Senior Data Engineer - Pathogen

Senior Data Engineer, EIT Pathogen Program

The Ellison Institute of Technology (EIT) tackles humanity's greatest challenges by turning science and technology into impactful global solutions. Focused on areas such as health, food security, sustainable agriculture, climate change, clean energy, and robotics in an era of artificial intelligence, EIT blends groundbreaking research with practical applications to deliver lasting results.

A cornerstone of EIT's mission is its upcoming 300,000-square‑foot research facility at the Oxford Science Park, set to open in 2027. This campus will feature advanced labs, an oncology and preventative care clinic, and collaborative spaces to strengthen its partnership with the University of Oxford. It will also host the Ellison Scholars, driving innovation for societal benefit.

The Pathogen Mission highlights EIT's transformative approach, using Whole Genome Sequencing (WGS) and Oracle's cloud technology to create a global pathogen metagenomics system. This initiative aims to improve diagnostics, provide early epidemic warnings, and guide treatments by profiling antimicrobial resistance. The goal is to deliver certified diagnostic tools for widespread use in labs, hospitals, and public health.

EIT fosters a culture of collaboration, innovation, and resilience, valuing diverse expertise to drive sustainable solutions to humanity's enduring challenges.

• Ensure data in the platform is acquired, processed, curated, and made accessible to scientists, digital analytics products, bioinformatics, and AI at a high standard of quality and availability.
• Ensure data access adheres to FAIR principles (Findable, Accessible, Interoperable, and Re‑usable).
• Ensure data is secured and compliant with regulatory, legal, and data sharing requirements.
• Ensure efficient, performant, and high‑quality pipelines for data ingestion into the platform.
• Contribute to building data management components, including reference data management, de‑identification, data curation, pathogen and technical metadata catalogues, and data access controls.
• Ensure efficient, secure, scalable, available, and performant data storage components, including genomic variant storage, clinical data stores, and clinical imaging.
• Ensure robust ingest services capable of seamlessly integrating data from distributed sequencing devices, including real‑time telemetry streams.
• Ensure data is processed to enable optimal access and consumption by digital analysis products, bioinformatics pipelines, and researchers/scientists.

• Deep experience in building modern data platforms using cloud‑based architectures and tools.
• Experience delivering data engineering solutions on cloud platforms, preferably Oracle OCI, AWS, or Azure.
• Proficient in Python and workflow orchestration tools such as Airflow or Prefect.
• Expert in data modeling, ETL, and SQL.
• Experience with real‑time analytics from telemetry and event‑based streaming (e.g., Kafka).
• Experience managing operational data stores with high availability, performance, and scalability.
• Expertise in data lakes, lake houses, Apache Iceberg, and data mesh architectures.
• Proven ability to build, deliver, and support modern data platforms at scale.
• Strong knowledge of data governance, data quality, and data cataloguing.
• Experience with modern database technologies, including Iceberg, No
  
  SQL, and vector databases.
• Embraces innovation and works closely with scientists and partners to explore cutting‑edge technology.
• Knowledge of master data, metadata, and reference data management.
• Understanding of Agile practices and sprint‑based methodologies.
• Active contributor to knowledge sharing and collaboration.

• Familiarity with genomics and associated data standards.
• Experience with healthcare clinical data and standards such as OMOP and SNOMED.
• Familiarity with containerization tools such as Docker and Kubernetes.
• Familiarity with Git and CI/CD workflows.

• Strong collaborator with excellent communication skills.
• Comfortable working in a fast‑paced, dynamic environment.
• Eagerness to learn and…