Do you want to contribute to top quality medical research?

Our group does research on precision cancer medicine with the aim of optimizing treatments for individual cancer patients based on molecular profiling, spatial cellular maps and functional drug testing. Our goal is to develop a systems biology framework and process to match therapies using cell type and omics- profiling with drug testing.

Your mission

Your mission is to conduct bioinformatic analysis from a variety of high throughput drug testing assays and omics molecular profiles and image-based spatial biology maps. This position provides you with the opportunity to pioneer data integration and mining on drug testing data and with a unique chance to develop analysis pipelines together with wet lab scientists to find drug repurposing opportunities for cancer patients. Our data types include drug testing done using cell lines and patient-derived cells in well-based assays but also a wide selection of image-based data done on 2D and 3D models including live cell videos. For omics profiles we routinely conduct genomic, transcriptomic as well as single-cell sequencing experiments. To complement these data types, we also do multiplexed-immunohistochemical analyses to identify spatial relationships between cell types in diseased tissues.

The applicant will be expected to perform basic data analysis and to participate in routine choirs in data management, but be focused, curious and eager to develop novel integrative analyses using both image- and omics-based data for future precision cancer medicine. The successful candidate will regularly present and communicate the scientific results both in written and oral format, to both informaticians and wet lab scientists. You will be expected to communicate and present your results clearly in English and help in teaching to other group members as well as the research community as a whole. Many of our pipelines are created to be used continuously after initial publication and hence the ability and will to develop web-based tools is considered a bonus.

Your profile

You hold a PhD or relevant experience in industry in a suitable field such as bioinformatics, computer science, mathematical modelling, and deep/machine learning. You have strong data analysis skills and knowledge of statistics. Previous experience with image and/or -omics data along with single cell sequencing are beneficial. You have previously created relevant bioinformatics data analysis pipelines and have good understanding of data integration and network biology. We expect experience in working with biologists as well as in participating in multi-disciplinary collaborative work. Ability and motivation to communicate and collaborate widely across disciplines is important.

Excellent skills in R, Python and/or MATLAB along with expertise on databases (SQL) and version control (Git/Bitbucket) is needed. Working in a Linux environment, with experience in working with job scheduling resources (i.e. SLURM) and Docker/Singularity technologies is desirable. Also, knowledge on web frameworks (full stack) is considered as an advantage. Desired skills also include experience in purchase and administration of IT systems.

Motivation to develop web-based interactive tools enabling biologists to visualize and data-mine and carry out basic analyses is also highly appreciated. In our dynamic, multidisciplinary and collaborative team, the applicant should be self-driven, but possess excellent interpersonal and communication skills in spoken and written English.

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.

Your work will be carried out at the Science for Life Laboratory (SciLifeLab), that is a leading national infrastructure for next-generation life science research in Sweden. SciLifeLab is jointly operated by the four host universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University, and it has facilities in four other universities across Sweden. There are over 1 000 people working at SciLifeLab, either in research groups or in the infrastructure facilities, most of them in the KI Solna campus and in Uppsala.

Location: Solna

The position is temporary for one year with possibility for extension. 

SciLifeLab

Olli Kallioniemi

Application

Welcome to apply at the latest 2020-11-08.

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

Want to make a difference? Join us and contribute to better health for all

Type of employment Temporary position longer than 6 months
Contract type Full time
First day of employment As per agreement
Salary Monthly salary
Number of positions 1
Working hours 100%
City Stockholm
County Stockholms län
Country Sweden
Reference number STÖD 2-4429/2020
Contact
  • Päivi Östling, +46 (0)73 673 5762, paivi.ostling@scilifelab.se
Union representative
  • Helen Eriksson, OFR, 08-524 823 38
  • Andreas Lundqvist, SACO, 08-517 768 84
Published 09.Oct.2020
Last application date 08.Nov.2020 11:59 PM CET

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