Bioinformatics Research Engineer in Oat Genomics - Hiring in process/Finished, not possible to apply

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.

Work duties
We are seeking a motivated and experienced bioinformatician to join the ScanOats Industrial Research Center to perform work in the field of oat genomics. We have recently sequenced and assembled the hexaploid oat genome and now the in-depth analysis can begin. An enthusiastic outlook to scientifically tackling this 12.5Gbp hexaploid genome is absolutely necessary. Your role will involve developing computational approaches that integrate next generation sequence data to address the goals of ScanOats. Our areas of research on oat seed quality include: 1) lipids and lipases, 2) total fibers, 3) antioxidants, 4) proteins, and 5) Fusarium resistance.  You will interact with researchers from different backgrounds including biochemistry, plant breeding, biotechnology and bioinformatics, and also with researchers within the other work packages of ScanOats as well as the ScanOats industrial partners Lantmännen, Oatly and Swedish Oat Fiber.

Detailed description of the work duties, such as:

• Apply state-of-the art tools, skills, and methods in genome sciences to achieve the goals of ScanOats
• Develop novel algorithms and strategies to scale analysis and leverage cloud-computing resources.
• Understand the core scientific questions and design analyses to best address these questions.
• Participate in automated/manual annotation of the oat genome, synteny analysis, transcriptomics, identification of markers for mutant traits.
• Collaborate with academic/industrial researchers at national and international level.
• Assist in supervision of graduate students and doctoral students.
• Assist in the integration and interpretation of results from ‘omics’ datasets.
• System administration and big data management.
• Participate in the development of a genome browser.
• Apply for research grants when required
• Duty abroad to work with international researchers for weeks to months at a time could be possible.

Qualification requirements
As Research Engineer you must have:

• A degree in Plant Genetics, Evolutionary Biology, Bioinformatics, Computational Biology, Statistics or other related field.
• A broad understanding of the statistical aspects of bioinformatics and the underlying genetics.
• Experience with open source bioinformatics analysis programs.
• Demonstrated programming skills for novel analysis in Python and R.
• Experience with Linux and high performance computing environments.
• Experience in genome scale data analysis including RNA-Seq, genome annotation, biological sequence analysis or other relevant computational genomics experience.
• Motivation for interdisciplinary research and the ability to work independently as well as within a research group.
• Very good oral and written proficiency in English.

We will place great importance on personal suitability – a positive can-do attitude is important for our work environment. We are looking for someone who has good ability to interact with many different parties and has good ability to cooperate. You are flexible, have a good drive and independence. Consideration will also be given to how the applicant’s experience and skill complement and strengthen ongoing research within the institution, and how they stand to contribute to its future development.

Additional requirements:

• Experience in plant breeding.
• Experience in hands-on molecular biology.
• Experience in characterization of non-model genomes, preferably plants, preferably polyploids
• Interest in developing de-novo genome assembly pipelines.
• Ability/interest in developing/applying statistical or machine learning methods.
• Track record of publications.

Terms of employment
This is a full-time, fixed-term employment of 2 years. Our employment needs may be longer than 2 years.

Instructions on how to apply
Applications shall be written in English. Please draw up the application in accordance with LTH’s Academic qualifications portfolio – see link below. Upload the application as PDF-files in the recruitment system. Read more: http://www.lth.se/index.php?id=71223