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Two Postdoctoral fellowships (2 years) in bioinformatics, focused on metagenomics based biosurveillance of fungal pathogens of conifer trees
The Department of Ecology and Environmental Science (Umeå University, Sweden) invites applicants for two postdoctoral fellowships to a project focused on analyzing time series of shotgun metagenomics data aiming at producing forecasts of fungal pathogens of conifer trees that will be used by the industry to reduce the impact of this emerging threat. Application deadline is September 1st, 2019.
Project description
Forest pathogen invasions into Europe have increased strongly over the last 30 years. Protecting forests from risks posed by forest pathogens is essential since they are responsible for significant economic loss as well as detrimental effects on several ecosystem functions and services. Unintentional dissemination by commercial trade and airborne transmission are the dominating dispersal pathways of new alien forest pathogens. Many of the already occurring forest pathogens in the northern part of Sweden can disperse by wind and aerosols.
We are in this project (a collaboration between Umeå University, Swedish Defence Research Agency (FOI) and Swedish University of Agricultural Sciences (SLU)) using a unique archive of air filters that represents an unbroken 50-year line of samples collected weekly in northern Sweden. These filters were set-up and are used by FOI to monitor radioactive fallout. We have extracted high quality DNA from these filters and through DNA sequencing we can identify the organisms and cell fragments that are captured in the filter. The properties of the filters and the huge amounts of air passed (>100,000 m3/filter) make it possible to measure the relative abundance of all types of organisms (plants, animals, fungi, bacteria and viruses) from all types of environments (soil, water, land and air). For more information on the project see www.org.umu.se/swebits/.
The postdocs will be given opportunity to participate in assembling new draft genomes for a number of fungal pathogens and subsequently trace these organisms in the air filter data (~400 samples shotgun sequenced to a depth of 200-800 million 150 bp PE reads). Identified historical seasonal variation of the pathogens can then be compared to weather and land-use data in order to construct models that can be used to predict future seasonal patterns and long-term trends. The proposed research mainly include modelling and NGS data analyses. The postdocs will also have the freedom to contribute to other ongoing projects based on this unique biodiversity dataset and to develop own projects that are aligned with the group’s interests.
The fellowships are funded by a tax-free 2-year scholarship amounting to 294 000 SEK per year. The scholarships are for two years starting in Fall 2019, or according to agreement. The project will mainly be performed at Umeå University, but may include periods at Swedish Defence Research Agency (FOI) and/or Swedish University of Agricultural Sciences (SLU).
Qualifications
The candidates should have a PhD degree in bioinformatics, genetics, ecology, or a related field. We seek highly motivated candidates with a broad experience in genomics and NGS data analysis. To be eligible for this fellowship, you should have completed your doctoral degree a maximum three (3) years before the end of the application period. Good ability to co-operate as well as to work independently and take initiative are required. Good skills in written and spoken English are required.
Experience with large-scale sequence analysis is a merit, including familiarity with phylogenetic analyses, statistics and programming (e.g. Linux, R, Python). Experiences in various modelling approaches are also a merit.
Application
The full application should include:
Your complete application, marked with reference number Dnr: FS 2.1.6-1235-19, should be sent in a PDF-document to [email protected] (state the reference number as subject) on September 1st, 2019 at the latest.
Contact
For more information, contact Dr. Per Stenberg (per.stenberg[at]umu.se).
The Department of Ecology and Environmental Science (www.emg.umu.se) carries out research and postgraduate education in ecology, environmental science and physical geography. The department has about 150 employees, about 15 of whom are post-docs.
The Department of Ecology and Environmental Science (Umeå University, Sweden) invites applicants for two postdoctoral fellowships to a project focused on analyzing time series of shotgun metagenomics data aiming at producing forecasts of fungal pathogens of conifer trees that will be used by the industry to reduce the impact of this emerging threat. Application deadline is September 1st, 2019.
Project description
Forest pathogen invasions into Europe have increased strongly over the last 30 years. Protecting forests from risks posed by forest pathogens is essential since they are responsible for significant economic loss as well as detrimental effects on several ecosystem functions and services. Unintentional dissemination by commercial trade and airborne transmission are the dominating dispersal pathways of new alien forest pathogens. Many of the already occurring forest pathogens in the northern part of Sweden can disperse by wind and aerosols.
We are in this project (a collaboration between Umeå University, Swedish Defence Research Agency (FOI) and Swedish University of Agricultural Sciences (SLU)) using a unique archive of air filters that represents an unbroken 50-year line of samples collected weekly in northern Sweden. These filters were set-up and are used by FOI to monitor radioactive fallout. We have extracted high quality DNA from these filters and through DNA sequencing we can identify the organisms and cell fragments that are captured in the filter. The properties of the filters and the huge amounts of air passed (>100,000 m3/filter) make it possible to measure the relative abundance of all types of organisms (plants, animals, fungi, bacteria and viruses) from all types of environments (soil, water, land and air). For more information on the project see www.org.umu.se/swebits/.
The postdocs will be given opportunity to participate in assembling new draft genomes for a number of fungal pathogens and subsequently trace these organisms in the air filter data (~400 samples shotgun sequenced to a depth of 200-800 million 150 bp PE reads). Identified historical seasonal variation of the pathogens can then be compared to weather and land-use data in order to construct models that can be used to predict future seasonal patterns and long-term trends. The proposed research mainly include modelling and NGS data analyses. The postdocs will also have the freedom to contribute to other ongoing projects based on this unique biodiversity dataset and to develop own projects that are aligned with the group’s interests.
The fellowships are funded by a tax-free 2-year scholarship amounting to 294 000 SEK per year. The scholarships are for two years starting in Fall 2019, or according to agreement. The project will mainly be performed at Umeå University, but may include periods at Swedish Defence Research Agency (FOI) and/or Swedish University of Agricultural Sciences (SLU).
Qualifications
The candidates should have a PhD degree in bioinformatics, genetics, ecology, or a related field. We seek highly motivated candidates with a broad experience in genomics and NGS data analysis. To be eligible for this fellowship, you should have completed your doctoral degree a maximum three (3) years before the end of the application period. Good ability to co-operate as well as to work independently and take initiative are required. Good skills in written and spoken English are required.
Experience with large-scale sequence analysis is a merit, including familiarity with phylogenetic analyses, statistics and programming (e.g. Linux, R, Python). Experiences in various modelling approaches are also a merit.
Application
The full application should include:
- A cover letter describing why you are interested in the project and your suitability (max. 2 pages).
- A CV, including a list of your publications.
- Copies of your doctoral thesis and relevant publications (maximum 5).
- Copy of doctoral degree certificate and other relevant degree certificates.
- Names and contact details (mail and phone) of three reference persons.
- Any other documents you wish to refer to.
Your complete application, marked with reference number Dnr: FS 2.1.6-1235-19, should be sent in a PDF-document to [email protected] (state the reference number as subject) on September 1st, 2019 at the latest.
Contact
For more information, contact Dr. Per Stenberg (per.stenberg[at]umu.se).
The Department of Ecology and Environmental Science (www.emg.umu.se) carries out research and postgraduate education in ecology, environmental science and physical geography. The department has about 150 employees, about 15 of whom are post-docs.