Amsterdam UMC/AMC – Bioinformatician (postdoc)

What you are going to do
You will be responsible for executing our contribution to the iTHER2.0 project which is in close collaboration with the Princess Maxima Center for pediatric oncology.
You will implement functionalities in the R2 platform that are useful in personalized medicine, making use of Perl / R / JavaScript / Python programming / scripting languages. You will also setup and maintain a database that can be used for automatic prioritization of targetable mutations, copy number variations and/or gene expression changes, to assist in quick and reproducible assessment. Furthermore, you will participate in the development of a report that can automatically be generated from all analyses. Finally, you will help develop tools and new visualizations in the R2 platform that can be used in pre-clinical drug testing on patient derived models, that will be generated and tested in the project. It is expected that parts of the R2 platform will have to be refactored in order to scale with expected growth of data and addition of new, computationally intensive algorithms.

What we expect from you
To help extend the R2 platform for personalized medicine utility, our team is looking for a highly motivated postdoc in the area of applied bioinformatics. As such our ideal candidate is a well-organized and analytical thinker, who additionally has:

  • A Ph.D in (Bio)informatics, biology with a strong emphasis on bioinformatics, or equivalent (required);
  • Proficiency in English (required);
  • Excellent programming skills in Perl, Javascript, Python or equivalent languages (required);
  • Experience with database and software design (MySQL, UML);
  • Experience with version control systems, github;
  • Experience with open source software;
  • Affinity with molecular biology data and their translation towards the clinic;
  • Familiarity with Linux operating systems;

Where you are going to work
You will work within the group of Dr. Jan Koster, who has conceived the R2 platform and is leading a team of bioinformaticians within the department of Oncogenomics (AMC, Amsterdam). The group has been involved in many (inter-)national projects relating to various aspects of genomics (WGS, RNAseq, gene expression profiling, methylation profiling, etc). Much of our current work is in the field of pediatric cancer, with emphasis to neuroblastoma. However, we also collaborate with groups in other fields of oncology.

Our ambition
In this era of explosive high throughput (HT) data in molecular biology, there is a growing need for accessible software solutions that can help unlock biological/clinical characteristics from such data. With the biomedical researcher (with limited or no bioinformatics skills) in mind, we developed a comprehensive open access web-based platform called R2 (http://r2.amc.nl). R2 aids in the analysis and visualization of public as well as private/shielded high throughput data and their associated annotated features. Because the R2 bioinformatics team is embedded in a molecular biology research group, development of the platform was guided by requirements of molecular biologists, thereby contributing to its user friendliness.
Over the years the R2 platform has expanded greatly, offering analyses and visualizations for many types of omics data. The platform has been cited in PubMed >900 times and been used in publications including Nature and Cell. Next generation sequencing analyses of patient biopsies are increasingly being employed to identify targets for therapeutic interventions (personalized medicine). Our team currently has an opening for a team player who can help to further develop our platform for usage towards clinical implementation.

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