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:
For more information about the project and position contact either dr. Michel Westenberg or dr. Sandra Smit by e-mail: m.a.westenberg[at]tue.nl, sandra.smit[at]wur.nl.
For more information about the employment conditions contact our HR department, e-mail: pzwin[at]tue.nl or by telephone: +31 40 247 4315.
The application should consist of the following parts:
You can upload one file including all the required documents (max. 10 MB).
The selection process will start on November 1, 2019, and will continue until the position get filled. The position is fully funded and immediately available. The start date is flexible.