This interdisciplinary PhD project combines visual analytics and comparative genomics. Plant breeding companies need efficient tools to assess and use genetic diversity in their crop varieties to develop the crops of the future. Where traditional genome sequences fail to represent genetic variation, innovative pangenome data structures do incorporate this variation and thus pave the way for the efficient analysis of crop data. However, the wide adoption of pangenomics in the plant-breeding industry is hampered by a lack of visualization strategies for plant pangenomes.

The aim of this project is to develop a visual analytics toolkit for a state-of-the art pangenome approach, called PanTools, which will enable plant breeders to interactively view and analyze genetic variation in their crops. PanTools is geared towards large plant genomes and can handle significant genetic diversity. Innovative and biologically meaningful views and visual encodings of the pangenome data structure are necessary, as contemporary, mainly graph-based visualizations are not informative. Many existing solutions either target gene sets or sequence-level pangenomes, but not the hierarchical pangenomes, including annotations and functional/evolutionary relationships, as constructed by PanTools. Therefore, there is a clear need for pangenomic solutions with a wide interactive visualization repertoire to support breeding analytics and advance genomics-based plant breeding.

This project is a collaboration between the Visualization Group at Eindhoven University of Technology and the Bioinformatics Group at Wageningen UR, in close connection to industrial partners in plant breeding.

We are looking for motivated candidates that meet the following requirements:

• an MSc degree in visual analytics, information visualization, or closely related field;
• affinity with real-world problems and data from the life sciences;
• software development skills at least in one language, e.g. Python, Java, JavaScript;
• good communication skills in English, both in speaking and in writing;
• ability to work interdependently in a team of data scientists and interact with domain experts;
• being enthusiastic about working on this challenging project in a collaborative environment;
• willingness to work 1-2 days per week in Wageningen and 3-4 days in Eindhoven.

• A full-time temporary appointment for a period of 4 years, with an intermediate evaluation after 9 months;
• A gross salary of € 2.325 per month in the first year increasing up to € 2.972 in the fourth year;
• Tight collaboration between academia and industry with access to real data and domain expertise;
• Support for your personal development and career planning including courses, workshops, summer schools, etc.;
• Healthy travel funding for presenting your work at relevant (inter)national conferences and going on research visits;
• Excellent technical infrastructure;
• Additional employment benefits, e.g. child daycare and sports facilities, extra holiday allowance (8%, May), and end-of-year bonus (8.3%, December).