PhD Enhancing Plant Resilience through Biologically-Inspired Machine Learning

Join us in advancing the frontier of plant sciences and making a tangible impact on agricultural resilience through the power of machine learning!

Job description

We are seeking a highly motivated PhD candidate to join our research team focused on enhancing plant resilience using cutting-edge data analysis and machine learning techniques. This exciting opportunity will involve designing and integrating biological knowledge into machine learning models to uncover mechanisms controlling plant resilience. The ultimate goal is to connect these findings with simulation models to predict how plants respond to environmental stresses such as drought and extreme temperatures, supporting plant breeding industry to develop crops that can withstand combinations of stresses brought by a changing climate.

The project is part of the Crop-XR program, a highly collaborative 10-year national initiative of universities and industry, with a mission to grow resilient crops developed by a data-driven design.

Key Challenges:

• Develop and implement biologically-inspired machine learning algorithms aimed at identifying gene regulatory networks that influence plant resilience.
• Integrate spatial and temporal data to establish connections between gene modules and specific plant organs and developmental stages.
• Utilize predictive modeling to identify key genes with significant impacts on stress resilience, thereby pinpointing potential targets for the breeding of more resilient plant varieties.
• Collaborate closely with modelers and plant biology experimenters to validate and enhance computational models, ensuring their accuracy and applicability.
• Contribute to the integration of mechanistic and machine learning models to simulate how plants respond to environmental changes and leverage these simulations to propose new experiments that generate "smart data" for ongoing model refinement and improvement.

Benefits:

• Opportunity to work on cutting-edge research with significant real-world impact.
• Collaborative and dynamic research environment.
• Access to state-of-the-art facilities and resources.
• Support for professional development and attendance at international conferences.

This PhD position is positioned within the Delft Bioinformatics Lab, part of the Computer Science department of the Delft University of Technology under supervision of Prof. Marcel Reinders. The PhD will be done in close collaboration with the Bioinformatics Group at Wageningen University, and co-supervised by Prof. Dick de Ridder.

Requirements

• A Master's degree in Computer science, Artificial Intelligence (AI), Computational Biology, Bioinformatics, or a related field with an affinity to plant sciences.
• Strong background in machine learning and data analysis.
• Experience with biological data integration and simulation modeling.
• Excellent programming skills (e.g., Python, R) and familiarity with machine learning libraries.
• Strong analytical and problem-solving skills.
• Ability to work independently and as part of a multidisciplinary team.
• Strong interpersonal communication and collaboration abilities
• Good communication skills and proficiency in English.

Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis.

Conditions of employment

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1,5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2,5 years assuming everything goes well and performance requirements are met.

Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2770 per month in the first year to € 3539 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged.

For international applicants, TU Delft has the Coming to Delft Service. This service provides information for new international employees to help you prepare the relocation and to settle in the Netherlands. The Coming to Delft Service offers a Dual Career Programme for partners and they organise events to expand your (social) network.

TU Delft (Delft University of Technology)

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values and we actively engage to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

Faculty Electrical Engineering, Mathematics and Computer Science

The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines. Combined, they reinforce each other and are the driving force behind the technology we all use in our daily lives. Technology such as the electricity grid, which our faculty is helping to make completely sustainable and future-proof. At the same time, we are developing the chips and sensors of the future, whilst also setting the foundations for the software technologies to run on this new generation of equipment – which of course includes AI. Meanwhile we are pushing the limits of applied mathematics, for example mapping out disease processes using single cell data, and using mathematics to simulate gigantic ash plumes after a volcanic eruption. In other words: there is plenty of room at the faculty for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1000 employees and 4,000 students work and study in this innovative environment.

CropXR

CropXR was launched in 2023 to help make agricultural production less vulnerable to climate change and less dependent on artificial fertilizers and chemical pesticides. The institute is a joint venture of the universities of Amsterdam, Delft, Wageningen and Utrecht in partnership with Plantum, the Dutch plant breeding sector association. CropXR brings together efforts from different academic disciplines (such as plant sciences, computational and data sciences, and social sciences) and private industry to help bring about sustainable change. It receives support from NWO, the Dutch National Growth Fund, and the Foundation for Food & Agricultural Research.