Key Skills

Job Description

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 the treatment of pancreatic cancer patients. Your Main Tasks Will Include Develop and maintain a 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. For candidates interested in pursuing a PhD, this position may provide an opportunity to develop into a PhD trajectory, depending on the candidate’s ambitions and performance, project progress, and funding availability. 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 develops 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. You will join a highly multidisciplinary team (15 FTE) and work closely with fellow bioinformaticians, as well as scientists, pharmacists, clinicians, and technicians. Qualifications And Skills 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. Terms of employment A temporary 12-month contract with the intention to extend The gross monthly salary amounts a minimum of € 3.126,- and a maximum of € 4.182,- (scale 7). A salary increase of 3,5% from May 2027, according to the collective labor agreement (CLA). 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 Applying is easy via the application button. For more information about this position, please contact Willem de Koning by e-mail (mailto:e-mail:[email protected]), phone or WhatsApp, 06 158 581 03 (tel:0615858103).

Core Responsibilities

Develop and maintain a reproducible bioinformatics pipeline to identify tumor-specific mutations and predict neoantigens using sequencing data and machine learning. Integrate datasets, collaborate with laboratory scientists to validate predictions, and contribute to research publications and grant applications.

Requirements

A master's degree in bioinformatics or a related field is required, along with demonstrable experience analyzing high-throughput sequencing data and knowledge of mutation and gene expression data. Candidates should be proficient with bioinformatics tools, workflow creation, Linux, Bash, and either R or Python; experience with HPC, Git, immunology, cancer genomics, and machine learning is preferred.

Benefits

• 13th-Month Salary
• Individual Travel Expense Package
• Pension Insurance
• In-Company Physiotherapist
• Bicycle Repair Service
• On-Site Gym