Senior or Principal Data Engineer

We are looking for an exceptional data engineer with expertise in multi-omics end-to-end processing to help us uncover novel therapies for our patients. As a Senior Scientist in the Computational Innovation (@computationalinnovation) unit, you will work closely with cross-functional teams, including Computational Biology and AI/ML experts. Our mission is to leverage cutting-edge computational and engineering methods to drive target identification and deliver innovative therapies. Your role will focus on designing and implementing scalable pipelines for emerging omics modalities (e.g., proteomics, single-cell RNA sequencing, spatial omics) and ensuring the seamless delivery of high-quality, multimodal data for downstream analysis. Embedded in Boehringer Ingelheim’s growing CI unit, you will actively contribute to the discovery of breakthrough therapies that improve human health. As part of our team, you will not only create maintainable and sustainable data systems but also leverage agentic AI to streamline data ingestion, engineering, and workflow optimization, ensuring efficient and reproducible data processing across modalities.

Discover our Biberach site: xplorebiberach.com This position has a hybrid setup with approximately 2-3 days per week on site. This position can be filled either as Senior Scientist or Principal Scientist. This position is part time eligible with 80 %.

Tasks & responsibilities

As a member of the Data Excellence team within the Computational Innovation (CI) unit, you will play a key role in enabling the generation, processing, and integration of multimodal omics data to drive scientific discovery and innovation.

• In close collaboration with computational biology and AI/ML teams, you will design and implement scalable data pipelines, ensuring high-quality, standardized data assets for downstream analysis.
• You will leverage agentic AI to streamline data ingestion, engineering, and workflow optimization, driving efficiency and reproducibility across modalities.
• Furthermore, you will take ownership of complex data processing pipelines for omics modalities, including proteomics, single-cell RNA sequencing, spatial omics, and metabolomics, ensuring seamless integration into downstream workflows.
• You will collaborate with internal and external partners to establish robust data standardization processes, ensuring consistency in data quality and formats across diverse sources.
• You will work closely with cross-functional teams to define global standards for data processing, integration, and delivery, contributing to the development of a unified data ecosystem.
• You will actively contribute to the development and optimization of computational biology pipelines, databases, and data assets to support cutting-edge research initiatives
• Finally, you will strengthen stakeholder relationships through effective communication and alignment while driving operational excellence by identifying and implementing improvements to workflows, processes, and multimodal data capabilities.

Additional tasks for the Principal Scientist role

• You will lead strategic initiatives to define and implement best practices for omics data engineering across the organization.
• Moreover, you will identify and establish key partnerships for high-quality human data asset internalization, ensuring access to robust and reliable datasets to support research initiatives.
• You will drive innovation by identifying emerging trends and technologies in data processing and integrating them into the team’s workflows.
• You will mentor and guide junior scientists and engineers, fostering a culture of collaboration and technical excellence.
• You will represent the team in cross-functional discussions, contributing to high-level decision-making and long-term strategy development.

• PhD or Master’s degree in Bioinformatics, Computational Biology, Computer Science, or a related field with several years of relevant industry experience
• Proven experience in designing and implementing scalable pipelines for omics data processing
• Strong problem-solving and solution-oriented abilities, combined with critical thinking and the willingness to challenge existing practices are essential to drive innovation and efficiency
• Proficiency in programming languages such as Python or R as well as experience with workflow management tools (e.g., Nextflow, Snakemake) and cloud platforms (e.g., AWS, Azure), and familiarity with containerization technologies (e.g., Docker, Kubernetes)
• Solid understanding of omics data types (e.g., genomics, transcriptomics, proteomics) and associated tools, databases, and file formats
• Experience with agentic AI to streamline data ingestion, engineering, and workflow optimization is highly desirable
• Excellent communication and interpersonal skills to collaborate with cross-functional teams

Additional requirements for the Principal Scientist role

• Proven ability to align engineering solutions with strategic goals
• Extensive experience in pharmaceutical or biotech industries, with a proven track record of leading complex projects
• Demonstrated ability to drive cross-functional initiatives and influence organizational strategy
• Expertise in integrating multiple omics modalities and leveraging advanced AI/ML techniques for data analysis