Princess Máxima Center for Pediatric Oncology- Scientific programmer/bioinformatician (Bsc or Msc)

Organisation

The candidate will be part of both the Kemmeren group at the Princess Máxima Center as well as the Koster group at the AMC. The Kemmeren group uses bioinformatics and systems biology to understand the molecular mechanisms underlying genetic interactions in relation to cellular processes and complex human diseases. We also have extensive experience with setting up and coordinating bioinformatics infrastructures such as High-Performance Computing, workflow management systems and data sharing and collaboration facilities. The Koster group uses bioinformatics to gain insights from all kinds of omics data, with a focus in the domain of pediatric solid tumors. We have extensive experience in creating data mining solutions that can be used by biomedical researchers with limited bioinformatics skills, such as the R2 genomics analysis and visualization platform (r2platform.com).

Project

As part of the research conducted at the Princess Máxima Center, Next-Generation Sequencing (NGS) data is collected for individual patients, organoids, cell lines and model systems and stored within a centrally managed LIMS system and data warehouse. This NGS genomics platform is part of an integrated research infrastructure currently being developed at the Princess Máxima Center. This project focuses on the development, implementation and use of the NGS genomics platform and integration with the existing R2 platform developed at the Koster group. The web-based R2 platform provides a rich set of inter connected tools that help biomedical researchers to analyze, hypothesize and visualize all kinds of omics data sets in a user friendly way. The system will incorporate various kinds of NGS data, including DNA-seq, RNA-seq and ChIP-seq, using either bulk sequencing as well as single-cell sequencing technologies and will allow investigation of individual samples, entire patient cohorts as well as cross-tumor pan analyses.

Tasks and responsibilities

The candidate will play a significant role in the development, implementation and integration of the NGS genomics platform at the Princess Máxima Center and the R2 platform developed by the Koster group. The candidate will work in close collaboration with bioinformaticians in both the Kemmeren and Koster groups.

Specific tasks include:

  • Development and implementation NGS genomics platform using Molgenis, WDL, Cromwell, REST and large-scale computational infrastructures.
  • Development and implementation integration layer between the NGS genomics platform and the R2 platform.
  • Coordination of tasks between the Kemmeren and Koster groups. You will be working both at the Princess Máxima Center in Utrecht as well as the Koster group at the AMC in Amsterdam.
  • Setting up and supporting bioinformatic analysis pipelines and questions.

Education and skills

We expect a highly motivated candidate with a bachelor or master in bioinformatics or similar experience in bioinformatics or data science. Excellent technical and programming skills are required, preferably in R, perl, python, java and/or C. Knowledge about next-generation sequencing, genetics, statistics and large-scale computational infrastructures are also preferred. The candidate should also have good communication skills, be flexible, versatile and a good team player.

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