Karolinska Institutet, Institutionen för medicin, Huddinge

The Department of Medicine, Huddinge conducts preclinical and clinical research in a variety of areas and undergraduate and graduate education. The department is internationally oriented and consists of seven units with about 40 teams.

Job description
We are looking for a talented and highly motived data scientist/bioinformatican to take the lead on the data analysis on joint projects in the Jacobsen (http://ki.se/en/medh/sten-eirik-w-jacobsen-group) and Woll (https://ki.se/en/medh/petter-woll-group) laboratories aiming to understand cellular and molecular pathways regulating normal and malignant hematopoiesis. Technological advances allow us to perform these studies down to the single cell level, generating large and complex genomic data sets which can be mined for novel and import insight to normal and malignant hematopoietic stem and progenitor cell biology. Applicants are invited to submit applications for a two year research bioinformatician position with an initial fixed term of one year.  

The Jacobsen and Woll labs comprises an international collaborative team focused on understanding cellular and molecular pathways governing the earliest fate decisions in normal hematopoiesis (Carrhela et al, Nature, 2018; Luis et al, Nature Immunology 2016; Boiers et al, Cell Stem Cell 2013; Sanjuan-Pla et al, Nature, 2013) and how these are dysregulated in hematologic malignancies (Booth et al, Cancer Cell 2018; Giustacchini et al, Nature Medicine 2017; Woll et al, Cancer Cell, 2014; Mead et al, N Engl J Med 2012; Tehranchi et al, New Engl J Med, 2010). This is studied in mouse models, as well as in relevant patients. Key technologies applied towards these research questions include high-throughput DNA and RNA sequencing including single cell analysis, genetic fate-mapping using next-generation-sequencing technology, flow cytometry, mouse genetics and various in vitro and in vivo stem cell assays. The position and project is largely supported by a prestigious program grant from the Knut and Alice Wallenberg Foundation focused on biological and clinical studies on normal hematopoiesis and myelodysplastic syndromes.

Projects relating to human studies will also be performed at the Center for Hematology and Regenerative Medicine (HERM; http://ki.se/en/medh/herm), a newly formed center at the Karolinska Institute aspiring to create a strong translational research environment bringing together basic and clinical scientists focusing on normal and malignant hematopoiesis. Both Jacobsen and Woll are also affiliated with the Department of Cell and Molecular Biology (CMB; http://ki.se/en/cmb/startpage), the home of Center in Developmental Biology for Regenerative Medicine, a world-leading research center in developmental and stem cell biology (http://www.dbrm.se), where more basic research projects will be performed. The Jacobsen and Woll lab also have close interaction with world leading research groups, and the recruited bioinformatician will also benefit with ability to interact with this collaborative network. Of particular relevance, the bioinformatician will interact closely with the research group of Professor Seishi Ogawa, a world leader on next-generation sequencing of cancer (Yoshida et al, Nature, 2011; Kataoka et al, Nature, 2016), and a guest professor at the Karolinska Institute. 

The postholder will work closely with the group leaders, other scientists in the lab and external collaborators to jointly take the lead on the data analysis of projects aiming to resolve cellular and molecular pathways regulating normal and malignant hematopoiesis. The postholder will apply his/her computational expertise to identify appropriate analysis tools for single cell RNA and DNA sequencing approaches, targeted and unbiased DNA sequencing, and genetic fate mapping approaches which will be further analysed by data mining, mathematical modelling and graphical depiction. This is therefore an exciting position that allows the postholder to use and apply a variety of mathematical and bioinformatics techniques that can be applied to a wide variety of data sets, ranging from DNA sequencing from cell populations to single-cell RNA-seq analysis which together with wet-lab biologist will be used to support downstream functional studies.

The postholder must enjoy team work and interact well with others, including other members of lab, as well as collaborating scientists and clinicians. Good communication skills will also be required for data presentations and to represent the group at local or external conferences.

Entry requirements

Essential requirements

  • Degree in computer science, bioinformatics or a scientific discipline
  • Competency in programming languages using programs such as Python, Perl and R
  • Ability to learn new programming language as required
  • Ability to stay on top of the relevant research field
  • Ability to work and communicate with others, scientifically and collegiately
  • Ability to work independently but when required, seek input from other team members and collaborators
  • Efficiently meet deadlines
  • Ability to present research orally and written
  • Good knowledge of written and spoken English language

Desirable skills

  • MSc or higher in computer science, bioinformatics, machine learning or related field
  • Training in international leading laboratory
  • Strong publication track record for stage of career
  • Experience from hematopoiesis research
  • Experience in molecular and/or cellular biology
  • Experience in statistical analysis, analysis of complex data sets or developing analytical pipelines
  • Familiarity with developing in a UNIX/Linux environment
  • Experience using and developing databases such as Oracle, MySql
  • Experience with DNA and/or RNA sequencing analysis
  • Experience with single cell analysis

 Application process

An employment application must contain the following documents in English or Swedish:

  1. A maximum one page cover letter summarizing previous experience, research interest and motivation for position
  1. A complete curriculum vitae of current work and work history
  1. A complete list of publications
  1. Names and contact details of three references who are familiar with the applicants recent research and training

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

Type of employment Visstidsanställning längre än 6 månader
Contract type Full time
Number of positions 1
Working hours 100 %
City Huddinge
County Stockholms län
Country Sweden
Reference number 2-1914/2018
  • Petter Woll, petter.woll@ki.se
Union representative
  • Mats Rudling, SACO, mats.rudling@ki.se
  • Yvonne Edlund OFR/ST , yvonne.edlund@ki.se
Published 05.Apr.2018
Last application date 11.May.2018 11:59 PM CET

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