Clinical Data Engineer II/III

ClearNote Health; San Mateo, San Diego (CA, CA); On-site; USD 150,000 - 190,000; Full time

Benefits offered by this job

Stock options

Competitive benefits

Job summary

ClearNote Health, an early cancer detection company, seeks a Clinical Data Engineer II/III to own clinical data operations, data pipelines, warehouse, and reporting infrastructure. You will transform clinical, laboratory, and sequencing data into validated, audit-ready data in a regulated environment.

Responsibilities include building ELT pipelines, data contracts with partners, quality metrics, dashboards, and cross-functional collaboration with clinical and regulatory teams.

Qualifications

• 5+ years of hands-on data engineering in production data-transformation frameworks and cloud data warehouses.
• Deep SQL expertise and ability to identify subtle logic errors in complex queries.
• Experience with ELT and data-integration tools.
• Experience with designing, building and using containers.
• Proficiency in Python or a comparable scripting language.
• Familiarity with cloud IAM concepts (OAuth/OIDC, key-pair, workload federation).
• Proven ability to work in a regulated environment with documentation and audit trails.
• Desire to balance building new data systems with maintaining reliability.
• Strong written and verbal communication skills and documentation history.
• Familiarity with clinical data standards (CDASH/CDISC) preferred.

Responsibilities

• Build and maintain ELT pipelines from clinical source systems into our data warehouse, including ad hoc sources.
• Support bulk data transfer initiatives to external partners and define data contracts.
• Develop, test, and refactor data transformation models across core clinical schemas.
• Define data quality metrics and monitor data quality across clinical datasets.
• Own the reliability of clinical result data end to end and manage change control.
• Unify data from multiple sources into an authoritative record with data contracts.
• Serve as a trusted partner to clinical and lab operations and external stakeholders.
• Build and maintain dashboards and monitoring, including system validation.
• Work with Regulatory/QA to ensure data flow and warehouse compliance.
• Provide guidance and training to research and development teams.

Skills

5+ years data engineering

SQL expertise

dbt

Python

Cloud data warehouse

ELT/data integration

Containerization

Regulated environment

Documentation/change control

CDASH/CDISC familiarity

Tools

dbt

Docker/containers

Job description

ClearNote Health is an early cancer detection company focused on the development and commercialization of non-invasive epigenomic tests to detect cancer through a standard blood draw, earlier than existing methods and when the disease is still treatable. Leveraging its novel liquid biopsy technology, ClearNote Health is initially focused on high-mortality cancers with the greatest need for early detection, starting with pancreatic and ovarian cancers.

Position Summary

TheClinicalData Engineer II/IIIownsclinical Data Operations:thedatapipelines, data warehouse, and reporting infrastructure that transformclinical data,laboratorydata,and sequencing results into validated, audit-ready clinical and business data. Thispositionoperatesina regulated environment in which accuracy and traceability are as important as well-architected code. The role combines hands-on pipeline and data-modeling work with ongoing production data support for our clinical studyoperations andis central to the integrity of the data that informs our research and clinical decisions.

Key Responsibilities

• Build andmaintainELT pipelines from clinical source systems — and non-standard sources such as ad hoc spreadsheets — into ourdata warehouse, and design ingestion frameworks that adapt to evolving report formats
• Support bulk data transfer initiatives to external partners and client-facing destinations, including the definition of the data contracts those partners depend on
• Develop, test, and refactor data transformation models across core clinical schemas, implementing precise, well-specified business logic, and integrate clinical data with other corporate data
• Define methods and metrics for assessing data quality, and monitor andmaintaindata quality across clinical datasets
• Own the reliability of clinical result data end to end, tracing issues to their root cause and strengthening controls through documented change management
• Strengthen the resilience of data contracts and design reconciliation logic that unifies data from multiple sources into a single, authoritative record
• Serve as a trusted partner to clinical and laboratory operations and external stakeholders, resolving data questions and improving accuracy at the source
• Build andmaintaindashboards and monitoring, including those subject to formal system validation, and support the data needs of adjacent business systems
• Partner with the Regulatory/QA team to ensure clinical data flow and the data warehouse remain compliant with procedural and regulatory requirements
• Serve as a subject-matter expert on warehouse clinical data, providing technical guidance and training to research and development teams
• Provide project status updates to cross-functional stakeholders

Qualifications

• 5+ years of hands-on data engineering experience with production data-transformation frameworks (dbtpreferred) and a cloud data warehouse
• Software-engineering fundamentals and an expert understanding of database and data-warehouse concepts
• Deep SQLexpertise, including the ability toidentifysubtle logic errors in complex queries
• Experience with ELT and data-integration tools
• Experience with designing,buildingandusingcontainers
• Proficiencyin Python or a comparable scripting language
• Familiarity with cloud identity and access-management concepts (key-pair authentication, OAuth/OIDC, workload identity federation)
• Proven ability to work in a regulated environment, including precise documentation, change-control processes, and audit trails
• Enjoys a role that balances building new data systems with keeping production systems reliable and trusted
• Strong written and verbal communication skills, witha track recordof documenting your work
• Working knowledge of clinical or laboratory data systems is a plus
• Familiarity with clinical data standards (CDASH/CDISC) preferred
• Working knowledge of Good Clinical Practice (GCP) and the clinical trial process preferred
• Familiarity with cancer-related medical classifications and ontologies (e.g., ICD-10) a plus

On-site is preferred for this position, in either our San Diego or San Mateo office. Theanticipatedsalary range for this position is $150,000 - $190,000. The actual salary will be dependent onvarious factorsthat may include experience level, knowledge,skills,and abilities.

ClearNote Health offers a competitive salary and benefits package.

Come join us in addressing large healthcare needs through precision epigenomic medicine!

ClearNote Health is an exciting life science company that is reinventing non-invasive molecular diagnostic testing using next generation epigenomic technologies. We are passionate and dedicated to discovering and developing medicines that will make a significant difference in cancer and other epigenomic-driven diseases. Our technologies provide novel insight and quantitation of human health and disease, with our focus on precision medicine applications improving both clinical and health system outcomes. Our company was founded based on pioneering work in the Stanford laboratory of Stephen Quake, with advisors from Stanford and UCSF.

We look for extraordinary lifelong learners with a passion and growth mindset for these areas, and for combining biological ingenuity with AI and data analysis. Led by a team with decades of experience bringing products from concept to market, we are an equal opportunity employer and value diversity at our company.

We provide generous benefits to all employees including stock options. We are building a world-class company, based in San Diego and San Mateo.

Our commitment to Diversity, Equity, Inclusion, and Belonging

We celebrate diversity in perspectives and backgrounds, and this is reflected in our innovation, our mission, and values. Our differences make us unique, help us innovate, and allow us to persevere. We strive to achieve representation and inclusion and redefine the possible in patients living longer lives.