Sr. Automation Engineer

Veracyte•San Francisco, CA

1d•Onsite

About The Position

The Position: Veracyte is seeking a highly motivated and experienced Senior Automation Engineer to join our growing Automation and Process Engineering team. This is a dynamic and impactful role where you will lead the development, optimization, and validation of automated liquid handling workflows—particularly using Hamilton platforms—for the implementation of molecular Laboratory Developed Tests (LDTs) in a regulated clinical laboratory environment. You will collaborate cross-functionally with R&D, Clinical Operations, Software, and IT teams to design and deploy innovative automation solutions that improve throughput, reproducibility, and efficiency. This is a unique opportunity to shape the future of molecular diagnostics through cutting-edge automation and process innovation. This is an onsite position based in our South San Francisco office. Responsibilities Design, program, and validate automated workflows for molecular assays using liquid handling platforms (eg. Hamilton) and other automated laboratory instruments Translate manual molecular protocols (e.g., RNA/DNA extraction, NGS library prep) into robust, high-throughput automated methods. Collaborate with Product Development, Clinical Operations, and Software teams to integrate automation with LIMS, bioinformatics pipelines, and data management systems. Lead portions or entire cross-functional projects from concept through implementation, ensuring timelines and deliverables are met. Collaborate with Equipment Engineering and Operations and QA on equipment qualification (IQ/OQ/PQ), calibration, and preventive maintenance procedures. Contribute to the development of custom 3D printed parts, software scripts, workcells, and novel automation technologies. Document workflows, SOPs, ERDs, and process maps in accordance with quality and regulatory standards. Provide technical mentorship and collaborate with internal stakeholders and external vendors. Who You Are: You’ve worked with both manual and automated molecular assays and feel right at home programming Hamilton systems. You might also have experience with microarray prep, NGS library prep, or RNA/DNA extraction from sample types like FFPE, blood, or cultured cells—that’s a big plus. You know how to build automation workflows that work in a high-throughput, CLIA-regulated lab—not just in theory. You’re good at spotting potential issues before they become problems, and you’re the kind of person who enjoys figuring out how to fix things when they don’t go as planned. You manage your time well, stay organized, and aren’t afraid to try new approaches or take calculated risks. You enjoy working with others, sharing ideas, and solving tough problems as a team. Most of all, you’re excited about using your skills to help push the boundaries of what’s possible in molecular diagnostics.

Requirements

Bachelor’s degree in Life Sciences, Engineering, or related field.
Minimum 5-7 years of industry experience in laboratory automation, with deep expertise in Hamilton Robotics platforms (preferred).
Strong background in molecular biology techniques such as PCR, RNA/DNA extraction, microarray, and NGS.
Proven experience designing, programming, and troubleshooting automated workflows in a clinical or regulated lab.
Familiarity with CLIA, CAP, GxP, and 21 CFR Part 11 compliance.
Excellent organizational, communication, and documentation skills.
Ability to work independently and collaboratively across multidisciplinary teams.
Proficiency in MS Office (Word, Excel, PowerPoint).

Nice To Haves

Experience with scripting languages (e.g., Python, C#) and database integration.
Familiarity with Agile/Scrum methodologies and tools like Jira and Confluence.
Experience with CAD design and 3D printing.
Proficiency with Microsoft Power Platform and modern AI tools.
Experience integrating automation with cloud-based data systems and bioinformatics pipelines.

Responsibilities

Design, program, and validate automated workflows for molecular assays using liquid handling platforms (eg. Hamilton) and other automated laboratory instruments
Translate manual molecular protocols (e.g., RNA/DNA extraction, NGS library prep) into robust, high-throughput automated methods.
Collaborate with Product Development, Clinical Operations, and Software teams to integrate automation with LIMS, bioinformatics pipelines, and data management systems.
Lead portions or entire cross-functional projects from concept through implementation, ensuring timelines and deliverables are met.
Collaborate with Equipment Engineering and Operations and QA on equipment qualification (IQ/OQ/PQ), calibration, and preventive maintenance procedures.
Contribute to the development of custom 3D printed parts, software scripts, workcells, and novel automation technologies.
Document workflows, SOPs, ERDs, and process maps in accordance with quality and regulatory standards.
Provide technical mentorship and collaborate with internal stakeholders and external vendors.

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