Bioinformatician – translational leukemia/proteomics bioinformatics

Karolinska Institutet

Application deadline

March 5, 2024

Bioinformatician – translational leukemia/proteomics bioinformatics

Karolinska Institutet, Department of Oncology-Pathology, Lehtiö research group

At the Department of Oncology-Pathology basic, translational and clinical research and educational activities related to cancer is carried out. Approximately 300 people from over 40 nations are currently working at the department. About 30 research groups with various cancer research profiles are involved and we have around 110 PhD students. The Department of Oncology-Pathology is responsible for undergraduate courses in Pathology, Oncology and Forensic Medicine for medical students, as well as for Tumor biology courses for biomedicine students and Pathology courses for opticians.

The bioinformatics work will be conducted in the Cancer proteomics Mass spectrometry research group headed by Professor Janne Lehtiö at Science for Life Laboratory (SciLifeLab). Karolinska Institutet is one of the four founding universities for SciLifeLab which is today a national infrastructure and research center in technology driven life sciences. Lehtiö group is a translational group of scientists with a drive to improve human proteome analysis by developing and using new proteomics methods that can be applied to improve personalized cancer treatment. We now need to strengthen our leukemia sub-group with a bioinformatician within the field of multi-omics data analysis and cancer research. We offer a very stimulating and diverse working atmosphere in a team of very motivated cancer researchers.

Your mission

We are looking for an outstanding candidate with focus on bioinformatics and experience in omics data analysis. The position requires solid expertise in genomics, transcriptomics and/or proteomics data analysis and communication skills and willingness to work in a team environment. The current position offers great possibility for innovative research combining proteomics and genomics data, together with a dedicated group of scientists.

The bioinformatician will work on integrative and translational analysis of multiple levels of omics data derived from various lymphoid malignancies such as AML and ALL cell lines as well as clinical specimens with the aim of identifying novel therapeutic and resistance biomarkers. The focus will be on developing and applying ‘omics’ methods on biologically/clinically oriented research questions and to analyze the acquired data as well as to validate the findings using public domain data. This includes both applying established data analysis steps as well as investigating new strategies and solutions for the analysis of quantitative biological data.

Important components of the work are experimental design, development of proteomics/ genomics/transcriptomics pipelines and statistical analyses of quantitative data and development of software and tools for data visualizations. It is expected that the applicant is well acquainted with software and programming languages related to omics data analysis. The candidate is expected to take a strong lead in managing and driving the project(s) as well as writing manuscripts.

Tasks for the position:

  • Drive and run integrative multi-omics data analyses tasks within the group.
  • Manage of multi-omics in-house and external data related to research projects (big data storage, security and access).
  • Help to meet the controlled data management guidelines.
  • Help in maintenance and handling of bioinformatics resources (server, HPC, cloud storage, and software).
  • Help interns, graduate students and technical personnel in running bioinformatics tools and pipelines.
  • Participate in tutorials and workshops organized within the research group.
  • Apply for external funding – both national and international.
  • Actively participate in meetings and discussions related to laboratory development and improvement.

Your profile


  • PhD in bioinformatics or computational biology.
  • Documented experience in bioinformatics, including experience in NGS, MS based proteomics, drug sensitivity/resistance screens or analysis of data from other high-throughput / high-dimensionality generating methods.
  • Strong publications record in reputed and high-impact factor journals.
  • Working experience in systems biology/systems medicine, large-scale data analysis, integration and visualization (e.g. GATK, nf-core,… etc).
  • Documented programming experience in: R/Python and Bash scripting.
  • Experience in workflow/pipelines management systems as well as packages management: Nextflow, Docker, Singularity and Conda.
  • Experience in utilize job scheduling systems such as Slurm or PBS to efficiently manage computational resources and execute bioinformatics workflows on high-performance computing clusters.
  • Experience in building data visualization and data navigation portals: Shiny or Dash.
  • Knowledge in statistical methods.
  • Ability to interpret omics data in a biological context.
  • Excellent communications skills
  • Fluent in English language.

Additional merits

  • Knowledge and working experience in MS based proteomics and proteogenomics is an advantage.
  • Knowledge and working experience of AML and ALL biology is ideal.
  • Knowledge of cancer biology and current translational cancer research
  • Knowledge/experience of drug discovery and development methods
  • Experience on building and handling interactive user-friendly web-based visualization tools
  • Experience in using and working in GitHub is an advantage

Since the position involves close interaction with several researchers, emphasis is placed on personal skills such as:

  • Very good collaborative skills
  • Excellent communication skills and analytical skills
  • Curious and eager to solve biological questions
  • Able to assist on-demand small tasks in research settings.

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: Science for Life Laboratory in Solna

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Welcome to apply at the latest 5th March.

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.

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Last updated: 2024-02-22

Content Responsible: Hampus Persson(