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 (one year, with a 3-year extension on good performance) 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
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.
All applications should be submitted through our online vacancy system: www.wur.nl/en/vacancy/postdoc-position-on-cross-species-translation-of-gene-regulation-modules.htm