The PhD project 'Prediction of Candidate genes for Traits using interoperable genome annotations and literature' aims at solving important questions in crop species: which gene (networks) are candidate for traits of interest and should be introgressed to breed improved cultivars by incorporating knowledge from previous QTL studies, available in literature, with annotations from de novo assembled genomes.
In this project, the goal is to develop statistical, genetic and bioinformatic tools for extracting breeding information from literature, utilizing computational (semantic web) approaches to combine this information with knowledge from other resources, further develop the correct ontologies to do so, and reasoning (knowledge discovery) to prioritize likely candidate gene (networks). Can we devise strategies which lead to faster discovery of candidate genes for traits of interest to plant breeders?
Student life at Wageningen University
- You will work in close cooperation with other PhD students and researchers involved in related (national) projects on the development of data integration approaches. The project team includes an eScience engineer of the NWO eSience center. You will be in regular contact with plant breeding companies, who are members of the 'Virtual lab for Plant Breeding' foundation.
Requirements
An ambitious PhD student with an MSc Degree in Bioinformatics, Computer Science, Statistics, Biotechnology, Biology or Plant Sciences. The candidate is highly motivated to develop a scientific career and is able to perform independent research, but values collaboration with other PhD students and researchers. The candidate is fluent in English and has excellent communication, scientific writing and presentation skills. For this position, the candidate should in particular demonstrate:
- appropriate knowledge of genetics, genomics, bioinformatics and statistics
- to be able to work in a highly multi-disciplinary team
- a good understanding of semantic web technologies and data interoperability
- proficiency in the bioinformatics analysis, interpretation and scientific visualization of large data sets
- proven proficiency in programming (preferably with Python and Java)
- knowledge of and experience with statistics software®
Terms of employment
- We offer the research environment of a dynamic group with a strong international profile and large numbers of PhD students; a state-of-the art computational infrastructure; close collaboration with the NWO eScience center and with other PhD students, researchers and plant breeding companies involved in analysis of genomics and genetics data; and the possibility to further develop your scientific education with courses, training, 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 € 2125,- per month rising to € 2717,- in the fourth year for a full-time appointment.
Contact
Dr. Richard Finkers or Prof. Dr. Richard GF Visser, Wageningen UR Plant Breeding, Wageningen University & Research Centre, tel:+31 317 484164, email: [email protected]
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