Bioinformatician in translational genomics

Lund University, Faculty of Medicine, Dept. of Laboratory Medicine, Lund

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 44 000 students and more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition.

Lund University welcomes applicants with diverse backgrounds and experiences. We regard gender equality and diversity as a strength and an asset.

Description of the workplace
The Center for Translational Genomics, CTG, is a prioritized research infrastructure at the Faculty of Medicine, Lund University, which is part of the Clinical Genomics platform within SciLifeLab, Sweden’s national research infrastructure in molecular life sciences. The Clinical Genomics platform aims to offer translational and clinical researchers access to the latest methods in genomics and single-cell sequencing technologies, and to quickly translate new research findings into clinical utility in collaboration with healthcare.

We are now looking for a driven and team-oriented bioinformatician with interest in developing and providing cutting-edge research services in genomics, transcriptomics and single-cell sequencing. As a workplace, we safeguard a positive work environment with respect and consideration in our relations with one another.

What we offer
Lund University is a public authority, which means that you will have special benefits, generous annual leave and an advantageous occupational pension. We also have a flexitime agreement that creates good conditions for work/life balance. Read more on the University’s website about being a Lund University employee, Work at Lund University

Work duties and responsibilitiesThe main tasks of the position focuses on data analysis, data delivery and internal project management of sequencing projects, primarily based on the Illumina and Oxford Nanopore Technology sequencing platforms. Services currently offered at the facility include both genomics (e.g., gene panels, WES and WGS), transcriptomics (RNA-seq) and a wide variety of single-cell sequencing applications, primarily based on the 10X Genomics technology platform. Depending on experience and background, the duties may include one or several of the above-mentioned service areas.     

The work will be based on a close collaboration with the bioinformatics team, currently consisting of 3 people, the laboratory staff (7 people), as well as with translational and clinical researchers, most often associated with Lund University or the regional healthcare. The work may include anything from smaller tasks, such as compilation of quality control (QC) data and delivery of raw data, to the development of entirely new bioinformatics workflows and in-depth analysis, where you will have the overarching responsibility for bioinformatics and data analysis. More specifically, your duties will include:

• Daily responsibility for existing bioinformatics routines and workflows.
• Development of new – and continuous optimization – of existing bioinformatics workflows and data analysis methods.
• Further development and integration of data management systems (LIMS and project management) to ensure seamless and automated data processing from project initiation and sample submission to the laboratory to data delivery to the customer.
• Providing bioinformatic expertise in genomics, transcriptomics and/or single-cell sequencing development projects between CTG and local as well as national collaborators.
• Active contribution to project meetings with customers of the facility as well as scientific collaborators
• Opportunity to participate in national cutting-edge collaborations in genomics and bioinformatics, e.g. via SciLifeLab and the Swedish national sequencing initiative Genomic Medicine Sweden (https://genomicmedicine.se).

Qualifications
The requirements for the position are:

• Adequate university degree (i.e. with bioinformatics, genomics or equivalent as a specialization)
• experience of working with large-scale sequencing data (DNA and/or RNA based)
• experience working in terminal-based Linux environment and in at least one scripting language (e.g.Python, Perl or R)
• excellent oral and written communication skills in English

Great emphasis will be placed on personal suitability. The tasks require that you have an excellent ability to collaborate and communicate, an excellent ability to structure and prioritize in the work, and an excellent ability to work independently as well as develop new methods, even where existing routines are lacking.

Additional merits for the position are:

• PhD from relevant research field (i.e. bioinformatics, genomics or equivalent)
• experience in analyzing genomics- and/or transcriptomics data
• experience in analyzing single-cell sequencing and/or spatial omics data
• experience of applying workflow managers (e.g. Nextflow or Snakemake)
• demonstrated working experience with containers (e.g., Singularity or Docker)
• experience of working with a high-performance computing (HPC) cluster
• experience of working with, or having developed, project management systems and/or databases

Further information
The employment is a full-time permanent position, to start as soon as possible. Probationary employment can be applied.