Senior Automation Engineer II

BillionToOne•Union City, CA

9d•Onsite

About The Position

Ready to redefine what's possible in molecular diagnostics? Join a team of brilliant, passionate innovators who wake up every day determined to transform healthcare. At BillionToOne, we've built something extraordinary—a culture where transparency fuels trust, collaboration drives breakthroughs, and every voice matters in our mission to make life-changing diagnostics accessible to all. We don't just aim for incremental improvements; we strive to build products that are 10x better than anything that exists today. Our people are our greatest asset: talented scientists, engineers, sales professionals, and visionaries 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—every innovation you contribute helps remove fear of unknown from some of life's most critical medical moments. If you're driven by purpose, energized by innovation, and ready to help build the future of precision medicine, this is where you belong. We are looking for a Senior Automation Engineer II to join our growing Process Engineering team responsible for innovative solutions to support the high-complexity and high-growth clinical laboratory. This is a high-growth role & will lead and manage projects to design and implement automation systems, as we continue to scale our laboratory by 10x over the next 12 months. This is a dynamic, start-up environment that requires adaptability and the ability to quickly learn and apply new concepts. The Senior Automation Engineer II role is a full-time onsite position and reports to the Associate Director, Service & Automation Engineering.

Requirements

BS or MS in Engineering (Biomedical, Mechanical, Systems), Biology, or a related field.
7+ years of hands-on experience in laboratory automation, with at least 2 years in a technical leadership or project management capacity.
Deep expertise scripting on at least two major platforms (e.g., Hamilton Venus, Beckman Biomek, Agilent VWorks, or Tecan Evoware).
Proven experience integrating third-party devices (readers, peelers, sealers) and interfacing with LIMS/LIS systems.
Proficiency in at least one software language used for data parsing or system integration (Python, C#).
Demonstrated ability to manage multiple concurrent projects using PM tools (e.g., Jira, Smartsheet) without direct supervision.
Strong understanding of molecular biology workflows, specifically NGS library preparation (fragmentation, adapter ligation, enrichment).

Nice To Haves

Training certificates from major vendors (e.g., Hamilton Venus, Beckman Biomek).
Experience with SQL database querying or cloud infrastructure (AWS/Azure) as it relates to lab data.
Project Management Professional (PMP) or Agile/Scrum certification.
Previous experience bringing automated assays live in a regulated clinical diagnostic environment (CLIA, CAP, ISO 13485).
Previous success in a high-growth, fast-paced start-up environment where wearing multiple hats was required.

Responsibilities

Lead Automation Programs: Drive the roadmap for laboratory automation projects from concept to deployment, managing timelines, scope, resource allocation, and risk assessments.
Cross-Functional Collaboration: Act as the primary liaison between Clinical Ops, R&D, and Informatics/LIMS teams to translate biological requirements into technical specifications.
Process Optimization: Analyze existing workflows to identify bottlenecks; design and implement robust process improvements to increase throughput and reduce error rates.
Platform Engineering: Design, script, and validate complex protocols on major liquid handling platforms (Hamilton STAR, Beckman Biomek i-Series, Agilent Bravo).
LIMS & Data Integration: Lead integration efforts between liquid handlers and LIMS; utilize APIs/drivers to ensure seamless bi-directional data transfer and sample tracking.
Validation & Compliance: Author and execute comprehensive validation packages (IQ/OQ/PQ), Standard Operating Procedures (SOPs), and user guides in compliance with CLIA/CAP/FDA regulations.
Troubleshooting & Support: Serve as the final escalation point for complex hardware/software failures; provide advanced training and technical mentorship to junior engineers and lab operators.

Benefits

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 new parents (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 a (1) base pay range (actual amount offered is based experience and salary/equity options split that the candidate chooses) (2) generous equity options offering, on top of (3) industry leading company benefits (free healthcare options, 401k match, very generous fully paid parental leave etc.).
For this position, the base pay range is: $163,681-$184,801 per year