Senior Data Engineer - Pathogen

Ellison Institute of Technology Oxford; Oxford; On-site; GBP 60,000 - 80,000; Full time

Benefits offered by this job

Competitive salary

Enhanced holiday pay

Pension

Life Assurance

Income Protection

Private Medical Insurance

Hospital Cash Plan

Therapy Services

Perk Box

Electric Car Scheme

Job summary

A leading research institute in Oxford seeks a Senior Data Engineer for their Pathogen Program. Candidates should have deep experience in building cloud-based data platforms and be proficient in Python and SQL. The role includes ensuring data quality and accessibility for scientists, and contributing to data management components. Benefits include a competitive salary and enhanced holiday pay, among others.

Qualifications

• 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.

Responsibilities

• Ensure data in the platform is acquired, processed, curated, and made accessible to scientists.
• Ensure data access adheres to FAIR principles.
• Contribute to building data management components.

Skills

Data platform development

Cloud-based architectures

Python

ETL

SQL

Real-time analytics

Data governance

Agile practices

Tools

Oracle OCI

AWS

Azure

Kafka

Docker

Kubernetes

Git

Job description

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.

Key Responsibilities

• 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.

Requirements

Essential Knowledge, Skills and Experience

• 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, lakehouses, 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, NoSQL, 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.

Desirable Knowledge, Skills and Experience

• 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.

Key Attributes

• Strong collaborator with excellent communication skills.
• Comfortable working in a fast‑paced, dynamic environment.
• Eagerness to learn and cross‑train in new technologies.
• Proactive and hands‑on approach to exploring new tools and developing proof of concepts (POCs).

Benefits

• Competitive salary on offer.
• Enhanced holiday pay.
• Pension.
• Life Assurance.
• Income Protection.
• Private Medical Insurance.
• Hospital Cash Plan.
• Therapy Services.
• Perk Box.
• Electric Car Scheme.

Why work for EIT

At the Ellison Institute, we believe a collaborative, inclusive team is key to our success. We are building a supportive environment where creative risks are encouraged and everyone feels heard. Valuing emotional intelligence, empathy, respect, and resilience, we encourage people to be curious and to have a shared commitment to excellence. Join us and make an impact!

Terms of Appointment

• You must have the right to work permanently in the UK with a willingness to travel as necessary.
• You will live in, relocate to, or be within easy commuting distance of Oxford.
• During peak periods, some longer hours may be required and some working across multiple time zones due to the global nature of the programme.