Director, Automation Engineering

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.