PhD position on machine learning-based prediction of protein-protein interactions

PhD position on machine learning-based prediction of protein-protein interactions

Published Deadline Location
9 May 5 Jun Wageningen

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Job description

Are you looking for a PhD position and like to participate in an exciting interdisciplinary research project to discover how proteins select their partners to interact with? Are you a bioinformatician with interest in machine learning, and its application to predict protein interactions? Then this PhD vacancy may be of interest to you.

Biological processes are controlled by transcription factor proteins (TFs), which interact in many different combinations to regulate gene expression. However, it is still largely unclear how the specificity of protein-protein interactions is encoded in protein sequence and structure and how this determines which combinations of proteins with unique functions can be formed. Ultimately, this knowledge is important to steer and control biological processes, and investigate for example the cause of human diseases or govern modern plant breeding approaches.

In the framework of the NWO-M2 project ‘Machine learning-based prediction of transcription factor protein-protein interactions’, two PhD candidates will collaborate to develop a robust computational method to predict protein-protein interactions of TFs with complex evolutionary histories. The method will be developed based on the MADS-domain transcription factor family, which regulates important plant processes such as flowering and fruit development. One of the PhD candidates will work in the Bioinformatics Group, the other PhD candidate in the Plant Developmental Systems group of the Laboratory for Molecular Biology to perform wet-lab experiments aiming to gain insight into the specific requirements for protein-protein interactions.

This vacancy only applies to the PhD position in the Bioinformatics group at Wageningen University. This PhD student will develop a computational method, based on machine learning, to predict MADS-domain TF protein-protein interaction specificity. This method will be used to identify features that influence protein interaction, and identify amino acid residues essential for MADS-domain TF protein-protein interaction specificity. As such, the PhD student will work in close collaboration with the PhD student at Plant Developmental Systems, where input for the model will be generated and model predictions will be tested.

The research is embedded within the Bioinformatics Group of Prof. Dick de Ridder, (web page). Your daily supervisor will be Dr. Aalt-Jan van Dijk.

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, algorithm development (including the application of machine learning to study protein function and interaction), and tool construction. There are many national and international collaborations with researchers studying plant development, biotechnology and genomics.


Wageningen University & Research


You have
  • A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline
  • Demonstrable experience in applying machine learning to biological data
  • Good statistical and mathematical skills
  • Proficiency in programming (e.g. in Python)
  • Affinity with molecular biology and be interested in collaborating with researchers in this discipline
  • Perseverance in problem solving

You are an independent person, but also a team player who enjoys working in a multidisciplinary team.

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. More information can be found here.

Conditions of employment

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.


Wageningen University & Research

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.

Read the 5 reasons why your future colleagues enjoy working at WUR and watch this video 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.


  • PhD
  • Natural sciences
  • max. 38 hours per week
  • University graduate
  • P1223227-1


Wageningen University & Research

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Droevendaalsesteeg, 6708 PB, Wageningen

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