Bioinformatician to Section for Molecular Diagnostics in Lund
Make a difference. Every day.
The medical unit of clinical genetics and pathology has over 400 employees in four locations in Skåne and consists of the Sections for Clinical Genetics, Clinical Pathology, and Molecular Diagnostics. The Section for Molecular Diagnostics has just over 80 employees, and our mission is to conduct highly specialized and modern laboratory diagnostics in many different method areas and to introduce new methods and analyses to meet the growing needs of healthcare. Our work takes place in close collaboration with Lund University and within the framework of national initiatives such as Genomic Medicine Sweden.
The Section for Molecular Diagnostics includes the Center for Molecular Diagnostics (CMD), where the work is primarily focused on massive parallel sequencing (MPS/NGS). CMD conducts routine diagnostics in several areas, such as NIPT, gene panels, and whole genome sequencing, but is at the same time very development-intensive. In 2020, more than 6000 NGS analyses were performed at CMD, focusing on cancer, hereditary diseases, and microbiology. At CMD, about 20 employees work with expertise in NGS, bioinformatics, and various disease areas.
The bioinformatics team comprises 8 people with different specialist competencies, who together handle the development and operation of everything from bioinformatics pipelines and infrastructure to IT systems, lab integration / automation and software for interpreting analysis results. The team also works in close collaboration with bioinformatics within the Center for Translational Genomics at Lund University. The work takes place in Linux-based environments, including a dedicated cluster with 1272 CPU cores for high performance computing specifically built for the organization. Nationally, work is underway to implement a large-scale cloud-based solution ("National Genomics Platform") which will be a resource for calculation, analysis, and storage for all regions in the country. Data is generated at CMD in one of Sweden's larger machine parks for short-read sequencing, which includes an Illumina NovaSeq 6000.
We are now looking for driven and solution-oriented employees for our bioinformatics team. Your responsibilities can partly be adapted and designed based on your qualifications together with the unit leadership. The main tasks are as follows:
• Development of new bioinformatics workflows within, among other things, whole genome and transcriptome analysis on everything from viruses to humans.
• Responsibility for operation and continuous improvements of established bioinformatics workflows.
• Development, operation, and improvement of software for visualization and evaluation of bioinformatics results.
• Support for geneticists/molecular biologists regarding the interpretation of genetic data and in technical issues concerning sequencing or bioinformatics.
• Work in national cutting-edge collaborations in genomics and bioinformatics.
Our work is at the technological forefront, and therefore in principle all development of new analyses takes place on site, from the ground up. New analyses are set up on an ongoing basis and as a bioinformatics expert you participate in all aspects from planning, to implementation and validation, and maintenance of robust pipelines. Within the group and in national networks, there is a diversity of expertise in bioinformatics, programming, and systems administration. We share much of our work publicly via github (https://github.com/Clinical-Genomics-Lund) and we use open source software wherever possible.
You have a bachelor's or master's degree in an adequate subject area, i.e. with bioinformatics and genomics as a foundation, or alternatively at least four years' relevant work experience in bioinformatics from industry, healthcare, or academia. You have good knowledge of Swedish and/or English, both verbally and in writing. To be successful in this role you also need experience of:
• Analysis of sequencing data (DNA and / or RNA based).
• The version control system git.
• A terminal-based Linux environment.
• At least one scripting language, such as Python, Perl, or R.
In addition to this, it is an advantage if you have a doctoral education in an adequate research area, i.e. in bioinformatics, genomics or equivalent. It is also beneficial if you have experience of:
• Working with containers (eg Singularity and Docker) and workflow managers (e.g. Snakemake and Nextflow).
• Working in a quality management system controlled environment with documentation requirements, such as in an accredited laboratory.
• Working in a common code base.
• Databases (SQL or mongodb).
The role requires good communication- and collaboration skills, as well as an ability to prioritize your work. You solve problems in your daily work, are thorough and are able to work independently even when existing routines are missing. Great emphasis will be placed on personal suitability.
Please note that this advertisement is also published in Swedish and that this advertisement is linked to a main advertisement.
We apply continuous selection in this recruitment, we look forward to your application.
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