Postdoc Position in Integrating Plant Microbiome Omics Data for Causal Inference

Do you enjoy using computational approaches to study biological problems? Are you interested in developing and applying methodology to investigate plant-microbiome-interactions? We invite enthusiastic and dedicated candidates to join our cutting-edge research team as a postdoctoral researcher to work on developing novel methodology to integrate plant microbiome and omics data.

Join us!
This position is part of MiCRop a government-funded research programme in the Netherlands that includes world-leading research institutes and private partners. You will actively interact with a vibrant community of PhD candidates and postdocs, and apply your methodologies to the rich datasets available within the consortium. The programme builds on and fosters many national and international collaborations with researchers studying plant and microbial interactions, metabolism, ecology, and (meta-) genomics.

The focus of this project is on the inference of causal relationships based on various microbiome, metabolome, transcriptome, and phenotype measurements, in order to understand how microbial communities impact plant health, growth, and resilience. In doing so, we will make use of biological knowledge related to these various omics datasets, e.g. related to microbial functions or pathways. The results from applying the developed approaches will be utilized to facilitate the identification of modules of microbial species, genes, or metabolites significantly associated with plant phenotypes. These can in turn be experimentally tested by MiCRop partners.

What you will do
You will work on the following research objectives:
1) Develop methodology for the inference of causal relationships based on microbiome, metabolome, plant transcriptome and phenotype measurements.
2) Incorporate biological knowledge, e.g. related to microbial functions or pathways, into this inference approach.
3) In collaboration with other researchers in the project, apply the methodology to datasets of interest within the MiCRop consortium.
Tasks and responsibilities
You will:

• develop computational methodology for causal inference;
• make use of available and newly obtained omics datasets as input for your approaches;
• collaborate with both experimental researchers as well as with bioinformatics/systems biology researchers (e.g. other postdocs/PhD students working in the MiCRop project);
• provide data analysis support within MiCRop, e.g. by organizing training events or Q&A sessions;
• be an active member of the research group and take responsibility for shared tasks; discuss your work with the group members and during BDA and MiCRop meetings; incorporate feedback and give input to others;
• take a leading role in writing manuscripts.

What we look for
You are passionate about science and have a particular interest in the development and application of computational methodology in biology. You enjoy close collaboration with domain experts. You have a creative mind and look forward to work at the cutting-edge of computational technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of computational researchers and microbiome scientists.
You have/are:

• a PhD in Data Science, Artificial Intelligence, Bioinformatics, Systems Biology or similar;
• experience with multivariate data such as omics or microbiome data; experience in causal inference is a plus
• able to communicate with non-experts on bioinformatics and/or statistics issues;
• professional command of English.

What we offer you
We offer a temporary contract for 38 hours per week for the duration of 12 months. After satisfactory evaluation the contract will be extended with 36 months. The preferred starting date is May 1st, 2025. The salary, depending on relevant experience before the beginning of the employment contract, will be between € 3.378 – 5.331 gross per month, based on a fulltime contract (38 hours a week). This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:

• 232 holiday hours per year (based on fulltime);
• multiple courses to follow from our Teaching and Learning Centre;
• the possibility to follow courses to learn Dutch;
• help with housing for a studio or small apartment when you’re moving from abroad.

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

Where you will work
The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.

You will be part of the Biosystems Data Analysis group (BDA) of the Swammerdam Institute for Life Sciences at the University of Amsterdam (UvA). BDA works on the development of methodology for data mining, machine learning/deep learning, data fusion, and modelling and application of these methods to answer biological questions, in close collaboration with domain experts. Want to know more about our organisation? Read more about working at the University of Amsterdam.

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 15 March 2025. Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• the names and email addresses of two references who can provide letters of recommendation.

A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). Only complete applications received within the response period via the link below will be considered. The interviews will be held in the second half of March 2025.

Do you have any questions or do you require additional information? Please contact:

• Prof. dr. Aalt-Jan van Dijk
• E-mail: a.d.j.vandijk@uva.nl
• T: +31 20 525 5519

38 hours per week

Science Park 904