Automation Engineering Manager Jobs in California

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.
The Automation Service Engineering Manager will oversee the design, deployment, and maintenance of automation systems within our molecular diagnostics labs and production facilities, providing service support to the oncology laboratory operations team. This role will manage a team of service engineers, ensuring smooth operation and optimization of automated systems, as well as the troubleshooting, maintenance, and repair of laboratory equipment utilized in the Next Generation Sequencing workflow. The ideal candidate will have a strong technical background in automation systems, team management experience, and the ability to work cross-functionally to ensure the reliability and scalability of operations. This role will report to the Director of Process & Development, Oncology. This is considered an onsite role and will require the majority of days to be spent in the office at the Menlo Park site.
Responsibilities:

• Team Leadership & Scheduling: Lead, mentor, and manage a team of automation service engineers, fostering a culture of collaboration, innovation, and continuous improvement. Manage and develop careers for the automation service engineers and associates. Oversee a team that needs to cover different production shifts (including AM and PM shifts) to ensure continuous laboratory support.
• System Maintenance: Ensure all automated equipment and systems are running optimally by overseeing routine maintenance, troubleshooting, and repairs. Troubleshoot, conduct root cause analysis, and problem solve on lab instruments.
• Deployment & Integration: Oversee the design, installation, and integration of new automated systems, ensuring alignment with company needs and industry standards. Carry out Installation, Operational, and Process Qualifications on new equipment as necessary.
• Process Optimization: Work closely with the operations, R&D, and production teams to identify areas where automation can enhance efficiency, quality, and throughput. Collaborate with Quality Control to ensure all documentation is completed accurately and in accordance with regulatory requirements.
• Vendor Relations: Manage relationships with automation vendors, negotiate contracts, and ensure timely support and delivery of equipment and services. Effectively coordinate with vendors as required for equipment issues.
• Inventory & Budgeting: Oversee the budget for automation services, ensuring cost-effective solutions while maintaining high performance and reliability of systems. Maintain equipment parts inventory and well-organized equipment records.
• Compliance & Safety: Ensure all automated systems are compliant with relevant industry standards, safety protocols, and regulatory requirements. Implement and enforce safety procedures for the operation of automated equipment.
• Data Analysis & Reporting: Monitor and analyze key performance indicators (KPIs) of automated systems, providing regular reports to senior management and recommending improvements based on data insights.

Requirements:

• Bachelor's degree in Engineering, Automation, or a related field (Master's degree preferred), or a BS degree in a scientific discipline.
• Proven 2+ years experience as an Lab Automation Service Engineering Manager or in a similar leadership role within a manufacturing or diagnostics environment.
• 4+ years of experience in operating and troubleshooting laboratory equipment, preferably high-throughput molecular biology equipment, especially liquid handlers.
• Extensive knowledge of automation systems, including robotics, PLCs, sensors, and control systems, with hands-on experience with installation, maintenance, and troubleshooting of automated equipment.
• Strong customer focused service experience with proficiency in problem-solving with limited direction and making confident decisions.
• Strong leadership and team management skills, with a track record of successfully leading and developing high-performing teams.
• Familiarity with compliance and safety standards in a highly regulated environment (e.g., FDA, ISO), and experience working in a CLIA or similar regulated environment is preferred.
• Strong communication and interpersonal skills, with the ability to collaborate across departments and communicate technical concepts to non-technical stakeholders.

Nice-to-Haves:

• STRONGLY PREFERRED: Familiarity with Molecular Biology techniques, including next generation sequencing.
• Experience in troubleshooting complex scripts is an added advantage.
• Experience with data science / data engineering in an automated laboratory environment.

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)
• Free 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 a (1) base pay range (actual amount offered and leveling are based on experience and salary/equity options split that the candidate chooses), (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 up to $274,016 per year, including a base pay range of $158,401 - $203,651 per year.
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