Bioinformatician in genomics and single-cell sequencing (PA2022/2243)

Updated: 4 days ago
Job Type: FullTime
Deadline: 14 Aug 2022

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, and to quickly translate new research findings into clinical utility in collaboration with healthcare.

We are now looking for a driven and solution-oriented bioinformatician in genomics, with a special focus on single-cell sequencing and spatial sequencing applications. 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 areas of responsibility
The 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 platforms. Both from the laboratory and bioinformatics perspectives, the areas of responsibility are divided into genomics, transcriptomics, single-cell and spatial applications. The focus of the current position is on single-cell sequencing (e.g. 10X Genomics-based), but depending on experience, the areas of responsibility in the new position can be partially adapted in dialogue with those responsible for the unit.

The work will be based on a close collaboration with the laboratory staff, as well as with translational and clinical researchers, most often associated with Lund University or the regional healthcare. The work may include everything 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 overall responsibility for bioinformatics and data analysis.

More specifically, your duties will include:

  • Daily responsibility for existing bioinformatics routines and workflows for data from the latest sequencing technologies, with a special focus on single-cell applications (e.g. mRNA, CITE-seq, ATAC-seq, multiomics).
  • Development of new, and continuous optimization, of existing bioinformatics workflows and data analysis methods, especially in single-cell sequencing (genomic applications) and spatial omics methods (e.g. 10X Genomics Visium).
  • Providing bioinformatic expertise in single-cell sequencing development projects between CTG and local and national 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.

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 qualifications for the position are:

  • PhD from relevant research field (i.e. bioinformatics, genomics or equivalent)
  • experience of working with genomics- and/or transcriptomics data
  • experience of working with single-cell sequencing and/or spatial omics data
  • experience of working with workflow managers (e.g. Nextflow or Snakemake)
  • experience of working 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. 

How to apply
You apply for the position via the University’s recruitment system. The application is to include a personal letter describing how you meet the qualification requirements and why you are interested in the position. The application is also to include a CV with a list of publications, a general description of previous research work, a copy of your doctoral degree and any other documents to which you wish to draw attention (copies of degree
certificates, grade transcripts, details of referees, letters of recommendation, etc.)

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