Clinical Data Scientist

Exagen Inc.; Carlsbad (CA); On-site; USD 130,000 - 160,000; Full time

Job summary

Exagen in Carlsbad, CA seeks a Clinical Data Scientist (CDS) to translate clinical, serologic, and laboratory data into analysis-ready datasets and ML applications accelerating validation studies and product development.

The CDS will own dataset curation across the registry, biobank, and study data, applying ML/AI approaches with the data science team, and provide clinical data management support for sponsor studies under mentorship.

Qualifications

• BS degree in a quantitative field with at least 5 years of clinical data experience.
• Proficiency in Python and SQL for data manipulation and reproducible workflows.
• Experience applying ML to high-dimensional clinical data.
• Familiarity with AI tools and LLM-assisted workflows.
• Interest in GCP/ICH EDC and clinical data management practices.

Responsibilities

• Design and maintain analysis-ready clinical datasets from multiple sources.
• Develop reproducible Python/SQL data pipelines with documentation.
• Apply ML methods to serologic and clinical data for assay interpretation.
• Develop AI-assisted workflows with human review and policy compliance.
• Collaborate with biostatistics to deliver clean datasets for analyses.
• Prepare data quality reports, study metrics, and dashboards.

Skills

Python

SQL

Machine Learning

AI tooling

Data visualization

Communication skills

Education

Bachelor's degree in bioinformatics or related field

Tools

EDC platform

LIS

SQL database

CDISC

Cloud computing

Job description

Overview

About our Company:

Exagen is a patient-focused and discovery-driven life sciences company dedicated to transforming the care continuum for patients suffering from debilitating and chronic autoimmune diseases. Our goal is to enable rheumatologists to improve care for patients through the differential diagnosis, prognosis, and monitoring of complex autoimmune and autoimmune-related diseases, including lupus and rheumatoid arthritis. By leveraging our proprietary Cell-Bound Complement Activation Products, or CB-CAPs, technology, we help get to the real cause of a patient’s symptoms and guide their journey to improved health.

About the Opportunity:

The Clinical Data Scientist (CDS) turns Exagen’s clinical, serologic, and laboratory data into analysis-ready datasets, reproducible pipelines, and machine learning applications that accelerate our validation studies, publications, and product development. The CDS owns dataset curation and clinical database development across the Company’s registry, biobank, and study data; applies machine learning and AI approaches—including large language model (LLM)-assisted workflows—in partnership with the data science team; and delivers analysis-ready data to biostatistics. In a supporting capacity, the CDS provides clinical data management for studies sponsored by Exagen and studies where Exagen serves as a central laboratory, with mentorship from the Clinical Affairs team and the opportunity to grow into broader clinical study operations.

Responsibilities

Primary Responsibilities:

Note: Other duties may be assigned.

• Design, build, and maintain analysis-ready clinical datasets from the Company’s SQL databases, EDC platform, laboratory information system (LIS), registry, and biobank sources in support of validation studies, publications, and regulatory deliverables.
• Develop and maintain reproducible data preparation and quality-control pipelines in Python and SQL, with appropriate documentation and version control.
• Apply machine learning approaches to multi-analyte serologic and clinical data to support assay interpretation and algorithm development, in partnership with the data science team.
• Develop and evaluate AI-assisted workflows (e.g., LLM-assisted literature surveillance, structured data extraction, and medical affairs content support) with appropriate human review and in compliance with Company policies.
• Partner with biostatistics to deliver clean, well-documented, analysis-ready datasets supporting statistical analyses of clinical and validation studies, including curation and harmonization of registry, biobank, and real-world data across the Company’s autoimmune disease areas.
• Prepare data quality reports, study metrics, and internal dashboards, and ensure data handling practices comply with applicable GCP/ICH guidelines, HIPAA, CLIA requirements, study protocols, and SOPs.

Supporting Responsibilities:

Note: These activities are shared with, and mentored by, the Clinical Affairs team; candidates are not expected to arrive with deep expertise in every area.

• Provide clinical data management for studies sponsored by the Company and studies where Exagen serves as a central laboratory, including data management plans, data reconciliations, release of data clarification forms, query resolution, dataset locks, manual release of test reports, and preparation of reports for invoicing, in coordination with study sponsors and/or CROs.
• Assist in the design of CRFs and the management of study builds, edit checks, and data exports within the EDC platform used by the Company.
• Support day-to-day operations of Company-sponsored studies in compliance with GCP/ICH guidelines, study protocols, SOPs, and other regulatory requirements, including maintenance of the Trial Master File (TMF) system.
• Support communications with investigative sites and maintain logs of study activities, including patient enrollment, completion of case report forms, and documentation of clinical research study samples received in the lab.
• Work with the data engineering team to ensure that data collected via the EDC and other instruments is captured, versioned, and quality-controlled in the Company’s SQL database.
• Assist in training research coordinators and investigators on study activities and on the EDC platform used by the Company.
• Contribute to team efforts in drafting and editing of scientific manuscripts and conference posters, including generation of figures, tables, and supporting analyses.
• Assist in writing and editing SOPs related to clinical data management and bioinformatics workflows.
• Comply with all company SOPs and safety standards.
• Perform other related duties as needed and required by supervisors.
• Maintain confidentiality of customer and patient information.

Qualifications

Minimum Qualifications:

• B.S. degree in bioinformatics, data science, biostatistics, computer science, or a related quantitative field and a minimum of 5 years of experience preparing, managing, and analyzing clinical or biological datasets in an academic or corporate setting; an advanced degree may substitute for up to 2 years of experience.
• Proficiency in Python and SQL for data manipulation, quality control, and analysis, including reproducible workflows and version control.
• Demonstrated experience applying machine learning methods to biological, clinical, or other high-dimensional datasets.
• Working familiarity with modern AI tooling, including practical experience with large language models.
• Interest in clinical research operations and willingness to develop working knowledge of ICH/GCP, EDC platforms, and clinical data management practices with mentorship.
• Must have excellent attention to detail and organizational skills.
• Must have good written and verbal communication skills.

Preferred Qualifications:

• M.S. or Ph.D. in a quantitative or life-science discipline.
• Experience supporting clinical trials, including EDC platforms, clinical data management practices, and working knowledge of ICH and GCP.
• Experience in a CLIA-certified laboratory, diagnostics, or other regulated clinical environment.
• Experience with immunology, autoimmune serologies, or rheumatology-related clinical data.
• Familiarity with CDISC data standards, R, and cloud computing environments.
• Clinical research or clinical data management certification (e.g., SCDM CCDM) preferred but not required.

Pay Range: $130,000 - $160,000 / Annually