Doctoral student in Bioinformatics with specialization on 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.

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

 Admission requirements
A person meets the general admission requirements for third-cycle courses and study programmes if he or she:

• has been awarded a second-cycle qualification, or
• has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second cycle, or
• has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

A person meets the specific admission requirements if he or she has: 1. at least 30 credits in the subject, of which at least 15 credits from the second cycle and a specialised project of at least 15 second-cycle credits in the subject, or 2. an MSc in Engineering, other Master’s degree or other comparable degree that included basic or applied bioscience

 To be successful in this role you should have:

• A Masters degree in Bioinformatics, Computational Biology, Statistics or other related field
• A good understanding of the statistical and computational aspects of bioinformatics and the underlying genetics
• Experience with open source bioinformatics analysis programs.
• Programming skills for novel analysis in Python, Perl, Java, C++, R or other language
• Experience with Linux and high performance computing environments
• Experience in genome scale data analysis including RNA-Seq data, genome annotation, biological sequence analysis or other relevant computational genomics experience

 Assessment criteria
We will place great importance on personal suitability – a positive can-do attitude is important for our work environmet. Consideration will also be given to good co-operative ability, drive and independence. The applicant, through his/her experience and competence, is expected to supplement and strengthen ongoing research within the institution as well as contribute to its future development.

 Additional merits:

• Experience in characterization of non-model genomes, preferably plants, preferably polyploids
• Previous work with oat genomics is an advantage
• A genuine interest in developing pipelines/tools e.g. de-novo genome assembly
• Experience in plant breeding
• Experience in hands-on molecular biology

Motivation for interdisciplinary research, excellent English communication skills (oral and written), and the ability to work independently as well as within a research group

Terms of employment
Only those admitted to third cycle studies may be appointed to a doctoral studentship. Third cycle studies at LTH consist of full-time studies for 4 years. A doctoral studentship is a fixed-term employment of a maximum of 5 years (including 20% departmental duties). Doctoral studentships are regulated in the Higher Education Ordinance (1993:100), chapter 5, 1-7 §§.

Instructions on how to apply
Applications shall be written in English and include a cover letter stating the reasons why you are interested in the position and in what way the research project corresponds to your interests and educational background. The application must also contain a CV, degree certificate or equivalent, and other documents you wish to be considered (grade transcripts, contact information for your references, letters of recommendation, etc.).