Bioinformatician: Neoantigen prediction for therapeutic purpose

Job description

Within the Department of Pulmonary Medicine, we are seeking a highly motivated and enthusiastic bioinformatician who will join us in developing neoantigen peptide-based cancer vaccines for treatment of pancreatic cancer patients.

Your main tasks will include:

• Develop and maintain bioinformatics pipeline for neoantigen identification.
• Analyze next-generation sequencing data (WES, RNA-seq) to identify tumor-specific mutations.
• Implement and optimize machine learning algorithms for neoantigen prediction.
• Integrate public and proprietary datasets to improve pipeline accuracy.
• Collaborate with wet-lab scientists to validate predicted neoantigens.
• Maintain and document computational workflows to ensure reproducibility.
• Contribute to research publications and grant applications.

Work environment

The Neoantigen Peptide group is part of the Solid Tumor Immunology Research Rotterdam (STIRR) group at the Department of Pulmonary Medicine. The STIRR performs fundamental, translational, and clinical research to unravel the prerequisites for effective anti-tumor immunity and the mechanisms behind resistance to immunotherapies. Our research focuses on various types of cancer, including lung cancer, mesothelioma, pancreatic cancer, and melanoma.

The Neoantigen Peptide group strives to develop novel neoantigen peptide based cancer vaccines for the treatment of pancreatic cancer, a highly lethal neoplasm with a poor 5-year survival rate of <10% for which new treatment options are urgently required.

In addition, you will collaborate closely with other departments such as the Radiopharmaceutical Chemistry (RPC) group and the Department of Pharmacy.

Qualifications and skills

• Bachelor's or Master's degree in Bioinformatics, Life Science, Engineering, Computer Science, Information Systems, or equivalent.
• Demonstrable experience with high-throughput sequencing data analysis, including data processing, quality control, and interpretation.
• Knowledge of mutation data and gene expression data.
• Proficiency in bioinformatics tools, workflow creation, and Linux-based systems.
• Strong skills in bash scripting and programming in either R or Python.

In addition, you preferably have:

• Experience with HPC infrastructure.
• Experience in Git for version control Knowledge of immunology and cancer genomics.
• Familiarity with machine learning techniques.

Before you apply please check our conditions for employment.

Terms of employment

• Depending on the work experience, either a temporary 12 month contract with the intend to extend.
• The gross monthly salary amounts a minimum of € 2.932,- and a maximum of € 3.923,- (scale 7).
• Excellent fringe benefits, such as a 13th month that is already paid out in November and a individual travel expense package.
• Pension insurance with ABP. We take care of approximately 2/3 of the monthly contribution.
• Special benefits, such as a incompany physiotherapist and bicycle repairer. And there is also a gym where you can work on your fitness after work.

More information

For more information about this position, please contact Koen Bezemer, projectmanager, 06 234 601 08 or k.bezemer@erasmusmc.nl.

If you are excited by the thought of this position and would like to apply, please do so by using the application form on our website.

No agencies please.