PhD Position Computational breeding for potato performance and resilience

Become part of the new research institute CropXR and use mathematics to develop eXtra Resilient (XR) crops for durable agriculture.

Job description

This vacancy is a part of the CropXR Potato program. Computational breeding aims at the construction of prediction models for yield and quality traits that combine phenomic, genomic and enviromic data. More specifically, in this project the goal is to create a hybrid model that will help to breed high performing new potato varieties resilient to drought and Nitrogen-deficiency. The hybrid model will combine features of machine learning and statistical models with those of physiological and quantitative genetic models.

The PhD candidate will study the available physiology-informed and data-based potato crop growth models and identify major genotype-specific parameters that control the performance and resilience of crop traits, such as tuber yield and quality traits with respect to drought and Nitrogen-deficiency. Next, the candidate will construct a predictive hybrid model by (a) retrieving estimates for performance and resilience-defining parameters from experimental time-series data about canopy and tuber yield for a diversity panel of potato cultivars and (b) model the genotype-specific growth parameters as functions of molecular marker profiles. This research is on the intersection of dynamic crop growth models and genomic prediction and may involve mathematical disciplines as ordinary differential equations, continuous optimization, ill-posed problems, linear and nonlinear mixed-effect models, overparameterized regression, Bayesian models and regularization. On the biological side, some knowledge of crop physiology, plant breeding and quantitative genetics will be useful.

This is a 4-year PhD position based jointly in Delft University of Technology (TUD, DIAM, Numerical Analysis) and Wageningen University & Research (WUR, Biometrics). You will be formally employed by TUD, but will receive supervision at both TUD and WUR and are ready to travel between the campuses. You should be motivated to function in an interdisciplinary research environment and to interact and collaborate with diverse partners at WUR, Utrecht University (UU), and in the potato industry. You are expected to communicate results with scientific peers, project partners, and the general public.

As a PhD candidate, you will:

• Lead the model development efforts in the Crop XR Potato project within CropXR, and coordinate model development with other PhD students in the Crop XR Potato project,
• communicate with potato physiology, microbiology and experimental research scientists, data acquisition and phenotyping specialists,
• contribute to the applied mathematics education at TUD,
• complete the Doctoral Education Programme of the TUD Graduate School.

Job requirements

You are:

•  a pleasant team player with proactive attitude and strong work ethics, 
•  an applied mathematician and/or applied statistician with interest in research, 
•  eager to work with real-world applications and experimental data.

You possess: 

• MSc degree in applied mathematics and/or applied statistics,
• knowledge of deterministic and statistical modeling methods (systems of ordinary and partial differential equations, probability, numerical methods, linear algebra, statistics, ANOVA and regression, mixed models, Bayesian methods, machine learning),
• propensity for or experience with applied and cross-disciplinary research,
• ability to program in Python, familiarity with R,
• some experience with data analysis,
• strong collaborative skills.

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.

Click here to go to the website of the Faculty of Electrical Engineering, Mathematics and Computer Science.

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 € 2901 per month in the first year to € 3707 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.  

Will you need to relocate to the Netherlands for this job? TU Delft is committed to make your move as smooth as possible! The HR unit, Coming to Delft Service, offers information on their website to help you prepare your relocation. In addition, Coming to Delft Service organises events to help you settle in the Netherlands, and expand your (social) network in Delft. A Dual Career Programme is available, to support your accompanying partner with their job search in the Netherlands.  

Additional information
If you would like more information about this vacancy or the selection procedure, please contact Neil Budko, Associate Professor or Fred van Eeuwijk, Professor, WUR, via n.v.budko@tudelft.nl, fred.vaneeuwijk@wur.nl.

Application procedure
Are you interested in this vacancy? Please apply no later than April 20, 2025 via the application button and upload the following documents:

• Motivation letter (explaining why you want to pursue this PhD, 1 page).
• CV (including links to your Bachelor/Master theses, publications if any, and at least one reference with name/e-mail).
•  Diploma and transcript of records (Bachelor and Master).

You can address your application to Neil Budko, Associate Professor.

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. For more details please check the Graduate Schools Admission Requirements. 

Please note:

• You can apply online. We will not process applications sent by email and/or post. 
• A pre-employment screening can be part of the selection procedure.
• For the final candidates, a knowledge security check will be part of the application procedure. For more information on this check, please consult Chapter 8 of the National Knowledge Security Guidelines. We carry out this check on the basis of legitimate interest.
• Please do not contact us for unsolicited services.