Bioinformatician at Karolinska Institutet

Do you want to contribute to top quality medical research?
Department of Oncology-Pathology

https://ki.

se/forskning/barntumorbanken, or in English: The Swedish Childhood Tumor Biobank, is a national infrastructure, research project and sample collection dedicated to childhood tumors. BTB performs deep sequencing and analysis on collected samples in collaboration with the https://www.scilifelab.se/units/ngi/ (NGI) at https://www.scilifelab.se/(SciLifeLab), a national centre for large-scale life science research with advanced technological infrastructure. The aim of BTB is to promote research and increase understanding of disease mechanisms for childhood tumors, ultimately improving patient care and treatment.

Currently, BTB is also co-coordinating the national initiative https://genomicmedicine.se/(GMS) for paediatric cancer. This project aims to implement whole genome sequencing in clinical practise for patients with childhood tumors. To support our mission, we are now looking for a motivated bioinformatician to contribute in developing data analysis pipelines and providing computational, and data handling support for the projects BTB manages and takes part in.

This is an opportunity to work in a multi-disciplinary environment, continuously evolving with the latest technologies in the field to support and enable high-quality genomic research on childhood cancer.

Your mission
As a bioinformatician, you would be focusing on developing, testing, implementing, and maintaining analysis pipelines for the sequencing data both for basic research and clinical application. The data is then mainly generated internally in collaboration with NGI/SciLifeLab and within the GMS-project. This would include develop/install/run software and pipelines for analysis, visualization and interpretation of results concerning childhood tumors and paired normal samples. You will be also be heavily involved in developing in-house databases to compile a vast amount of genomic data from unstructured data sources to build interactive database web applications. Tasks includes as well data management, data transfer and documentation.

The work will be performed at BTB/Dept. of Pathology-Oncology together with colleagues of different expertise. A part of the job is also to keep up to date and in contact with the appropriate collaborators for NGS-data management.

Your profile
Requested requirements:

- Ph.D. or similar experience in computational biology, bioinformatics or computer science.
- Knowledge of working with next generation sequencing pipelines and experience in handling, analysis, and annotation of very large biological datasets (e.g., WGS, WES, RNA-seq), both exploratory and in form of pipelines.
- Experience working with various bioinformatics tools and statistical methods (eg GATK, STAR, BWA, Manta, FastQC/MultiQC, DESeq/edgeR). 
- Experience with web-based bioinformatics tools and public databases of biological data.
- Proficiency in R or Python and knowledge and experience of BASH/UNIX.
- Experience with data analysis and data mining to produce meaningful data visualizations.
- Experience in designing and implementing databases (e.g., MySQL or MongoDB)
- Great communication skills, including research report writing, code documentation, and oral presentation, with excellent attention to detail.
- Ability to work independently and successfully in a matrix environment, prioritize and manage multiple tasks simultaneously, integrate cross-functional issues, and balance competing priorities effectively.
- Fluent in spoken and written English.

Preferred qualifications:

- Experience from research in human genomics and transcriptomics, preferably in cancer biology.
- Experience in high-performance computing (HPC) cluster, and use of job schedulers (Slurm/PBS).
- Experience with workflow management software such as Nextflow or SnakeMake.
- Experience with development, generation, and use of software containers (e.g., Docker, Apptainer/Singularity)
- Experience with version control software (e.g., Git).
- Experience in database design and management.
- Experience in developing project technical specifications.
- Ability to work independently, be organized, and take initiative.
- Excellent analytical and problem-solving capabilities.
- Excellent communication, and interpersonal skills and team player.
- Great emphasis will be placed on personal competence and suitability.

What do we offer?
A creative and inspiring environment with wide-ranging expertise and interests. 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 a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. And you get to practice freely in our modern wellness facilities, where trained staff are on site.

Location: Solna 



Application
Welcome to apply at the latest 13th of april. 

The application is to be submitted through the Varbi recruitment system.In this recruitment, you will apply with your CV without a personal letter. Instead, you will answer some questions about why you are applying for the job in the application form. 

Permanent position is initiated by a six months trial period.

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