Bioinformatician in Translational Genomics

Lunds universitet, Medicinska fakulteten, Inst för laboratoriemedicin

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 46 000 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 at SciLifeLab. The Clinical Genomics platform offers state-of-the-art genomics-based services (e.g. novel single cell applications) to translational and clinical researchers across Sweden as a whole and promotes rapid translation of new research findings into clinical utility through close collaborations with the regional healthcare providers. The unit is localized at BMC D14 in Lund and currently consists of a multi-disciplinary team of 14 people.

We are now looking for one to two highly driven and team-oriented bioinformaticians, interested 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.

We offer

Lund University is a state authority, which means you get special benefits, generous holidays and a favorable occupational pension. Read more on the university’s website about being employed by us Work with us.

Duties and areas of responsibility

The main tasks of the position include data analysis and processing, and internal project management, of massively parallel sequencing (MPS)-based projects, primarily based on the Illumina sequencing platform. Services currently offered at the facility include both genomics (e.g., WGS), transcriptomics (e.g. RNA-seq) and a wide variety of single-cell sequencing and spatial transcriptomics applications, primarily based on the 10X Genomics technology platforms.

Depending on experience and background, the duties may include one or several of the above-mentioned service areas. The work is versatile and may include one or several of the following duties:

• Daily responsibility for existing bioinformatics routines and workflows
• Development of new bioinformatics workflows and data analysis methods, e.g. in single-cell applications and spatial transcriptomics
• Integration of data management systems (LIMS and project management) to ensure seamless and automated data processing from project initiation to data delivery
• Providing bioinformatic expertise in genomics, transcriptomics and/or single-cell sequencing as well as spatial omics 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

Qualifications

We are looking for someone who meets the following requirements.

Requirements for the position are:

• Master or equivalent within a relevant field (i.e. bioinformatics, engineering, genomics or equivalent)
• experience of working with large-scale sequencing data (DNA and/or RNA based)
• experience of working in a terminal-based Linux environment
• experience in at least one scripting language (e.g. Python or JavaScript)
• 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 to 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-based data
• experience in analyzing single-cell sequencing and/or spatial omics data
• experience of applying workflow managers (e.g. Nextflow)
• experience of working with containers (e.g., Singularity or Docker)
• experience of collaborating in a version control system (e.g. Git)
• 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 permanent full time employment with the desired starting date September 1st or as soon as possible upon agreement. Probationary employment of 6 months may be applied.

How to apply

The position is applied for via the university’s recruitment system. The application must contain a personal letter in which you describe how you meet the qualification requirements and why you are interested in the position. The application must also contain a CV, including a list of publications, a general description of previous research work, a copy of the doctorate and anything else you wish to refer to (copies of diplomas, grades, information for references, letters of recommendation, etc.)

The Faculty of Medicine is a part of Lund University, and is responsible for education and research within medicine and healthcare. Our academic programs are closely linked with the healthcare system and are firmly anchored in the faculty’s strong research tradition. Our research spans a broad field within experimental preclinical research, near-patient clinical research and health sciences research. The Faculty of Medicine, with its 1,800 employees and 2,700 students in Lund and Malmö, is a knowledge-intensive meeting place for students, teachers and researchers from all over the world.

The Department of Laboratory Medicine is one of six departments at Lund University’s Faculty of Medicine. We conduct leading research, both broad and specialised, within the field of laboratory medicine, focusing on the onset of disease and how we can improve diagnostics and treatment for patients. Some of our strongest areas with world-class research deal with cancer, genetics and blood.

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