Senior Clinical Data Scientist

Sr. Clinical Data Scientist

Karius is a life science, venture-backed clinical metagenomics company, focused on elevating patient care through microbial insights. We are committed to advancing diagnostic science and technology to optimize the diagnosis and treatment of infectious diseases. Through the use of genomics and AI, we are driven to improve the diagnostic landscape for infectious diseases. Karius delivers unprecedented diagnostic insight detecting microbial cell-free DNA circulating in the body to assist physicians to make rapid treatment decisions.

The Sr. Clinical Data Scientist will serve as the primary data architect for Karius's large-scale commercial real-world evidence registry. This role sits at the intersection of clinical research and health informatics, responsible for designing and operationalizing EHR data extraction pipelines across participating health systems, translating clinical research requirements into structured data specifications, and transforming heterogeneous real-world data into analysis-ready datasets that support biostatistics and clinical development.

The ideal candidate is equally comfortable negotiating data specifications with a site's Epic Clarity team and working alongside biostatisticians to structure complex longitudinal datasets.

Karius aims to conquer infectious diseases through innovations around genomic sequencing and machine learning. The company's platform is already delivering unprecedented insights into the microbial landscape, providing clinicians with a comprehensive test capable of identifying more than a thousand pathogens directly from blood, and helping industry accelerate the development of therapeutic solutions. The products Karius offers today are some of the most advanced solutions available to physicians who aim to deliver better care to many otherwise ineffectively treated patients.

Our tests are the result of some incredible work done by our scientists, statisticians, engineers, and physicians, all driven by the same mission. You, as part of the Karius team, will be able to see how directly your work has a life-changing impact on people, and at scale.

Primary Responsibilities

• Own EHR data extraction specifications for the AXIS registry, including data element definitions, data dictionaries, field mappings, and site-specific translation logic across heterogeneous EHR environments.
• Serve as the primary technical liaison to site informatics and IT teams, translating clinical research data requirements into executable data queries and extraction protocols; primary experience with Epic Clarity and/or Caboodle required.
• Design and validate data extraction pipelines that ingest structured EHR data (diagnoses, medications, labs, procedures, utilization) from multiple health systems into a harmonized, analysis-ready format.
• Perform data quality assessment, anomaly detection, and cross-site consistency validation; implement processes to identify and resolve data integrity issues with sites.
• Partner closely with the biostatistics team to deliver clean, structured, well-documented datasets; support data preparation, variable derivation, and dataset specifications for statistical analysis plans.
• Collaborate with clinical operations on site onboarding for clinical site data integration, including support for data governance agreements, BAAs, and technical feasibility assessments.
• Build and maintain the registry data model, data lineage documentation, and codebook to ensure reproducibility and audit-readiness.
• Apply working knowledge of real-world data standards (OMOP CDM, HL7 FHIR, SNOMED, ICD-10, LOINC) to support data harmonization across sites with diverse EHR configurations.
• Support seamless integration between EHR data, the registry EDC, and Karius' standardized internal clinical database.
• Support broader clinical research data analytics across programs, including integrating datasets from multiple sources, building analysis-ready analytic files, and data visualization to support clinical development and biostatistics teams
• Contribute to the design of data collection strategies for future real-world evidence studies and registry expansions.

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