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. 37 research groups with various cancer research profiles are involved and we have around 120 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 research group
Professor Jonas Bergh´s research group is performing leading breast cancer research of highest scientific level. Within the research group and associated/collaborating teams most aspects of breast cancer research are covered including basic tumor biology, pathology, bioinformatics and clinical trials. The research group has access to a well-characterized comprehensive tumor biobank as well as several clinical study cohorts. Many projects are run as multidisciplinary, global collaborations.

Your main tasks will be to develop and setup analytical pipelines for NGS-data with focus on genomics (WGS, WES and targeted sequencing) but also on transcriptomic (RNA-seq) data and their integration. You will be working with several highly unique clinical cohorts such as longitudinal primary tumor-metastatic samples and therapy-resistant versus therapy-naive tumors.
The position will involve applying advanced bioinformatics and statistical methods for analysis and interpretation of large datasets and high-dimensional genomic and transcriptomic data. You will be reporting directly to the PI and/or the associated project leader.


Absolute Requirements

  • PhD (or MSc with 3+ years of related experience) in computer science, bioinformatics or similar with emphasize on genomic data analysis.
  • Strong background in large-scale NGS data analysis using tools such as GATK, VarScan, MuTect, Cufflinks, Kallisto etc.
  • Programming skills in statistical software environments, preferably in R and/or Python. Should be well-versed in visualizing high-dimensional data, for instance, using packages such as ggplot2, matplotlib etc.
  • Working experience in UNIX/Linux environment and bash scripting, for instance, for automating large-scale analyses.
  • Experience in public bioinformatics databases (UCSC, Ensembl etc) and associated analytical pipelines.
  • A successful candidate should possess excellent interpersonal communication skills (written and verbal English), have the motivation to work in multidisciplinary teams and should be willing to work on multiple projects in parallel.
  • Experience in biostatistics.
  • Excellent documentation skills.

Preferred Requirements

  • Experience in NGS data pipelines and related packages in Bioconductor
  • Experience in integration of genomic and transcriptomic data
  • Experience in cancer-related databases such as TCGA, COSMIC, dbSNP etc.
  • Experience in precision cancer medicine and drug response profiling will be big plus
  • Experience in cancer genomics, especially related to breast cancer, will be very valuable
  • Experience in high-performance computing (cluster computing, parallelization, etc).
  • General knowledge in molecular biology and breast cancer research

Form of employment
This is a fixed term employment for 6 month, with possibility of extension for 18 month.

Application process
The application is to be submitted on the MyNetwork recruitment system.

Type of employment Visstidsanställning 3-6 månader
Contract type Full time
City Solna
County Stockholms län
Country Sweden
Reference number 2-770/2018
  • Johan Hartman, 073 976 02 42,
Union representative
  • Mimmi Shoshan, SACO, 46 8 517 754 60
  • Andreas Lundqvist, SACO, 46 8 517 768 84,
  • Helen Eriksson, OFR, 46 8 517 762 79
Published 23.Mar.2018
Last application date 20.Apr.2018 11:59 PM CET

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