Utrecht University
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Postdoc in AI Foundation Models for Crop Microbiomes at Utrecht University Utrecht University in Netherlands
Degree Level
Postdoc
Field of study
Computer Science
Funding
Postdoctoral position initially for 1 year, extendable by 3 years after positive evaluation. Gross monthly salary between €3,706 and €5,760 depending on qualifications and experience, plus 8% holiday pay, 8.3% year-end bonus, pension scheme, partially paid parental leave, flexible employment terms, and additional benefits. Based on a 38-hour working week.
Deadline
Oct 17, 2026
Country
Netherlands
University
Utrecht University
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About this position
Utrecht University is advertising a Postdoc Position in AI Foundation Models for Crop Microbiomes within the Faculty of Science, Department of Information and Computing Sciences, in close collaboration with the Plant-Microbe Interactions group. The project is part of the European Innovation Council (EIC) Pathfinder consortium NOAH, which develops ARCA, an AI foundation model for crop microbiomes.
The post sits at the intersection of computer science, artificial intelligence, deep learning, bioinformatics, microbial ecology, microbiome biology, and agriculture. The successful candidate will design, train, and benchmark foundation-model architectures for sparse, high-dimensional microbiome data, including transformer-based and masked-autoencoder approaches, self-supervised learning objectives, and generative components such as autoencoder- or diffusion-based methods. The work also includes interpretable AI, reproducible workflows, and downstream prediction for crop-relevant outcomes.
The research environment is highly interdisciplinary, involving Utrecht University’s AI Technology for Life and Plant-Microbe Interactions groups, with access to GPU/HPC infrastructure and large curated microbiome and microbial genome datasets. The project also connects with partners at Aarhus University, Niab, INRAE, and The Hyve, and model predictions will be tested experimentally in greenhouse and field settings.
This is a postdoctoral opening, not a PhD or master’s call. Applicants should have a PhD, or be close to completion, in machine learning, AI, computational biology, bioinformatics, computer science, or a related field. Strong Python and PyTorch skills are expected, along with experience in deep learning and working with biological or omics data. Experience with microbiome or metagenomics data is an advantage.
The position starts in January 2027, initially for one year and extendable by three years after positive evaluation. The salary is listed at €3,706–€5,760 gross per month (scale 10, CAO NU), plus holiday pay, year-end bonus, pension, and other employment benefits. The application deadline is 17 October 2026.
To apply, use the Utrecht University vacancy page and submit a CV, motivation letter, two references, and proof of PhD status/completion. For questions about the position, contact Dr Ronnie de Jonge at [email protected]; application procedure questions can be sent to [email protected].
Funding details
Postdoctoral position initially for 1 year, extendable by 3 years after positive evaluation. Gross monthly salary between €3,706 and €5,760 depending on qualifications and experience, plus 8% holiday pay, 8.3% year-end bonus, pension scheme, partially paid parental leave, flexible employment terms, and additional benefits. Based on a 38-hour working week.
What's required
A PhD, or a PhD close to completion, in machine learning, artificial intelligence, computational biology, bioinformatics, computer science or a closely related field. Strong hands-on experience with deep learning and modern representation learning is expected, preferably including transformers, self-supervised learning, foundation models, autoencoders or related architectures. Applicants should have strong Python programming skills and experience with PyTorch and GPU/HPC training and evaluation. Experience with high-dimensional biological, omics, ecological or similarly sparse and heterogeneous data is required or a clear motivation to develop this expertise. Interest in interpretable AI, rigorous benchmarking, reproducible research, and cross-disciplinary collaboration is important. Experience with microbiome data, microbial genomics, metagenomics or multimodal biological data is an advantage.
How to apply
Apply via the Utrecht University application portal using the “Apply now” button. Enclose your CV, a motivation letter addressing your expertise and approach to the tasks, names and contact details of at least two references, and a copy of your PhD certificate or a letter stating when your defence will take place.
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