PhD in Virus diversity in natural plant ecosystems to develop bioinformatics methods to analyze plant virus metagenome data
You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus genomes are highly diverse and evolve rapidly. To know which role plant viruses play in shaping natural plant communities, we must characterize their biodiversity and evolution.
You might be familiar with the phenomenon that plant virus infections are often asymptomatic, i.e., they do not cause overt disease, and can even be beneficial for the host. Recently, plant virus research expanded from the study of individual virus-host systems into characterizing global diversity using metagenomics, i.e., sequencing the genetic content of environmental samples without the need for prior virus isolation. Metagenomics led to the surprising observation that virus infections are ubiquitous, that there is a high incidence of mixed infection, and that most plant viruses identified in crops also occur in wild plants. There is growing evidence that viruses can impact plant ecosystems, which calls for a reappraisal of the role of viruses in natural ecosystems and accentuates the need to understand virus genomes and their function and evolution.
The aim of this project is to develop bioinformatics methods to analyze plant virus metagenome data that has been sampled from wild plants in the Netherlands. This (and potentially your) project will contribute to understanding plant virus diversity and evolution in natural Dutch ecosystems. You will contribute to developing bioinformatics methods to discover and reconstruct virus genomes from high-throughput plant virus sequencing data and to analyze ecological and evolutionary properties of these viruses. To this end, we aim to analyze the effect of host range and mixed infections on intra-host diversity and estimate how recombination and selection impact virus genome evolution.
Beyond the scientific and potentially application merits, you will build a wide network for your future career both within and outside Wageningen University.
The research is embedded within the chair group of Bioinformatics at Wageningen University which is led by Prof. Dick de Ridder (https://www.bioinformatics.nl/). You will be supervised by Dr. Anne Kupczok (https://annecmg.github.io/). The research will be carried out in close collaboration with Dr. Mark Zwart at the Netherlands Institute of Ecology (NIOO-KNAW) (https://nioo.knaw.nl/nl/employees/mark-zwart). The position is for four years and funded by the graduate school Experimental Plant Sciences (https://www.graduateschool-eps.info/).
We ask
You have:
- a successfully completed MSc degree in bioinformatics or a related field
- excellent background in high-throughput sequencing analysis and comparative genomics
- affinity with ecology, evolution, and population genomics
- interest in close collaborations with experimental biologists and ability to work effectively as a team member and to carry out individual research
- For this position your command of the English language is expected to be at C1 level.
We offer
Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:
- study leave and partially paid parental leave;
- working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
- the option to accrue additional compensation / holiday hours by working more, up to 40 hours per week;
- there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
- a fixed December bonus of 8.3%;
- excellent pension scheme.
In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.
The gross salary for the first year is € 2.443,- per month rising to € 3.122,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.
There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.
You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “ Best University ” in the Netherlands for the 17th consecutive time.
Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees. Applicants from abroad moving to the Netherlands may qualify for a special tax relief, known as the 30% ruling. Our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. Wageningen University & Research’s International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about helping your partner to find a job, housing, schooling, and other issues.
Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. For more information please go to our inclusivity page. A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment.
More information
Do you want more information?
For more information about this function, please contact Anne Kupczok (staff member of the WU Bioinformatics group) by e-mail; anne.kupczok@wur.nl .
For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.
General information about the Bioinformatics group can be found on https://www.bioinformatics.nl/.
Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.
This vacancy will be listed up to and including Monday 6 June 2022.
We hope to schedule the first job interviews in the week of 13 June 2022. The starting date for this position is 1 July 2022 or later.
In this first round, please only send your resume and motivation letter. Any other documents will not be taken into consideration at this stage.
We are
The mission of Wageningen University and Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment.
With its roughly 30 branches, 6.800 employees and 12.900 students, Wageningen University & Research is one of the leading organisations in its domain. An integrated approach to problems and the cooperation between various disciplines are at the heart of Wageningen’s unique approach. WUR has been named the best university of the Netherlands by students for the 17th time in a row.
Read the 5 reasons why your future colleagues enjoy working at WUR and watch this video to get an idea of our green campus!