Bioinformatician / computational microbiologist

Bioinformatician / computational microbiologist

A permanent full time position is available at the Department of Clinical Microbiology, Odense University Hospital from May 1st 2021

We are looking for a skilled bioinformatician with ambitions within microbiology and the ability to apply theory to practice.

Our department

The Department of Clinical Microbiology is a cross-disciplinary, clinical laboratory department of 130 employees at Odense University Hospital (OUH), which serves hospital departments at OUH as well as the primary health care sector with microbiological diagnostics and counselling, including infection control. Find out more at:

Department of Clinical Microbiology

About the position

You will be a part of a team with strong ambitions to implement microbial NGS for surveillance, outbreak investigations, pathogen typing and diagnostics.

Initial focus will be on improving current implementation of bioinformatic pipelines for Coronavirus SARS-CoV-2 genome assembly, lineage, clade and variant calling and reporting.

The position will involve a multitude of projects and tasks including:

-Implement sound data storage solutions for NGS data
-Code maintenance, database management
-Responsibility to establish and maintain bioinformatics pipelines and databases for use in surveillance, outbreak investigations, pathogen typing and diagnostics.
-Implementation of various new bioinformatics tools including genome comparisons, metagenome analysis
-Teaching and capacity building of co-workers.
-Participate in the Department's research projects including supervising bachelor, master and PhD-students.
-Engage in national and local networks of bioinformaticians from other para-clinical departments at Odense University Hospital, other Danish Departments of Clinical Microbiology and Statens Serum Institute.

Required qualifications

You are a bioinformatician (MSc or PhD) and have experience in programming (Linux bash, Python and R) and handling microbial next generation sequencing data sets.

You are an enthusiastic and creative person with an interest in combining bioinformatics and microbiology and a drive to be an integral part in establishing sound workflows for clinical NGS to solve both large and small clinical problems. You have excellent cooperation and communication skills and are able to apply theory to practice.

The ideal candidate

-Strong competences with various programming languages and SQL-databases
-Dual experience within bioinformatics and molecular biology
-Documented experience with building programs and pipelines analyzing Illumina and Oxford Nanopore data
-Experience with working with software version control and managed releases
-PhD-degree and a relevant publication list
-Post-doctoral experience within clinical microbiology bioinformatics
-Skilled in statistical analysis of large datasets
-Strong network within the international microbial NGS and bioinformatics research community

We are offering a positive work environment with an inspiring cross-disciplinary collaboration between medical doctors, molecular biologists, laboratory technicians, infection control nurses, and secretaries.

Terms of employment follow Danish collective agreements.

Working language: Danish. New employees who are not fluent in Danish will be required to pass a three month Danish course during the first months of employment.

The application must be written in English or Danish. CV and contact information on two references must be included.

Deadline for application: Thursday March 18th 2021

Interviews will be held on Tuesday March 23rd 2021 in the afternoon. Online participation can be arranged.

If you need further information on the position, please contact MD, Ph.D. Thomas Vognbjerg Sydenham (+45 65414797) or Head of Department Anette Holm (+45 40 29 35 39).