Postdoctoral researcher (2 years) in conifer genomics

Umeå universitet, Teknisk-naturvetenskaplig fakultet

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Postdoctoral researcher (2 years) in conifer genomics 

A postdoctoral position is available at the Department of Plant Physiology at Umeå university, which is a part of Umeå Plant Science Centre, (see www.upsc.se). The position is funded by the Norway spruce and Scots pine genome project. The employment is full-time for two years in the group of Nathaniel Street (http://streetlab.upsc.se). The position start date is by agreement, but the position is immediately available.

Duties 

The candidate will work with bioinformatics in a joint research environment of the Department of Plant Physiology, Umeå University, and in collaboration with research groups at SciLifeLab (Science for Life Laboratory), National Bioinformatics Infrastructure Sweden (NBIS) and the Norway spruce and Scots pine genome project team. The work will involve performing analysis of epigenetics data and comparative genomics analyses including of protein coding genes, non-coding RNAs, pseudogenes and repetitive elements (primarily LTRs) in addition to general bioinformatics analysis and support. There will be an emphasis on the role of chromatin conformation in gene regulation and synteny and comparative expression analyses using RNA-Seq data, which will include the use of co-expression networks. Available project data includes Illumina RNA-Seq, PacBio Iso-Seq, Ribo-Seq, Hi-C, ATAC-Seq and DNA methylation profiling. Duties will include data analysis, result interpretation and writing original research publications. 

Qualifications

To be appointed under the postdoctoral agreement, the postdoctoral fellow is required to have completed a doctoral degree or a foreign degree deemed equivalent to a doctoral degree. This qualification requirements must be fulfilled no later than at the time of the appointment decision.

To be appointed under the postdoctoral agreement, priority should be given to candidates who completed their doctoral degree, according to what is stipulated in the paragraph above, no later than three years prior. If there are special reasons, candidates who completed their doctoral degree prior to that may also be eligible. Special reasons include absence due to illness, parental leave, appointments of trust in trade union organizations, military service, or similar circumstances, as well as clinical practice or other forms of appointment/assignment relevant to the subject area. Postdoctoral fellows who are to teach or supervise must have taken relevant courses in teaching and learning in higher education.

For this position, it is required that you hold a doctoral degree in bioinformatics, molecular biology, computational biology, plant science or equivalent. 

Experience and knowledge in implementing efficient high-performance cluster pipelines is a requirement and you must be competent in job scheduling systems. Experience in scripting (in e.g. python, bash etc.) is required as well as implementation of reproducible pipelines using code sharing platforms (for example Git, which is used extensively in the project). Excellent oral and written communication skills in English, a willingness to learn new skills and to work collaboratively are also essential.

Meriting qualifications would include experience in any of the following: analysis of high throughput sequencing gene expression data, whole genome sequence alignment and synteny analysis, analysis of non-coding RNA and/or pseudogenes including methods for functional annotation, repeat analysis, differential expression analysis, transcript/alternative splicing analysis and co-expression network inference and analysis. Further, skill in R programming for data analysis and visualisation is highly desirable. Experience in working with plant species, in particular non model species, in particular species with large genomes, is highly desirable. All code developed will be shared publicly and must adhere to transparent and reproducible research principles. Exact details of the analysis to be performed are flexible and can be adjusted to match the qualifications and interest of the selected candidate.

Application

The application should contain:

• A Curriculum Vitae.
• A cover letter that must include describing yourself, your previous relevant research achievements, clear links to demonstrated examples of implemented tools and code and reasons for applying to this position (max 2 pages).
• Certified copies of doctoral degree certificate or equivalent, or documentation that clarifies when the degree of doctor is expected to be obtained,
• A list of publications including a link to your PhD thesis.
• Certified copies of grades and degree certificates.

The application must be written in English or Swedish. The application is made through our electronic recruitment system. Documents sent electronically must be in Word or PDF format. Apply via our recruitment system by the button at the bottom of the page.   Application deadline is 2023-09-13.

Terms of employment

The employment is full-time and is limited to two years. Access according to agreement.

Contact

For more information please contact Dr Nathaniel Street, nathaniel.street@umu.se or +46-(0)70-322 0136.

 
We look forward to receiving your application!

The Department of Plant Physiology carries out research and postgraduate education in different fields of the plant sciences including, ecology, biochemistry, physiology and development, and genomics. The department is part of the Umeå Plant Science Centre, which hosts close to 200 employees and 40 principal investigators, representing about 35 nationalities. For more information please visit http://www.plantphys.umu.se/english/ and http://www.upsc.se.

Umeå University strives to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment.

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