Pangenome mining for quarantine organisms

Wageningen University
Bioinformatics Group
Netherlands Wageningen


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.


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;
- a very good level of oral and written English.

Start date

To be determined

How to Apply

Please apply through the online form on our website,