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Plant breeding has progressed enormously over the last decades, but the development of new varieties is very time consuming as it depends on meiotic recombination to generate crossovers and thus genetic variation. In the EU Horizon 2020 INNOVATIVE TRAINING NETWORKS (ITN) programme, the Meiotic Control of Recombination in Crops (MEICOM) project will build on earlier research, in (among others) Arabidopsis and tomato, to study crossover formation in crops and to devise ways of influencing the frequency and location of crossovers. Within this project, you will study meiotic recombination crossover profiles using genome bioinformatics and machine learning methods. Your task will be to analyse crossover formation in crop genomes using novel combinations of high-throughput sequencing (Illumina, PacBio, Oxford Nanopore, 10X Genomics) and optical mapping (BioNano Genomics) data, to learn about crossover frequency in haplotypes, genome structure and structural variation in parental lines and offspring of crops such as tomato, potato, melon, and lettuce. Sequence and genome structural data will be mined using machine learning techniques to find features influencing recombination. With project partners, you will then study the link between structural diversity, genetic diversity and cross over frequency with variation for particular agronomic important traits.
As an ITN researcher, you will be offered a number of secondments to partners (University of Amsterdam; University of Birmingham; SESVanDerHave, Belgium) and enjoy regular ITN meetings. Furthermore, you'll have the opportunity to actively communicate and promote your research via international meetings and, if applicable, at private parties such as breeding companies.
Wageningen University & Research
We are looking for an ambitious, enthusiastic team player and result-driven scientist with:
- an excellent academic record (MSc) in bioinformatics, computer science or a related area;
- demonstrable skills in mathematics, statistics and programming;
- proven proficiency in algorithm development, preferably related to machine learning;
- affinity with genomics and next-generation sequencing data analysis;
- excellent oral and written communication skills in English.
EU ITNs are meant to train young researchers and increase their mobility. Therefore, candidates should have obtained their MSc degree no longer than four years before the starting date (i.e. after March 1, 2014), cannot yet hold a PhD or equivalent degree. Moreover, candidates may not have resided or carried out their main activity (work, studies, etc.) in The Netherlands for more than 12 months in the 3 years immediately prior to the starting date (short stays not taken into account).
Conditions of employment
We offer a dynamic and driven research environment with a strong international profile and a growing 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 € 2222,- per month rising to € 2840,- in the fourth year for a full-time appointment.
Wageningen University & Research
Wageningen UR has a global reputation for its ground-breaking research and innovative education in the fields of food and health, sustainable agrosystems, the rural environment, and societal development - all of which make an essential contribution to the quality of life, i.e. the supply of safe and healthy food and drink, on the one hand, and the chance to live, work and play in a balanced ecosystem with a large variety of plants and animals on the other. Within Wageningen UR, the Plant Sciences Group brings together science education and scientific, strategic and applied research in the fields of biology, of plants in relation to their environment, of plant-related organisms and of plant production.
This project is a collaboration of the Wageningen University Bioinformatics Group and the Wageningen Research Applied Bioinformatics cluster.
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.
The Applied Bioinformatics cluster adopts the latest in high throughput DNA sequencing and analysis technology to delivering genomes that can be directly used for research and, especially targeting complex genomes. This is combined with state-of-the-art computational infrastructure focussing on high-quality assembly, annotation, data integration as well as development and use of appropriate tools and technologies.