Vacancies

Title Data Scientist/Bioinformatician (Msc)
Start Date 2020-11-06
Location Utrecht, Princess Máxima Center for Pediatric Oncology
Job Information

The Princess Máxima Center for Pediatric Oncology is a research hospital concentrating healthcare, research and education of pediatric cancer in a single location in Utrecht. The institute aims to provide the highest level of care for all children with cancer and has the ambition to cure all children of cancer and improve quality of life. The center brings together the best possible care and scientific research, creating a unique interdisciplinary institute for pediatric oncology in Europe.

The candidate will be part of the Big Data Core at the Princess Máxima Center. This unit is responsible for performing and developing bioinformatic data analyses with regard to our institute-wide biobanking and clinical genomics activities. The Big Data Core is at the fore-front of using next-generation sequencing technologies in research including exome sequencing (WES), whole-genome sequencing (WGS) and RNA-seq based analyses for all patients as well as DNA methylation-based classification of brain tumors. Implementation of novel applications using long-read technologies and other sequencing-based assays are under active development. We have extensive experience with implementing novel technologies in a mixed diagnostic and research setting as well as coordinating bioinformatics infrastructures such as High-Performance Computing, workflow management systems and data sharing and collaboration facilities.

Project

As part of diagnostics and biobanking conducted at the Princess Máxima Center, WES, WGS, RNA-seq and DNA methylation array data are generated for patients treated at the institute. The genomics platform is part of a shared diagnostics and research infrastructure developed at the Princess Máxima Center. The candidate will be responsible for further development of the data infrastructure, optimizing the data flows, efficiency scaling and integration with other data reporting and interpretation tooling.

Tasks and responsibilities

The candidate will play a significant role in the further development, implementation and integration of the genomics platform at the Princess Máxima Center. Within the team, we are using an Agile/Scrum methodology for achieving our goals. The candidate will work in close collaboration with bioinformaticians and laboratory specialists in both the Kemmeren group, diagnostics lab as well as other research groups in the institute.

Specific tasks include:

  • Continued development, implementation and support of the genomics platform using Molgenis, WDL and Cromwell.
  • Optimize the use of large-scale computational infrastructures using provisioning tools such as ansible and containerization platforms such as docker/singularity.
  • Optimizing computational data flows for NGS analyses.
  • Integration and support of data querying, reporting and interpretation tools such as TranSMART/Glowing Bear and cBioPortal.
  • Facilitate biobank data requests.

 Education and skills

We expect a highly motivated candidate with a master in data science or similar experience in data science or bioinformatics. Excellent technical and programming skills are required, preferably in Linux, R, python and java. 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 in a dynamic environment.

We offer

A temporary, full time position (36 hours a week for one year with the intention to extend after this period for three years) as a data scientist/bioinformatician at the Princess Máxima Center. You will be working in a very stimulating and cross-disciplinary clinical and research environment, combining cutting-edge clinical care with state-of-the-art bioinformatics. Gross monthly salary will depend on experience and background with a maximum of (€4.227,- per month, FWG 55). The Princess Máxima Center is covered by the collective labor agreement “algemene ziekenhuizen”.

Contact and application

For more information contact Dr. Patrick Kemmeren p.kemmeren@prinsesmaximacentrum.nl. You can apply for this position using the orange apply button “solliciteer direct”.

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