Bioinformatician to the Center of Translational Genomics (CTG)

Lund University


December 12, 2021


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.

The Research Group The Center for Translational Genomics (CTG) is a prioritized research infrastructure at the Faculty of Medicine, Lund University, part of the Clinical Genomics platform at SciLifeLab. The platform aims to offer translational and clinical researchers access to state-of-the-art methods in genomics and transcriptomics (e.g. WGS, RNA-seq and new single cell analyses) and to quickly translate new research findings into improved clinical utility in close collaboration with the regional healthcare. Locally, this is performed through close interactions with the Section for Molecular Diagnostics at Region Skåne. Within CTG, there is great expertise in Next Generation Sequencing (NGS) technologies, bioinformatics and several different disease areas, and seen from both a national and international perspective, the unit is at the technological forefront with access to very powerful sequencing instruments (e.g.Illumina NovaSeq 6000). For data processing, the center uses a dedicated high-performance computing cluster at Lund University.

At the national level, CTG and Clinical Genomics Lund are also involved in a Swedish initiative for precision medicine; Genomic Medicine Sweden, where the development of new methods for tomorrow's research and diagnostics is coordinated with the corresponding large-scale sequencing facilities at the country's other university hospitals.

We are now expanding our bioinformatics group with a driven and team-oriented bioinformatics specialist. The position is a full time position time limited to 1 year starting January 1, 2022, or according to agreement.

Work duties and area of expertise You will be responsible for bioinformatics activities related to the Genomic Pandemic Preparedness Portfolio (G3P) project, which is a part of SciLifeLab´s Pandemic Laboratory Preparedness program.

Originating from some of the top genomics research infrastructures in Sweden, the G3P project aims at creating a resilient and nationally coordinated preparedness with regards to genomics-based analysis methods, applicable to both the current and future pandemics of viral pathogens. The methods developed may be used for multiple needs throughout a pandemic, e.g. to monitor global spread of different strains or to design more targeted and scalable diagnostic tests at earlier stages, or to identify potential vaccine escape mutations at later stages.

Within the project CTG and Clinical Genomics Lund is responsible for a work package aimed at improving existing SARS-CoV-2 bioinformatic pipelines of short-read whole-genome sequencing (WGS) data, and to develop software analysis tools for user-friendly data visualization. Depending on your background, the role may include both back- and front-end design of a web application for monitoring of viral-agnostic WGS data.

Work duties may also include more general bioinformatics tasks within the facility.

Qualifications The position requires:

  • University degree from a relevant field (i.e. with bioinformatics and genomics as a basis) or equivalent (at least 4 years) working experience in bioinformatics, from business, healthcare or academia
  • Bioinformatics experience in working with sequencing data (DNA- and/or RNA-based)
  • Experience in working in a terminal-based Linux environment and in at least one scripting language (eg 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 are structured and have an excellent ability to prioritize at work. The work is very team-based - both internally and externally - and therefore requires very good communication and collaboration skills. In addition, you need to have the ability to work independently. We are looking for you who are unpretentious and have a service-oriented approach.

    The following are desired for the position:

  • Basic knowledge about clinical and translational microbiology, with particular focus on viral agents
  • Experience in working with back- and/or front-end web design (e.g. Flask or React)
  • Experience in working with containers (e.g. Singularity or Docker)
  • Experience in working with bioinformatics workflow managers (e.g. Snakemake or Nextflow)
  • Excellent oral and written communication skills in Swedish
  • Instructions for your application The application must contain a personal letter describing how you fulfill the desired qualifications, a CV and diploma.

    Other The university applies individual salary setting. Please indicate your salary claim in your application.

    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.

    We kindly decline all sales and marketing contacts.

    Type of employment Temporary position longer than 6 months

    Contract type Full time First day of employment January 1, 2022, or according to agreement Salary Monthly salary Number of positions 1 Working hours 100 City Lund County Skåne län Country Sweden Reference number PA2021/3794 Contact

  • Markus Heidenblad, recruiting manager, 046-2220000
  • Emelie Falck, HR coordinator, 046-2220000
  • Published 25.Nov.2021 Last application date 12.Dec.2021 11:59 PM CET

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