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Doctoral student in Bioinformatics with specialization on oat genomics

Doctoral student in Bioinformatics with specialization on oat genomics

Lund University, Sweden


ScanOats is a newly established industrial research centre in collaboration between the academy and the industry. We conduct basic and applied research on oats and oat-based products. Oat is an important crop both for the Swedish agriculture and for the food chain. ScanOats is unique in the sense that we cover the entire chain from basic research, genome sequencing, cultivar development, field testing, mild processing and fractionation, and clinical health trials.

Subject description
We are looking for a highly motivated bioinformatician to work with the characterisation of the oat genome, with an emphasis on lipids. We have recently sequenced and assembled the hexaploid oat genome and now the analysis can begin. From an industrial processing point of view, we are also interested in better understanding the mechanism behind rancidity during oat storage. We will utilize a collection of oat mutants and collaborate with researchers from around the world to reach our goals. An enthusiastic outlook to scientifically tackling this 12.5Gbp hexaploid genome is absolutely necessary.

The work will be conducted in collaboration with researchers within the other subprojects of Scanoats as well as with the ScanOats industrial partners Lantmännen, Oatly and Swedish Oat Fiber.

Work duties
The main duties of doctoral students are to devote themselves to their research studies which includes participating in research projects and third cycle courses. The work duties may also include teaching and other departmental duties (no more than 20%).

We are seeking a motivated individual with a genuine interest in laying the foundation for their academic career in crop genomics to join the ScanOats Industrial Research Centre. You will begin your PhD in the field of oat genomics by developing computational approaches that integrate NGS data to identify and characterize the genetics associated with oat lipids, lipases, antioxidants, and other factors involved in rancidity during oat storage. You will interact with researchers from different backgrounds including biochemistry, plant breeding, biotechnology and bioinformatics.

  •  Apply state-of-the art methods in genome sciences to achieve the goals of your PhD
  • Utilize new and existing approaches to gene prediction to improve automated annotation of your assigned gene families
  • Analysis of gene family evolution and comparative genomics
  • Investigate NGS data from oat mutants and identify markers/genes affecting the phenotype
  • Develop novel algorithms and strategies to scale analysis and leverage cloud-computing resources
  • Take the lead in, or participate in, the development of a genome browser
  • Collaborate with academic/industrial researchers and be willing to work abroad with international researchers for weeks to months at a time.
  • Investigate the distribution and possible effects of transposable elements adjacent to your assigned gene families
  • Assist in supervision of ungraduate students
  • Integrate and interpret ‘omics’ datasets when required for your goals
  • Assist in system administration and big data management when required
  • Apply for research grants when required


More information to be found here

Lund University, SE

Printed from on 25/06/18 06:37:50 PM

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