Senior research engineer in comparative genomics - ,

The candidate will be employed by 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 and the position start date is by agreement, but the position is immediately available. For more information about the research group, see: http://streetlab.upsc.se. 

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 Service (NBIS) and the Norway spruce and Scots pine genome project team. The work will involve performing comparative genomics analysis 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 syntney and comparative expression analyses using RNA-Seq data, which will include the use of expression networks. Available project data includes Illumina RNA-Seq, PacBio Iso-Seq, Ribo-Seq, Hi-C, ATAC-Seq and DNA methylation profiling.

Qualifications 

To be eligible for this position, the applicant must hold a PhD in bioinformatics, molecular biology, plant science or equivalent. The candidate must have experience and knowledge in implementing efficient high-performance cluster pipelines and must be competent in job scheduling systems and database creation and management. The candidate must have experience in complex scripting (in e.g. python, C etc.) and will have proven experience and expertise in the development of reproducible pipelines using code sharing platforms (for example Git, which is used extensively in the project). Very good oral and written communication skills in English, a willingness to learn new skills and to work collaboratively are essential. As the candidate will offer general bioinformatics support within the department, proven experience in a broad range of bioinformatics skills is required.

Beneficial qualifications would include experience in 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 and data analysis is highly desirable. Experience in working with plant species, in particular non model species or species with large genomes, is highly desirable. In order to make resources from these genome projects publicly available, experience in full-stack development is highly attractive (e.g. php, node.js, MySQL, HTML5, JavaScript). 

All code developed will be shared publicly and must adhere to transparent and reproducible research principles.

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.
• A list of publications including a link to your PhD thesis.
• Certified copies of grades and degree certificates.

Apply via our recruitment system by the button at the bottom of the page. Application deadline is 5 May, 2022.

Terms of employment

The employment is full-time and is limited to 2 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!