Bioinformatician to the Single cell core facility of Flemingsberg Campus (SICOF), Department of Medicine, Huddinge

Updated: about 1 month ago

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The single cell core facility of Flemingsberg Campus (SICOF)

We are a team of several research engineers, as well as senior scientists working together at the Single cell Core Facility of Flemingsberg (SICOF), where we define cells though their transcriptome as a service to Karolinska Institute. Our main technological focus is single cell sequencing using Smart-seq2/3 chemistry and the commercially available 10x genomics single cell solution. Our working group is made up of a mix of complementary skills in order to quickly and effectively drive research projects forward. We are currently looking for a bioinformatician with laboratory manager duties to primarily strengthen our team in the area of data analysis.

Department of Medicine (MedH)

The department of Medicine, Huddinge conducts graduate and post-graduate education, as well as research, within a wide range of the medical field, covering all internal medicine specialties, infectious diseases and dermatology. The department consists of seven units with a total of nearly 60 research groups. Our ambition is to be the leading department for medical research and education.

Duties

The position of bioinformatician with lab management duties at SICOF includes the following tasks:

  • General day-to-day management of data generated by SICOF, where a lot of projects are running in parallel.
  • Maintaining of the SICOF computing server, including safeguarding data organization and backups. Excellent knowledge of server architecture and data management is critical.
  • Data exchange between the customers of SICOF and the core server. Upload/download data to and from the customers.
  • SICOF has as one of its pillars of service the conversion of raw single cell sequencing files to analyzed clustered data that can be interpreted by researchers without relying on bioinformatical expertise. The position therefore entails the use of this pipeline and the continuous development of this analysis pipeline, making sure that the analysis stays up to date with new advances in single cell data clustering techniques.
  • Assist the other group members in the Smart-seq2/3 pipeline: Preparation of 384-well plates containing RNA-lysis buffer. Handling of single cell RNA extracts in 384-well plates and organizing the acquisition, tracking and progress of a large number of plates. The position therefore requires a strong track record in laboratory skills and substantial experience in wet lab techniques is mandatory
  • Advising users in the proper isolation techniques and cell sorting strategies. Prior experience with single cell isolation from primary tissues is therefore a demand for this position.
  • Plate-based single cell sequencing is dependent on proper deposition of single cells in a 384 well plate using a FACS. We therefore are looking for a person that has extensive experience in FACS operation. Prior experience with a BD FACSMelody is a strong merit.
  • Preparation of libraries for 10x Genomics sequencing. Prior experience with sequencing library preparation is therefore a merit.
  • Your profile

    We are looking for an experienced person with extensive bioinformatical knowledge in the field of single cell sequencing. The applicant should have substantial proficiency working in a Linux environment, as well as possess expertise in the coding languages of Python and R. Experience of working with a computing server is required. Strong understanding of single cell clustering algorithms is required and prior experience with Smart-seq2/3 data and 10x Genomics data is paramount.

    A major step in single cell sequencing experiments is the isolation of primary cells and their deposition in a 384 well plate using a FACS. The applicant should therefore have good documented use of FACS machines and primary isolation techniques. Prior experience with a BD FACSMelody is a strong merit, as well as practical knowledge on primary cell isolation from mouse models.

    SICOF has many projects running on cell heterogeneity of the central nervous system and as thus, knowledge in this area qualifies as a merit.

    Qualifications

    We are looking for a Bioinformatician who is able to work dynamically at MedH, an international and multidisciplinary research department. As communication with the user base is paramount, excellent communication skills in the English language is of utmost importance. Personal suitability will be a strong selection criterion. The applicant will be assessed on basis of technical competence, as well as past experience.

    What do we offer?

    Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote better health for all. At Karolinska Institutet, we conduct innovative medical research and provide the largest range of biomedical education in Sweden. Karolinska Institutet is a state university, which entitles employees to several benefits such as extended holiday and a generous occupational pension. Employees also have free access to our modern gym and receive reimbursements for medical care.

    Location: Flemingsberg

    Application

    Welcome to apply at the latest 2021-04-09.

    The application is to be submitted through the Varbi recruitment system.  

    Permanent position is initiated by a six months trial period.


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