In a collaboration between the Princess Máxima Center and partnering international hospitals we will be implementing (Nanopore) long read sequencing to improve the molecular diagnostics of pediatric cancer patients. The candidate will play a significant role in developing diagnostic grade tumor analysis pipelines for both methylation and variant calling. This analysis will be integrated into the genomics cloud platform at the Princess Máxima Center, and also shared for implementation at other hospitals.
Tasks and responsibilities
The candidate will work in close collaboration with bioinformaticians and laboratory specialists in both the Big Data Core and the Molecular Diagnostic laboratory. Specific tasks include:
- Implementation of analyses for (Nanopore) long read sequencing.
- Further development and implementation of the genomics cloud platform using Nextflow or (WDL, Cromwel), REST and large-scale computational infrastructures.
- Support data resources used for clinical data analysis.
- Deployment of analysis pipelines to cloud infrastructure.
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 Linux, R, python and java. Knowledge about next-generation sequencing, genetics, statistics and large-scale computational infrastructures are also preferred (including cloud computing). These skills should include deployment, orchestration and monitoring of workflows on cloud infrastructure, as well as awareness of cloud policy and security. The candidate should also have good communication skills, be flexible, versatile and a good team player in a dynamic multidisciplinary and international environment. The candidate should be able to work in a structured manner with an attention to details and perferrably have experience in software lifecycle and agile project management.
Our job offer
A temporary, full time position (36 hours a week for one year with the option for an extension after this period upon satisfactory performance) as a clinical 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 (FWG 50 BSc, FWG 55 MSc). The Princess Máxima Center is covered by the collective labor agreement “algemene ziekenhuizen”.
Work environment
The candidate will be part of the translational bioinformatics team at the Princess Máxima Center. This team is responsible for performing and developing bioinformatic data analyses at the interface of clinical care and research. The translational bioinformatics team is at the fore-front of implementing next-generation sequencing technologies in clinical practice, performing a broad range on analysis for all patients. Implementation of novel analysis within existing workflows as well as long-read technologies and other sequencing-based assays are under active development. We have extensive experience with implementing novel technologies in a diagnostic setting and coordinating bioinformatics infrastructures such as High-Performance Computing, cloud compute environments, workflow management systems and data sharing.
The Princess Máxima Center
The Princess Máxima Center for Pediatric Oncology is an integrated hospital and research institute, which integrates healthcare, research and education on pediatric cancer, in a single location in Utrecht. Our institute aims to provide the highest level of care for all children with cancer, with optimal quality of life. The center brings together the best possible care and scientific research, creating a unique interdisciplinary institute for pediatric oncology in Europe.
Contact
Are you our new colleague? We are looking forward to meeting you! You can apply directly by clicking on the orange button on this page. For more information about this position, or to arrange an informal chat, please contact Dr. Jayne Hehir-Kwa.
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