Director, Automation Engineering
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Overview
Job Description
Director, Automation Engineering
Location: San Diego, CA
Job Type: Full-Time
Salary Range: $230,000 - $245,000
Position Overview
We are seeking a Director of Automation to lead the design, development, and scaling of automated workflows for sample preparation. This role is critical to building a robust, scalable, and cost-efficient automation platform.
You will own the end-to-end automation strategy from system architecture through implementation and validation working at the intersection of engineering, assay development, and laboratory.
Key Responsibilities
Automation Strategy & Architecture
Define and lead the automation strategy for sample preparation workflows
Architect integrated systems leveraging liquid handling robotics and supporting instrumentation
Drive innovative system design to achieve:
Low cost per sample
High sample success rates
Operational robustness and uptime
Design systems that scale from early-stage development to high-throughput production
Workflow Development & Validation
Translate assay requirements into automated workflows
Lead the implementation, optimization, and validation of automated processes
Establish performance metrics, QC strategies, and validation protocols
Ensure workflows meet clinical, regulatory, and operational requirements as applicable
Systems Integration
Lead integration of automation platforms with LIMS and data systems
Ensure seamless sample tracking, data integrity, and process traceability
Collaborate with software and informatics teams to build scalable infrastructure
Team Leadership
Build and lead a high-performing team of automation engineers
Set technical direction, prioritize projects, and mentor team members
Foster a culture of innovation, accountability, and continuous improvement
Cross-Functional Collaboration
Partner closely with assay chemistry and R&D teams to co-develop automation-ready assays
Collaborate with operations and quality teams to ensure successful deployment
Serve as a key bridge between wet lab science and engineering
Qualifications
Required Experience
PhD (10+ years), MS/MA (14+ years), or BS/BA (17+ years) in Engineering, Science or Technology
10+ years of demonstrated experience in lab automation, robotics, or related fields
Deep expertise with liquid handling systems (e.g., Hamilton, Tecan, Beckman, etc.)
Proven track record of designing and deploying automated sample prep workflows
Experience integrating automation platforms with LIMS or similar systems
Demonstrated success in scaling laboratory processes to high throughput.
Leadership & Innovation
Experience leading and managing small, high-impact engineering teams
Strong history of cross-functional collaboration, especially with assay development teams
Demonstrated ability to innovate at the system architecture level, improving throughput, reliability, and cost efficiency
Technical Skills
Workflow design, scripting, and automation control systems
Process validation and performance optimization
Understanding of workflows and molecular biology techniques
Familiarity with data integration, APIs, and lab informatics systems
Nice to Have
Experience in clinical diagnostics or regulated environments (CLIA/CAP/FDA)
Background in scaling to high sample throughput
Experience with DOE (Design of Experiments) and process optimization
Exposure to manufacturing or production-scale lab environments
Why Join Us
Influence the foundational technologies and strategies of a company poised to shape the future of clinical genomics and healthcare.
Work in a dynamic, collaborative environment where innovation and scientific rigor are deeply valued.
Join a seasoned and multidisciplinary team tackling high-impact problems at the intersection of science and engineering.
Competitive compensation and equity package, comprehensive benefits, and flexibility to support work-life integration.
We are an equal opportunity employer. We thrive on diversity and collaboration.
Automate your job search with Sonara.
Submit 10x as many applications with less effort than one manual application.
