PhD Position in Pangenome Mining for Quarantine Organisms

Wageningen University


PhD Position in Pangenome Mining for Quarantine Organisms

Published on
April 13, 2021

Location Wageningen

We are looking for

We are looking for a PhD student to work on the development of comparative and pangenomic strategies, using machine learning, for monitoring and diversity analysis of high-risk plant pathogens and pests, so-called quarantine organisms.

Within a project on the development of new detection strategies and analysis of quarantine organisms (q-organisms), we have a vacancy for a PhD student in the field of bioinformatics. This PhD student will be responsible for the construction, annotation, and analysis of the pangenome of various q-organisms. This includes the development of machine-learning methodology on pangenome graphs, to identify important features associated to pathogenicity or host specificity for instance, and visualizations to support genome analysis and outbreak management. Novel methods will be added to the software package PanTools (, developed at Wageningen University.

The PhD student on this TKI project will become part of a larger team aiming for the detection and tracing of q-organisms, which pose an unacceptable risk to crops, forest and the wider environment. The project addresses the need for novel genomics-based strategies that make use of the genetic diversity within these organisms, by exploiting smart collections that cover the full genetic diversity and include rich metadata, and analyzing them using pangenomic technology. The PhD student will work closely together with experts from the National Plant Protection organization (NPPO-NL) and industrial partners.

The student will work in the Bioinformatics Group of Wageningen University (, embedded in the comparative (pan)genomics team led by Sandra Smit and will work with the group of Theo van der Lee in the business unit Biointeractions and Plant Health (, This 4-year position offers the opportunity to apply your research skills in the domain of bioinformatics and algorithms, and includes time for personal development. Are you a skilled bioinformatician with a collaborative attitude, interested in genetic diversity of pathogens that could directly impact outbreak management? We look forward to your application. 

We ask

For this interdisciplinary collaboration we are looking for an ambitious, enthusiastic scientist with:

  • an MSc degree in bioinformatics, computer science or related area;
  • experience in algorithm development and machine learning, and demonstrable skills in mathematics, statistics and programming;
  • affinity with genomics and next-generation sequencing data analysis;
  • enthusiasm for working in an interdisciplinary team, bringing bioinformatics methodology to practical application;
  • good organizational skills;
  • you have a very good level of oral and written English. You are required to show us a certification of English skills. For more information about the required level please take a look at:;
  • you meet all the entry requirements of the  WUR PhD programme.

We offer

We offer a dynamic and driven research environment with a strong international profile and a large number of young researchers; a state-of-the art computational infrastructure; close collaboration with other PhD students, researchers in the plant and animal sciences and relevant companies; and the possibility to further develop your scientific education with courses, training and conferences. There will be opportunities to be involved in teaching at workshops or courses.

The position is full-time (38 hours/week), initially for 1 year after which a go/no-go decision will be taken on extension with another three years. The gross salary in the first year is € 2395,- per month rising to € 3061,- in the fourth year for a full-time appointment.

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

  • sabbatical leave, study leave, and paid parental leave
  • working hours that can be discussed and arranged so that they allow for the best possible work-life balance
  • the option to accrue additional flexible hours by working more, up to 40 hours per week
  • there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee
  • a fixed December bonus of 8.3%
  • excellent pension scheme
You will work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 16th consecutive time.

Coming from abroad

Wageningen University & Research is the university and research centre for the life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees. Applicants from abroad moving to the Netherlands may qualify for a special tax relief, known as the 30% ruling. Our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.

Feeling welcome also has everything to do with being well informed. Wageningen University & Research's International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about helping your partner to find a job, housing, schooling, and other issues.

More information

For more information about this function, contact dr. Theo van der Lee at, or dr. Sandra Smit at For more information about the procedure, please contact

Do you want to apply?

You can apply directly using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.

This vacancy will be listed up to and including May 9, 2021.

In this first round please only send your resume and motivation letter. Any other documents will not be taken into consideration at this stage.

We are

The mission of Wageningen University and Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment.

With its roughly 30 branches, 6.500 employees and 12.500 students, Wageningen University & Research is one of the leading organisations in its domain. An integrated approach to problems and the cooperation between various disciplines are at the heart of Wageningen’s unique approach. WUR has been named Best Employer in the Education category for 2019-2020.

These are the points our employees list as good reasons to come work at WUR: read the 5 reasons to come work at WUR.

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated. 

The business unit Biointeractions and Plant Health studies harmful and useful insects, viruses, bacteria and fungi and analyze their effect on plants. Both in a positive (biological control) and negative sense (damage to plants). We work on IPM: integrated pest management, we detect pests and diseases and we examine the health of bees. In our phytosanitary research, we work with advanced diagnostic tests to prevent contamination.

The Bioinformatics Group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, we develop and apply novel computational methods for the analysis and integration of –omics data. The group has a strong track record in genomics, algorithm development and machine learning. Still growing, the group currently holds 5 faculty and approx. 20 PhD students and postdocs, as well as 10-15 MSc students at any given time.

Equal opportunities

WUR is an equal opportunity employer. We are keen to receive applications from all sufficiently qualified people, regardless of their ethnicity, gender, functional impairment, religion/life philosophy, sexual orientation, or age. 

Apply now

In your application, please refer to


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