Bioinformatiker (m/w/d) in Hamburg

The Research Institute Children's Cancer Centre at the University Medical Center Hamburg-Eppendorf is looking for a highly motivated research assistant (PhD student) in the Computational Pediatric Oncology working group (headed by Prof. Dr. Michael Bockmayr) starting 01.11.2026. A later start can be accomodated in principle. We actively support and offer the chance to pursue a PhD alongside the project.

This position is part of a BMFTR-funded Junior Research Consortium conducted in close cooperation with the TU Berlin (Machine Learning Group/Dr. Mina Jamshidi Idaji) and the LMU München (Computational and Molecular Pathology/Prof. Dr. Philipp Jurmeister). The project focuses on developing novel ML methods for multimodal learning in computer-aided diagnostics. The goal is to integrate histopathological, clinical, and molecular data to optimize AI-based decision-making tools in oncology.

Strong individualized support is guaranteed throughout the entire period. In addition, you can expect a motivated and dynamic team of physicians, natural scientists, bioinformaticians, technical assistants, and students at the Research Institute, who are investigating pediatric cancers as part of various projects and with different approaches.

Your tasks

• Development and evaluation of clinically relevant multimodal classification algorithms using machine learning methods based on image data and high-dimensional omics datasets
• Integration of histological, molecular (genomics, epigenomics, transcriptomics at the bulk and single-cell levels), and clinical data
• Close collaboration with partners and other research groups at the Children’s Cancer Center
• Presentation of research results at international conferences and publication as first author in recognized journals

This position is temporary for three years due to third-party funding and project duration.

Requirements

• Proven programming experience, especially in Python, good knowledge of ML frameworks such as PyTorch or TensorFlow. Programming experience in R is a plus
• Excellent knowledge of current machine learning methods
• Excellent communication skills and ability to collaborate across disciplines
• Proficiency in written and spoken English; familiarity with German is a plus
• Experience with representation learning, transformer architectures, and explainable AI (XAI) is a plus
• Knowledge of omics data processing and basic molecular biology is a plus but not mandatory, as we care more about your computational skills
• Knowledge of UNIX-based operating systems and version control software is desirable

Fair and transparent compensation in accordance with our collective bargaining agreement (TVöD/VKA) (€ 63,600 - € 91,100), taking into account qualifications and professional experience. The salary range applies to a full-time position of 38.5 hours per week. The amounts listed are guidelines and do not constitute a salary guarantee.

Benefits

• Targeted and individualized professional development at both the technical and project levels is provided, offering long-term prospects in a meaningful work environment
• Comprehensive continuing education and training programs at our UKE Academy for Education and Career
• Opportunities to help shape our “UKE INside” personnel policy through cross-functional and cross-hierarchical projects
• Sustainable commuting: Subsidies for the Deutschlandticket as a job ticket and Dr. Bike bicycle service
• Excellent health, prevention, and sports programs
• Family-friendly work environment: Partnerships for childcare, free vacation care, counseling for employees with family members requiring care
• A secure job, meaningful work, and a supportive team environment
• Structured onboarding and open knowledge sharing within the team
• Our employee restaurant offers a wide variety of cu...