PhD student - Machine learning in bio- and cheminformatics

Your job

Are you looking for a PhD position at the intersection of biology, chemistry, and computer science? Are you interested in developing new machine learning methodologies in proximity to and collaboration with experimentalists? If yes, this fully funded PhD position might be an excellent match for you.

Molecules lie at the core of both chemistry and biology. They are the basis of all life and indispensable tools in medicine and agriculture. This broad range of molecular function is enabled by a vast diversity of molecular composition, structure, as well as the interaction within and between molecules. Therefore, the computational prediction of molecular functions requires a suitable computational representation of molecules and their interactions. Developing machine learning methodologies to learn suitable molecular representations is thus essential to the computational life sciences and lies at the core of our team's research. We aim to extend the current approach to data-driven machine learning in the life sciences, where molecules, including proteins, are commonly considered static entities, by introducing dynamics based on newly sourced data and constraints set by natural laws. Our goal is to implement machine learning techniques that have a truly beneficial impact on global health by decreasing drug development times and costs and that contribute toward making industrial chemical processes more sustainable.

As a PhD student, your work will focus on developing new biology- and chemistry-focused machine learning methodologies, enabling the computational representation of molecular composition, structure, dynamics, and associated expert knowledge and applying them to open problems in chemistry and biology. Specifically, you will adapt and implement methodologies from computer vision, such as neural radiance fields (NeRFs) or similar techniques, to our domains of interest. Furthermore, you will have the option to apply the developed methods in collaboration with experimentalists in the fields of synthetic biology/metabolism engineering, pharmacology, and agricultural chemistry.

As a PhD student embedded in a diverse group of international scientists, your responsibilities and opportunities will encompass:  

• Following, evaluating, and synthesising state-of-the-art machine learning, chemistry, and biology research;
• Connecting and collaborating with other national and international researchers in the life sciences and in computer science;
• Writing and presenting/publishing research papers at/in internationally renowned conferences/journals.

You will work here
The Probst Lab (https://probstlab.science) is embedded within the chair Bioinformatics Group (https://wur.eu/bif). You will be co-supervised by Daniel Probst and Dick de Ridder.

Your qualities

You are a computational biologist or computational chemist with proven expertise in programming with Python. You have also taken advanced courses on machine learning and applied it as part of your master's thesis. Alternatively, you are a computer scientist or mathematician with a proven understanding of the mathematics underlying machine learning and an interest in the life sciences. As a computational chemist or computational biologist, proven experience in molecular dynamics simulations is an advantage. As a computer scientist or mathematician, proven experience in computer vision is an advantage.

You possess:

• A successfully completed MSc degree in computer science, mathematics, biology, chemistry, or a related program;
• Proven experience in Python programming or high proficiency in another language such as C/++ or Rust. It is an advantage if you can provide a link to a code repository of a project where you were or are the main contributor;
• Experience in implementing and applying machine learning methodologies, specifically deep neural networks;
• An interest in applying state-of-the-art machine learning techniques to various fields in the life sciences;
• A collaborative attitude valuing the importance of interdisciplinarity and open science;
• The drive to present and share your work at international conferences;
• Excellent English writing skills and experience in scientific writing;

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.

We offer you

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

• 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 € 2.872,- per month rising to € 3.670,-  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 19th 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.

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. 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 position, please contact dr. Daniel Probst , daniel.probst@wur.nl or prof. Dick de Ridder, telephone +31 317 484074 or by e-mail, dick.deridder@wur.nl.

For more information about the procedure, please contact Noorien Abbas, corporate recruiter, vacaturemeldingen.psg@wur.nl

Do you want to apply?
You can apply directly 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 Januari 6th, 2024

Welcome, safe, and valued
Wageningen University & Research (WUR) highly values diversity and inclusion because we believe that different insights lead to innovative solutions. We create a work environment where everyone feels welcome, safe, and appreciated, regardless of background, identity, or experience. Together, we are building a culture where everyone's unique contribution adds to the success of our organization.

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.