PhD position in plant science with a focus on computational biology

Updated: 3 months ago
Deadline: 28 Feb 2022

The Department of Plant Physiology (Umeå University, Umeå Plant Science Centre, Sweden) invites applicants for a PhD position in plant science with a focus on computational biology. The expected starting date is spring 2022 or according to agreement.

Umeå Plant Science Centre (UPSC) is one of the strongest research environments for basic plant research in Europe. Research at UPSC covers a wide range of disciplines in plant biology including ecology, computational biology, genetics, physiology, biochemistry, cell biology and molecular biology (see www.upsc.se). A PhD student position is open at the Department of Plant Physiology, which is part of Umeå Plant Science Centre. Application deadline is February 28, 2022.


Project description

Crops are exposed to herbivores and diseases. In a climate change scenario, the growth zones that have previously dictated agriculture are about to move northward, and we do not know the risk of biological stress factors we may face under the novel growth conditions. Simultaneously, EU-legislation is emphasizing the need to ban the use of pesticides and instead promote and develop integrated pest management strategies.  The purpose of this project is to provide a foundation that prepares for changes in climate and agriculture in Sweden, emphasizing analyses of pests associated with potato and cereals. To predict colonization by and outbreaks of pests and diseases, solid crop system knowledge is required as well as are long time series that detail how climate affects the association between pests and crops. Surveillance systems that monitor risk of colonization and outbreak by selected pathogens and pests are usually also finetuned to capture a limited number of pests from a limited number of crops.

Our approach is to use a unique archive of air filters, collected weekly at six locations across Sweden since 1965. We have now produced a very large dataset that maps weekly biodiversity in Kiruna (sub-arctic region, Northern Sweden) from 1974 to 2008. By using shotgun DNA sequencing we can identify plant pests and pathogens among other types of organisms (plants, animals, fungi, bacteria, and viruses). We have generated high-resolution data that provide us with the unique opportunity to investigate how organisms are influenced by changes to the environment. We are currently working on extending the Kiruna time series until present day as well as producing a new time series from a filter station in Southern Sweden located in a temperate agricultural system.


About the position

The project will involve analyzing large scale sequencing data along with climate and land-use data to understand associations between two kinds of crops and the risk of outbreak in those. The project will also include collaboration with leading experts and associated networks including association with the SweBITS (Swedish Biodiversity In Time and Space) network with scientists from Umeå University, Swedish University of Agricultural Sciences and Swedish Defence Research Agency, the N’TOP Northern Tubers of Potato network with scientists from six Nordic countries, and UPSCb (the bioinformatics section at Umeå Plant Science Centre).

The employment is expected to result in a doctoral degree and the main assignment for the student is thus to be part of the research education, which includes participation in research but also taking relevant courses. Teaching and other departmental activities (up to a maximum of 20% time) are typically included as well. Employment is limited to four years at full time or up to five years if teaching and other departmental work is performed. The salary is fixed according to the established salary level for doctoral students.


Admission requirements

To be admitted for studies at third-cycle level the applicant must have completed a second cycle level degree, or completed course requirements of at least 240 ECTS, of which at least 120 ECTS are at second-cycle level and 30 clearly relevant to the project or have an equivalent education with relevant qualifications. To fulfil the specific entry requirements to be admitted for studies at third-cycle level in Plant Science at Umeå Plant Science Centre, the successful candidate must have completed 90 ECTS relevant to the doctoral thesis project. Out of this, at least 30 ECTS have to be in a subject closely related to the research topic of the graduate program. Applicants who have acquired equivalent skills in some other educational system in Sweden or abroad are also eligible.

For this position, we are looking for a person interested in computational biological analysis. We expect the candidate to have an academic background in Plant biology, Agronomy, Biotechnology or a related field as well as having a strong and documented experience in computational analysis (e.g. statistics and bioinformatics).

The successful applicant should have good skills in written and spoken English. Strong merits include experience with bioinformatics focused on the analysis of large scale sequencing data. We are looking for a creative and initiative rich person who can work independently but who can also collaborate within a larger research group. Evaluation of candidates will be based on the application and on interviews.


Application

You apply through our recruitment system Varbi on Februari 28, 2022 at the latest. The application may be written in English, Swedish, Norwegian, or Danish and should include:

  • A short (max 2 pages) description of why you are interested in the position
  • CV
  • Certified copies of certificates from higher education
  • List of completed university courses and the grades
  • Copy of publications/degree thesis

  • Contact

    If you have questions regarding the position, please contact Docent Benedicte Albrectsen benedicte.albrectsen@umu.se

    Documents should be sent electronically, in MS Word or PDF format, trough the recruitment system. The procedure for recruitment for the position is in accordance with the Higher Education Ordinance (chapt. 12, 2 §) and the decision regarding the position cannot be appealed. 

    The Department of Plant Physiology values the qualities that an even gender distribution brings to the department, and therefore we particularly encourage women to apply for the position.


    We look forward to your application!
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