Postdoc position on cross-species translation of gene regulation modules

Do you want to be part of the development of resilient crops that can continue to feed the world even when faced with climate change, reduced pesticide use, and reduced irrigation? Then you might be the ideal candidate to join our new, interdisciplinary research institute CropXR!

With a budget of 96 million euros over a period of ten years, CropXR focuses on creating eXtra Resilient (XR), sustainable, and climate-adaptive crops. By combining plant biology, simulation modelling, and artificial intelligence we aim to develop ‘smart breeding and cultivation’ methods. Thus, we try to speed up the breeding of complex resilience traits for several crops in different growing systems. This collaborative effort involves four universities and numerous companies. It encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding (learn more about CropXR at cropx.org).

This postdoc position at Wageningen University is part of the “Translator” work package within the core research programme of CropXR. Our goal is to develop computational methods to translate integrated plant models between species, combining machine-learning inferred gene regulation modules with mechanistic plant models. We will develop and demonstrate these methods by translating a model of the response to combined drought and heat stress on seedlings, from a model plant species (Arabidopsis thaliana), where data is abundant, to various crop species such as cauliflower, potato, tomato and lettuce, where data is much sparser.

This highly interdisciplinary, collaborative work package brings together experimentalists, providing measurement data for translation and testing model predictions; bioinformaticians, investigating evolutionary conservation of sequence, (co)expression and regulation; and modelers, developing crop-specific integrated plant models.

As a postdoctoral researcher in this team, you will be responsible for linking the bioinformatics work on sequence/expression conservation and the mechanistic modeling. You will develop machine learning/deep learning-based bioinformatics methods to translate gene regulation modules between species by integrating orthology, gene and genome annotation, (co)expression and known regulatory interactions.

Your duties and responsibilities include:

• developing methods to translate gene regulation modules and key regulators between species
• integrating translated modules with several crop-specific mechanistic models to be developed
• using the resulting models to propose new experiments for iterative model improvement
• maintaining and organizing close collaboration in the work package and more broadly in CropXR

Your team
You will be located at Wageningen University and be part of the Bioinformatics Group. However, you will collaborate with other researchers in the project, particularly with bioinformaticians and modelers at the Theoretical Biology & Bioinformatics group at Utrecht University.

You are a team player, motivated to help CropXR in working towards its mission, interested in collaborating with computational and experimental colleagues in academia and industry, and skilled and knowledgeable in bioinformatics and machine learning/deep learning.

You also have:

• a strong academic record and a PhD in bioinformatics, computational biology or related discipline
• proven proficiency in programming (Python) and machine learning/deep learning
• experience with (comparative) genomics and transcriptomics analysis
• an interest in working in an interdisciplinary team, towards application in plant sciences
• excellent oral and written communication skills in English

In our international working environment there is an increasing amount of communication in English. For this position this is approximately language level C1.

You will work here
Wageningen UR has a global reputation for its ground-breaking research and innovative education in the fields of food and health, sustainable agrosystems, the rural environment, and societal development - all of which make an essential contribution to the quality of life, i.e. the supply of safe and healthy food and drink, on the one hand, and the chance to live, work and play in a balanced ecosystem with a large variety of plants and animals on the other. Within Wageningen UR, the Plant Sciences Group (PSG) brings together science education and scientific, strategic and applied research in the fields of biology, of plants in relation to their environment, of plant-related organisms and of plant production.

This project will be carried out at the Bioinformatics Group within PSG. This research 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 (integrative) computational omics analysis, algorithm development, machine learning and scientific data infrastructure. There are many national and international collaborations with researchers studying plant and microbe metabolism, biotechnology and genomics, of which CropXR is one.

CropXR is a Dutch research consortium that was launched in 2023 to contribute to improving agricultural production by making it less vulnerable to climate change. Furthermore, it aims to reduce agriculture’s dependence on artificial fertilizers and chemical pesticides. This collaborative initiative brings together various academic disciplines (such as plant sciences, computational and data sciences, and social sciences) and numerous private industry companies to drive sustainable change. It encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding.

Together, they have a crucial mission: to develop innovative, climate-resilient crops that enable sustainable agriculture and contribute to food security. CropXR combines science and technology to achieve this impact and receives financial support from NWO, the Dutch National Growth Fund, and the Foundation for Food & Agricultural Research. Learn more about CropXR at cropx.org.

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;
• 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 of course receive a good salary. Depending on your experience, we offer a competitive gross salary of between € 3.378,- and € 5.331,- for a full-time working week of 38 hours, in accordance with the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale 10). Additionally, a contract for 0.8 or 0.9 fte can be discussed. As for your contract, we initially offer a one-year contract that can be extended with another 3 years on good performance.
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.

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 coming to Wageningen. Furthermore, our Welcome Center can assist you with any additional advice and information about for example housing, opening a bank account, dual career programs 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.

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.

For more information about the position, please contact Dick de Ridder via email: dick.deridder@wur.nl.

Questions about the procedure? Get in touch with vacaturemeldingen.psg@wur.nl.

Ready to apply?
Are you interested in the position but are you unsure whether you (already) meet all the criteria? Please do not feel discouraged to apply. We welcome bright minds with diverse skills and backgrounds. Meeting all the requirements from the start is not a prerequisite.

Click on the application button next to the vacancy on our website. Only applications submitted through our website will be considered.

You can apply until May 12, 2025. The first interviews are scheduled for May 28, 2025.

Procedure
As part of our selection process, an assessment may be incorporated within the procedure.

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.

For more information about the position, please contact Dick de Ridder via email: dick.deridder@wur.nl.

Questions about the procedure? Get in touch with vacaturemeldingen.psg@wur.nl.

Ready to apply?
Are you interested in the position but are you unsure whether you (already) meet all the criteria? Please do not feel discouraged to apply. We welcome bright minds with diverse skills and backgrounds. Meeting all the requirements from the start is not a prerequisite.

Click on the application button next to the vacancy on our website. Only applications submitted through our website will be considered.

You can apply until May 12, 2025. The first interviews are scheduled for May 28, 2025.

Procedure
As part of our selection process, an assessment may be incorporated within the procedure.

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.