Position in microbiological bioinformatics

Department of Microbiology at Oslo University Hospital is seeking a bioinformatician to work on analysis of high throughput sequencing data from patients with infectious diseases. The position is full time and for two years, with possibility for extension dependent on further financing. As part of an initiative to develop precision medicine within the field of infectious diseases, the candidate will have a key role in establishing the diagnostic offering at the department while also partaking in the exciting research going on in the department within areas such as antibiotic resistance and virology; and translating this to the diagnostic setting.
 
The position will offer interesting work with a great variety of tasks. The candidate will be working on planning and design of experiments and procedures, development of pipelines and analyses, conducting analyses and evaluating results. The position is well suited for candidates who want to tackle complex problems and develop quality-assured solutions that are suitable for medical diagnostics to the benefit of patients and society. The candidate will work within an interdisciplinary team of bioinformaticians, molecular biologists, bioengineers, and doctors within Department of Microbiology. The work will also be done in close collaboration with the large group of bioinformaticians at Department of Medical Genetics.
 
The position is placed at Section for Development, which is active at both Ullevål sykehus and Rikshospitalet campuses. The section has 12 employees, where 7 are molecular biologists (of which 3 have 50% positions), 2 bioinformaticians (20% positions), and 3 specialist bioengineers. The department has an accreditation according to ISO 15189. The candidate is expected to work at both campuses, and some remote work is also possible. Start date for the position is as soon as possible after January 1st.

Oslo University Hospital is a workplace with great diversity. We believe this is absolutely crucial to solving the tasks required of us. We therefore want this diversity to be reflected among the applicants for our positions and encourage everyone to apply regardless of who you are and what background you have. 

Duties and responsebilities

• Bioinformatic analysis of HTS (NGS) whole genome data for identification of microorganisms, determination of antimicrobial resistance genes and phylogeny, as well as metagenomic analyses for detection of microorganisms directly from sample material.  ?
• Development, quality assurance, automation, and deployment of bioinformatical pipelines/analyses, and generation of reports for presentation of results to research and routine diagnostics. 
• Development of analyses, databases, and data management in general in areas where the department has a national coordination role, including fungi and parasites, HIV, Cytomegalovirus, and syphilis.  
• Provide help and guidance with bioinformatic analyses, and contribute to building bioinformatic competence in the department

Qualifications

Required

• Master degree or PhD in bioinformatics or relevant disciplines 
• Documented experience within applied bioinformatics 
• Practical experience with Linux/CLI and good general knowledge of IT 
• Experience with programming (for example Python, R, Bash) 

Desirable

• Experience with relevant tools and analysis of sequencing data. Experience from a diagnostic setting and microbial whole genome sequencing, amplicon sequencing   and gene expression analysis is particularly relevant. 
  
• Knowledge of microbiology, especially microbial phylogeny, and genetic mechanisms for antimicrobial resistance 
• Practical skills within version control, use of containers, databases, and software/libraries for data analysis

Personal qualities

• Professional interest and curiosity for the field is a requirement. 
  
• The candidate is expected to collaborate closely with other personnel in the department, so good collaboration and knowledge sharing skills across disciplines and departments are deemed important 
  
• Ability to take initiative, work independently and acquire relevant knowledge, systematic and goal-oriented  
  
• Good English oral/writing skills, and ideally also some proficiency in Norwegian

We can offer

• An exciting and challenging academic environment, with a technology in rapid development  
  
• A key role in building and introducing precision medicine in the health sector  
  
• An open and welcoming work environment with nice colleagues