PhD Candidate in Integrated Modeling for Plant Life-History Traits

Faculty/Services:  Faculty of Science
Educational level:  Master
Function type:  PhD position
Closing date:  23.08.2024
Vacancy number:  13201

Do you enjoy using computational approaches to study biological problems? Are you interested in using a combination of machine learning and mechanistic modelling? We invite enthusiastic and dedicated candidates to join our cutting-edge research team as a PhD candidate to work on developing novel methodology to model plant life-history traits such as flowering time, fertility and seed germination. The position is part of the new, interdisciplinary research institute CropXR. 


In this project, you will work towards unraveling the regulatory networks controlling reproduction-associated transitions under temperature and drought stress. We will use the main model plant Arabidopsis, because of the wealth of existing information. In four accompanying experimental PhD-projects, data will be obtained on the effects of temperature and drought at the transcriptome and phenotype level. 

Your task will be to integrate these datasets, using a combination of mechanistic models and machine learning. This will aid selection of signaling processes to be targeted towards improving plant yield under suboptimal conditions. As part of the larger CropXR consortium, you will also collaborate with additional PhD candidates working on methodology for integrating machine learning and mechanistic modeling.


Your work will take place at the Swammerdam Institute of Life Sciences, one if the research institutes of the University of Amsterdam. 


What are you going to do?

You will work on the following research objectives: 

  1. Develop an integrated model of the regulatory networks controlling reproduction-associated transitions, starting with flowering time and the effect of temperature. An existing multiscale model will be expanded using machine learning derived modules, based on existing data.
  2. Improve the integrated model by adding additional core regulatory genes and data on epigenetic regulation, generation of additional modules using newly obtained data, and including environmental effects on fertility and seed germination.
  3. From the developed model, propose new experiments to our collaborators, and use the model to study the effect of stress on life-history traits.

Tasks and responsibilities

You will:
•    complete a PhD thesis within the official appointment duration of four years;
•    develop ODE-based models as well as supervised and unsupervised machine learning approaches, towards generating

     an integrated model for plant life-history traits;
•    make use of available experimental data and data newly obtained by our collaborators, in particular transcriptome sequencing;
•    closely collaborate with experimental researchers (PhD students working on the various traits) as well as with

     computational researchers (PhD students working on developing methodology for integrating mechanistic modeling and

     machine learning);
•    be an active member of the research group and take responsibility for shared tasks; discuss your work with the group members

     and during CropXR meetings, incorporate feedback and give input to others;
•    take a leading role in writing manuscripts;
•    participate in the Faculty of Science PhD training program; 
•    assist in teaching and supervise Bachelor and Master theses.

Your profile

You are passionate about science and have a particular interest in modelling. 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 plant scientists.


Your experience and profile

You have/are:
•    a MSc degree in Data Science, Artificial Intelligence, Computational Science, Bioinformatics/Systems Biology or similar;
•    experience in using differential equations to model biological systems and interested in using machine learning;

     or experience in using machine learning on biological data and interested in using differential equations to model biological systems;
•    able to communicate with non-experts on computational issues;
•    professional command of English.


Our offer

We offer a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is November 1st, 2024. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.


Based on a full-time appointment (38 hours per week) the gross monthly salary will range from € 2.770 in the first year to €3.539 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The Collective Labour Agreement of Universities of the Netherlands 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;
•    a complete educational program for PhD students;
•    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.


About us

The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.


The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain. 


The Swammerdam Institute for Life Sciences (SILS) is one of the Faculty of Science’s largest institutes. Its approximately 240 scientists and staff members work in 16 research groups that perform excellent research centred on four themes: Neurosciences, Cell & Systems Biology, Microbiology and Green Life Sciences.


With a budget of 96 million Euro over the next decade, 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 to speed up breeding for complex resilience traits in different growing systems for several crops. This collaborative effort involves four universities, numerous companies, and encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding. 


Want to know more about our organisation? Read more about working at the University of Amsterdam.



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


Job application

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 23 August 2024. 

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.


Only complete applications received within the response period via the link below will be considered.


The interviews will be held beginning of September 2024. 


A knowledge security check can be part of the selection procedure. 
(for details: national knowledge security guidelines



Studies show that women and members of underrepresented groups only apply for jobs if they meet 100% of the qualifications. Do you meet the educational requirements but do not yet have all the required experience? Then the UvA encourages you to apply anyway.