Automation Engineer Associate II

A Rare Opportunity to Shape the Future of Genomics

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.

Responsibilities:

• 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

Qualifications:

• 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

Nice-to-Haves:

• 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

Benefits And Perks:

• Working alongside brilliant, kind, passionate and dedicated colleagues, in an empowering environment, toward a global vision, striving for a future in which transformative molecular diagnostics can help millions of patients
• Open, transparent culture that includes weekly Town Hall meetings
• The ability to indirectly or directly change the lives of hundreds of thousands patients
• Multiple medical benefit options; employee premiums paid 100% of select plans, dependents covered up to 80%
• Extremely generous Family Bonding Leave for eligible employees (16 weeks, paid at 100%)
• Supplemental fertility benefits coverage 
• Retirement savings program including a 4% Company match
• Increase paid time off with increased tenure
• Latest and greatest hardware (laptop, lab equipment, facilities)
• Daily on-site lunches provided from top eateries
• A variety of perks on campus (state of the art gym, restaurant)
• Free on-site EV charging (compatible with all EVs, including Tesla)

At BillionToOne, we are proud to offer a combination of (1) competitive base pay, (2) generous equity options offering, (3) corporate bonus program, on top of (4) industry leading company benefits (free healthcare options, 401k match, very generous fully paid parental leave, etc.).

For this position, we offer a total compensation package of up to $105,737 per year, including a base pay range of $70,715 - $87,034 per year (based on the level and experience).

BillionToOne is an equal opportunity employer. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.

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BillionToOne is a next-generation molecular diagnostics company on a mission to make powerful, accurate diagnostic tests accessible to everyone. Our revolutionary QCT molecular counting technology enhances disease detection resolution by over a thousandfold using cell-free DNA,a breakthrough that has already transformed the lives of over half a million patients worldwide.

Our Impact

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.

Our Growth

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.

Our Recognition

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.

Our Future

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