PhD in Modelling yeast metabolis and regulated cell death

Different yeast species play a vital role in industrial biotechnology for the sustainable production of a wide range of products, for example ethanol as a biofuel or protein ingredients for alternatives to animal-based products. However, also the lifespan of these yeast cells is finite, and their death negatively impacts processes: for example, with regards to process duration or product quality.

Therefore, we developed an approach that integrates the disciplines of fundamental cell and molecular biology, systems and synthetic biology with bioprocess and metabolic engineering to improve both our understanding of these cell death processes as well as the survival and performance of different yeast species in industrial bioprocesses. 

In this project, you will:

• develop mathematical models on how yeast cell actors impact physiology and metabolism and how cell heterogeneity affects the cell population;  
• develop highly curated and predictive enzyme constrained Genome scale models (ecGEMs) of Saccharomyces cerevisiae and Komagataella phaffii that incorporate regulated cell death (RCD) pathways;
• extensively model yeast metabolism during RCD under industrially relevant conditions; 
• characterize molecular mechanisms and identify biomarkers. The models will be used to design strategies to postpone yeast cell death under industrially relevant conditions. 

You will work here

A consortium at seven host institutes (Wageningen Universiteit, Universidade do Minho, Danmarks Tekniske Universitet, Austrian Centre for Industrial Biotechnology, Imperial College London, Università degli Studi di Milano Bicocca and Chalmers Tekniska Högskola) together with fifteen associated partners, ranging from start-up to large biotechnology companies and renowned research institutes aims to understand how yeast cells die under industrial process conditions and use this knowledge to improve biomanufacturing. 

Your project, together with 12 other doctoral projects, will focus on a different aspect, but in strong synergy with the other projects. As such, each PhD will receive a strongly interdisciplinary training alongside performing exciting research. During this PhD project you will perform secondments to the Austrian Centre of Industrial Biotechnology (Austria) and Cambrium (Germany). 

Your research is embedded within the chair Systems and Synthetic Biology and you will be supervised by Prof. Dr Maria Suarez Diez and Dr Edoardo Saccenti. Within the project, you will collaborate with the other consortium members of UPsYDe and especially the Laboratory of Bioprocess engineering (BPE) at Wageningen University, the laboratories of Dr. Briggite Gasser (Austrian Centre of Industrial Biotechnology) (Viena, Austria) and of Dr Pierre Salvy at Cambrium (Berlin, Germany).

You have a passion for developing mathematical models of complex biological processes and are willing to develop multiscale models that link genomic information, regulatory pathways, cellular metabolism, and population dynamics. You have high standards for working accurately following findable, accessible, interoperable and reusable approaches to ensure reproducibility of computation work. You have the flexibility to work independently on challenging computational tasks and are willing to explore and develop combinations of methods for modelling biological systems. You are willing to communicate results to experts of different and related or more distant fields.  

You also possess:

• a successfully completed MSc degree in Bioinformatics;
• experience in developing and using genome scale constraint-based models to address complex biological questions and experinece in conducting research in genomics; 
• a background in statistical methods and machine learning approaches and their application in life sciences;
• a strong desire and ability to quickly master new computational techniques to effectively tackle complex, multidisciplinary scientific queries; 
• experience in using methods to enable collaborative programing in complex projects (git or other version control approaches) and to enable code reusability (containerization) will be strongly valued.   

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.

To be eligible for the positions general conditions apply, namely:

1. not be in possession of a doctoral degree at the date of the recruitment;
2. comply with the european mobility rules. No residence or main activity in the Netherlands for more than 12 months in the 36 months before the recruitment date.

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;
• 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 year-end 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 € 3.059,- per month rising to € 3.881,-  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 offers plenty of opportunities for growth and development, with a strong internal recruitment policy and excellent training programmes.

You will work on the greenest and most innovative campus in the Netherlands, in an international and open working environment. For 20 consecutive years, we have been voted the "best university" in the Netherlands! A place to be proud of.

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.

For more information about the position, please contact Prof. Dr. Maria Suarez Diez by email:  maria.suarezdiez@wur.nl.

Questions about the procedure? Get in touch with Evelien Janssen, Corporate Recruiter, by email: evelien.janssen@wur.nl.

Ready 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. Only applications submitted through our website will be considered.

To apply, please send the following documents (max. 3 pages in total for both documents):

• Complete and up-to-date curriculum vitae;
• Motivation letter.

The maximum length of the documents must not exceed 3 pages. If it exceeds, applications will not be considered. Additional files such as grades and transcripts are not required during this stage and will not be considered.

You can apply until 19 December 2025. The first interviews are scheduled shortly after the closing date. The intended starting date is 15 January 2026.

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.

​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.

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