Automation Engineer Associate II

Join a team of brilliant, passionate innovators determined to transform healthcare. At BillionToOne, we've built a category-defining, publicly traded company on Nasdaq where transparency fuels trust, collaboration drives breakthroughs, and every contribution moves the needle on our mission to make life-changing diagnostics accessible to all. We don't just aim for incremental improvements; we build products that are 10x better than anything that exists today.

Our scientists, engineers, sales executives, and visionaries are united by an unwavering commitment to changing the standard of care in prenatal and cancer diagnostics. This is where cutting-edge science meets human compassion, and every innovation you contribute helps remove the fear of the unknown from some of life's most critical medical moments.

If you're driven by purpose, energized by innovation, and ready to help shape the future of precision medicine at scale, this is where you belong.

We are looking for an Automation Engineer Associate II (level commensurate with experience and interview scores) to join our growing Process Engineering team responsible for innovative solutions to support the high-complexity and high-growth clinical laboratory. This is a dynamic, start-up environment that requires adaptability and the ability to quickly learn and apply new concepts. The Automation Engineer reports to the Automation Engineering Manager and is an onsite position. This role will help to build upon the strong technology and execution found within BTO’s walls, and will help us pave the way for replicating our prenatal success in the oncology space. This is considered an onsite role and will require the majority of days to be spent in the office at either the Menlo Park or Union City sites.

• →End-to-end development, design, integration, and validation of automation systems and protocols on liquid handling platforms (Hamilton, Lynx, Agilent Bravo etc.) in the clinical laboratory
• →Contribute to integration efforts between liquid handlers and LIMS, utilizing APIs/drivers to support bi-directional data transfer and sample tracking
• →Identify, develop, and implement process improvements to design and improve robust laboratory procedures
• →Collaborate with the clinical and R&D teams to transfer new products and procedures onto the automated platforms
• →Provide training and guidance to employees in the operation, maintenance, and troubleshooting of new equipment
• →Develop and prepare documentation for procedure changes, instrument validations, IQ/OQ/PQ, standard operating procedures, and related documents

• BS or higher in Engineering, Biology, Microbiology, Biophysics, Biochemistry, or related field
• 1 to 3 years of experience in assay automation on liquid handlers (i.e. Hamilton, Beckman, Agilent, Tecan, Dynamic Devices)
• Experience in a semi-automated laboratory environment
• Technical proficiency in laboratory automation and systems development
• Strong multi-tasking, project management, organizational, communication, and documentation skills
• Software development experience in one or more languages (Python preferred)
• Strong laboratory understanding with experience in next-generation sequencing library preparation

• Certification in one of the major liquid handling systems (Hamilton, Beckman, Agilent, Tecan)
• Experience working under regulatory environments such as CLIA, CAP, or FDA
• Experience with Clarity LIMS or other LIMS systems
• Experience with integrated systems

Unity Complete™ is the only non-invasive prenatal screen capable of assessing fetal risk for both common recessive conditions and aneuploidies from a single maternal blood sample.
Unity Confirm™ enables non-invasive confirmation for high-risk screening results through the capture of intact circulating fetal cells using BillionToOne’s Fetal Cell Capture™ Technology.
Our Northstar® liquid biopsy test uniquely combines treatment selection with real-time monitoring, giving oncologists unprecedented precision in cancer care.

From $0 to $400M+ annualized revenue run-rate in just 6 years. In 2025, we completed one of the most successful IPOs for a medical diagnostics company, building on nearly $400M in private funding,including our $130M Series D in 2024 and backed by world-class investors including Hummingbird, Adams Street Partners, Neuberger Berman, Baillie Gifford, and Premji Invest.

Forbes named us one of America's Best Startup Employers for 2025 and we're Great Place to Work certified, with 100% of our people willing to go the extra mile, even as we've scaled to over 700 employees.

Headquartered in Menlo Park with facilities in Union City, CA, and a new lab opening in Austin, TX in 2027, we're continuing to push the boundaries of what's possible in molecular diagnostics. We're just getting started.

Ready to help us change the world, one molecule at a time? Learn more at billiontoone.com