Are you looking for a PhD position and interested in research on protein evolution in bacteria? Are you a bioinformatician who wants to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this PhD vacancy may be of interest to you!

Job description: The Bioinformatics Group at Wageningen University is seeking a motivated and talented PhD researcher to join our team. In this role, you will delve into the fascinating world of orphan genes – genes that are unique to a single species, with no homologs found in other organisms.  

Even though more and more sequencing data is available, we cannot find homologs of these genes outside of that single species. The evolution of such genes is particularly intriguing, since they might arise from very fast divergence beyond recognition or entirely novel “from scratch” from a region that did not code for a protein before.

Alternatively, some might simply be artefacts of the automatic annotation. Orphan genes have been mainly studied in eukaryotes, where they are associated with organismal novelties and species-specific traits, and are generally thought to be important for adaptation. Much less is known about prokaryotic orphans. However, prokaryotes evolve rapidly and are exposed to changing environments, in which orphan genes might provide novel adaptations.

In this project, we will investigate orphans in human gut microbiome species. We will use state-of-the art machine learning approaches to study the properties of orphans and to learn about their evolutionary origin and potential function. In particular, we plan to use predicted protein structures to detect remote homology and to investigate the properties of proteins with potentially novel functions.

This work will contribute to a fundamental understanding of how proteins evolve. The research is embedded within the Bioinformatics Group. Your daily supervisors will be dr. Anne Kupczok and dr. Aalt-Jan van Dijk, with complementary expertise: molecular evolution of microbes (Anne Kupczok) and machine learning and protein structures (Aalt-Jan van Dijk).

Your qualities The ideal candidate must have the following qualities:

  • A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline;
  • Proficiency in programming (e.g. in Python);
  • Experience in applying machine learning to biological data;
  • Strong affinity with molecular evolution and/or prokaryote genomics;
  • Good statistical and mathematical skills;
  • Perseverance in problem solving;
  • Excellent writing and oral communication skills in English.

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language.

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, up to 40 hours 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.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.

The gross salary for the first year is € 2.541,- per month rising to € 3.247,- 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. 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. You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “ Best University ” in the Netherlands for the 18th consecutive time.

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.

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 helping your partner to find a job, housing, schooling. For instance under the “30% rule”, certain categories of international staff can receive tax exemption on approximately 30% of their gross salary.

Do you want more information? For more information about this position, please contact dr. Anne Kupczok by email: and dr. Aalt-Jan van Dijk by email
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 September 18, 2023. We hope to schedule the first job interviews in the week of September 25, 2023. The preferred starting date for this position is in November 2023.

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. 

Wageningen University & Research 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, 7,200 employees (6,400 fte) and 13,200 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.

About the group: The Bioinformatics Group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of –omics data.

The group has a strong track record in genome analysis (including evolutionary genomics), algorithm development (including the development and application of machine learning approaches to study proteins), and tool construction. There are many national and international collaborations with researchers studying molecular evolution and the application of machine learning in bioinformatics.

Apply now

Leave a Reply

%d bloggers like this: