Backend Developer to progress personalized medicine at department of Genomic Medicine, Rigshospitalet

The Department of Genomic Medicine at Rigshospitalet is looking for a computational scientist or bioinformatician to join our bioinformatics group that develops and maintains computational workflows for the analysis of patient genomes and transcriptomes.

The Department of Genomic Medicine holds a combined high-throughput DNA/RNA sequencing and bioinformatics platform that offers a wide-range of genomic and transcriptomic analyses, including human whole-genome sequencing, to all of Denmark as part of the National Genome Center.

For this position we are looking for a person with strong competence in backend development with interest in design, development and application. We work with docker, APIs, webapps, write mainly in Python but also have applications dependent on Java, JavaScript, Django and Vue; we create and maintain our own applications, and integrate with various hospital systems both commercial and locally sourced. You will be responsible for developing and maintaining workflows for data analyses and provide bioinformatics support to clinical department, and for developing and maintaining systems that support the complete journey from patient sample to diagnostics. Accordingly, responsibilities will range from making daily surveillance of automated data analyses workflows, designing, and building dataflow back-ends and minor contributions to research within genomic medicine.

You will be part of the Bioinformatics team that works in full DevOps, and consists of 15 full-time colleagues from various technical backgrounds within computer science, bioinformatics and software engineering. In the team we also have 3 student assistants and a number of project and PhD students, and all projects are collaborative efforts.

We offer a stimulating environment where developers, medical doctors, biomedical analysts, and bioinformaticians work together to deliver high-quality precision medicine and research. Moreover, there will be a unique opportunity to work with bioinformatics and computing tools on real clinical data. Our work has direct implications for diagnosis of patients leading to better treatment for a variety of rare and more common genetic diseases, infections, and cancer.

Qualifications:

• A degree in computer science, computational biology, bioinformatics, or similar.
• Proficient in general purpose programming, ideally in python. Proficient with Linux-based operating systems and shell scripting
• Experience with design and usage of relational databases
• Experience with version control using Git
• PhD in bioinformatics, genomics, or clinical data science is a plus
• Proficiency in lower level languages like C/C++ is a plus
• Fluency in English written and spoken
• You like to work in a team and are motivated by working in an interdisciplinary environment

Our work is primarily focused on processing and analyses of DNA sequencing data, and we are using SnakeMake for orchestration of a large variety of bioinformatics tools on a on-premise cloud infrastructure managed through Moab/Torque. Previous experience with this work, or aspects thereof, is a great advantage - just like scientific understanding of molecular biology.

The application should comprise the following, and must be uploaded in the application system (the blue link “søg job”):

1. A very brief introductory letter outlining how you see yourself as part of the bioinformatics group, with examples from past and present research and development activities, or contributions to other larger bioinformatics projects.
2. A curriculum vitae that includes by
   1. Full publication list (if relevant)
   2. Link to git repository, or an example of some code that you have developed or co-developed (university projects are just fine). If this is not possible, please describe in some detail your coding experience and contributions to collaborative development projects.
3. Master level transcripts

Please do not upload videos, nor use the video CV option.

Deadline for application is October 31st, 2024 at noon. The appointment is permanent and will be based on the collective agreement with relevant union. The place of work is Rigshospitalet, Blegdamsvej, Copenhagen.

For further information, contact Frederik Otzen Bagger (email: [email protected], 2855 0628