, you will formulate mathematical and computational models of phage evolution to explain observed patterns of diversity. You will refine these models based on the observations from the genomic data.

Beyond the scientific and potential application merits, you will build a network for your future career both within and outside Wageningen University.

You will work here
The research is embedded in two chair groups at Wageningen University: the Bioinformatics Group led by prof. Dick de Ridder and the Laboratory of Genetics led by prof. Bas Zwaan. Your daily supervisors will be dr. Hilje Doekes and dr. Anne Kupczok, with complementary expertise: mathematical biology and evolutionary modelling (Hilje Doekes) and bioinformatics and comparative genomics (Anne Kupczok). The position is for four years, and you will join the graduate school PE&RC, which offers PhD training and other activities.

Your qualities

You have:

  • a successfully completed MSc degree in bioinformatics, evolutionary biology, applied mathematics, or another related field;
  • proficiency in programming (e.g., python) ;
  • experience in high-throughput sequencing data analysis and comparative genomics or strong interest to develop it;
  • strong affinity with the development of mathematical models and their application to genomic data;
  • fascination for the evolution of microbes and their viruses and a quantitative mindset;
  • a proactive attitude and teamwork skills and are committed to obtaining a PhD ;
  • a very good level of oral and written English. You are required to show a certification of English skills. For more information about the required level please take a look at: PhD entry requirements.;
  • A PhD is a learning trajectory. If you do not yet have a track-record showing all the requirements but do have a strong motivation to acquire the skills necessary to make this project a success, we would like to encourage you to apply.

We offer you

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

  • sabbatical leave, study leave, and partially paid parental leave;
  • working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
  • the option to accrue additional compensation / holiday hours by working more, per week;
  • there is a strong focus on vitality, and you can make use of the sports facilities available on campus for a small fee;
  • a fixed December bonus of 8.3%;
  • excellent pension scheme.
The gross salary for the first year is € 2.770 - per month rising to € 3.539,-  in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

Wageningen University & Research encourages internal advancement opportunities and mobility with an internal recruitment policy. There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. Wageningen University & Research's International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

Do you want more information?

For more information about this function, please contact Hilje Doekes , staff member of the WU Laboratory of Genetics, by email: or Anne Kupczok, staff member of the WU Bioinformatics Group, by email: Applications are only accepted using the apply button on the vacancy page.

For more information about the procedure, please contact Noorien Abbas, Corporate Recruiter, by email:  

Do you want to apply?
You can apply directly by uploading your CV and motivation letter, using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.

This vacancy will be listed up to and including Monday 26 August 2024. We plan to schedule the first job interviews on 5 September 2024.

In this first round, please only send your resume and motivation letter. Any other documents will not be taken into consideration at this stage.

Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment.

We are

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,600 employees (6,700 fte) and 13,100 students and over 150,000 participants to WUR’s Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.

Read the 5 reasons why your future colleagues enjoy working at WUR and watch the video below to get an idea of our green campus!

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.