PhD Position Privacy for Crop Breeding

Do you want to contribute to privacy-preserving models for crop breeding? Join the Pattern Recognition and Bioinformatics section and work at the interface of model design and biological applications.

Job description

Genome sequence models are increasingly used in plant breeding and crop improvement pipelines. But training such models on private genomic data carries a risk: rather than learning general rules of sequence-function relationships, a model may simply memorize segments of the genomes it was trained on and later reproduce these. Since training data may be commercially sensitive, we need to understand when and why sequence models reproduce their training data and how to prevent it.

This project aims to characterize and mitigate memorization risk in sequence models to ensure privacy of training data. The PhD student will develop methods to quantify the degree to which a trained model reproduces specific training sequences, investigate how properties specific to plant genomes shape memorization behavior, design strategies that prevent leakage, and translate these findings into practical guidance.

The student will be embedded in the Pattern Recognition and Bioinformatics section, INSY department, TU Delft. In this project we work together with KeyGene, a research company for the development of breakthrough technology innovation for crop improvement. 

Job requirements 

To be considered for the position you must:

• have a master’s degree (or equivalent) in Computer Science.
• have proven affinity with (and preferably a degree in) Biology.    
• have strong computational skills in model design, implementation and testing.
• have experience with courses and projects in Bioinformatics.
• have good communication skills in English (both verbal and written).
• be eager to push yourself to learn new skills, exchange knowledge and collaborate where possible.
• be willing to teach and guide students. Prior teaching experience is appreciated.  

To thrive as a PhD candidate, it’s crucial to have a strong research mindset driven by curiosity and passion for your topic. Reflecting on your motivation for pursuing a PhD trajectory is essential, as this path involves unique challenges and uncertainties inherent to scientific exploration. Success requires dedication, adaptability, the ability to analyze complex problems, manage your time effectively, innovate and stay resilient under pressure. Combined with the ability and willingness to work independently and collaborate well, these qualities are indispensable for a fulfilling PhD journey. These experiences will build you as an independent researcher, expand your professional network, and pave the way for diverse career pave the way for diverse career paths, inside or outside academia.

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 €3059 - €3881 gross per month, from the first year to the fourth year based on a fulltime contract (38 hours), plus 8% holiday allowance and an end-of-year bonus of 8.3%.  

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 Dr. Jasmijn Baaijens, via j.a.baaijens@tudelft.nl.

Application procedure
Are you interested in this vacancy? Please apply no later than 20 July 2026 via the application button and upload the following documents:

• CV
• Motivational letter. The letter of motivation should summarise (I) why you want to do a PhD, (II) why the project is of interest to you, (III) evidence of suitability for the job, and (IV) what you hope to gain from the position. 
• Academic transcripts (both MSc and BSc degrees)
• MSc thesis (link or PDF)

You can address your application to Dr. Jasmijn Baaijens.

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. 
• As part of knowledge security, TU Delft conducts a risk assessment during the recruitment of personnel. We do this, among other things, to prevent the unwanted transfer of sensitive knowledge and technology. The assessment is based on information provided by the candidates themselves, such as their motivation letter and CV, and takes place at the final stages of the selection process. When the outcome of the assessment is negative, the candidate will be informed. The processing of personal data in the context of the risk assessment is carried out on the legal basis of the GDPR: performing a public task in the public interest. You can find more information about this assessment on our website about knowledge security.
• Please do not contact us for unsolicited services.