Senior Automation Engineer (Lab Automation Platforms)

Job Description

We are seeking a senior, hands-on Senior Automation Engineer to help define, evolve, and execute the technical vision for laboratory automation platforms. This role combines platform ownership and architectural leadership with deep, practical involvement in instrument integration, troubleshooting, and live lab operations.

The ideal candidate has shaped automation platforms or workcell architectures that scale across instruments, workflows, and teams, while remaining close to the lab and accountable for reliability in production. You translate long-term vision into pragmatic systems that scientists and operators trust. This is an onsite position in San Diego.

Primary Stack: .NET (C#), JavaScript, Relational Databases

Key Responsibilities:

Automation Platform Vision & Ownership

• Help shape the technical vision, architecture, and standards for laboratory automation software and workcell integration.
• Translate automation goals (scalability, reliability, flexibility) into concrete platform patterns and implementations.
• Act as a technical steward, balancing near-term operational needs with long-term platform health.

Hands-On Integration & Operational Support

• Design, implement, and support instrument drivers, control layers, and orchestration logic across diverse lab equipment.
• Troubleshoot complex failures spanning software, robotics, instruments, networking, and data flows.
• Support commissioning, validation, and rollout of new automation capabilities.
• Serve as an escalation point for complex or systemic automation issues.

Reliability, Usability & Operator Experience

• Architect robust communication, error handling, recovery, and observability patterns.
• Design systems that fail safely and recover predictably under real lab conditions.
• Guide operator-facing software to provide clear system state, actionable errors, and intuitive recovery workflows.
• Use operator and scientist feedback to drive continuous improvement.

Data & Informatics Integration

• Shape data models and workflows supporting traceability, QC, and analytics across automated runs.
• Influence relational database design and performance for workflows.
• Collaborate with informatics teams to align automation data with enterprise systems.

Technical Leadership

• Provide technical leadership during live operations and incident response.
• Mentor engineers and automation specialists.
• Influence roadmaps, priorities, and investments in reliability and platform health.

What Success Looks Like

• Automation systems are more reliable, scalable, and understandable.
• Operators trust the platform and can recover confidently from failures.
• Today's technical decisions clearly support the automation ecosystem 2-5 years out.

Education and Experience:

• PhD in software, computer sciences or related field and 2-5 years experience in life sciences, engineering or academia, or
• Master's Degree in software, computer sciences or related field and 5 years experience in life sciences, engineering or academia, or
• Bachelor's Degree in software, computer sciences or related field and 8 years experience in life sciences, engineering or academia
• Significant experience with:
  • C# / .NET
  • JavaScript / TypeScript
  • Relational databases (advanced SQL, schema design)

• Proven experience defining and delivering technical vision for complex automation or platform systems.
• Deep, hands-on experience with laboratory or industrial automation.
• Strong troubleshooting skills across software and physical systems.
• Experience in drug discovery or high-throughput laboratory environments.

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Pay Range:
$124,000 - $186,000

Disclosure Statement:

The range provided is based on what we believe is a reasonable estimate for the base salary pay range for this job at the time of posting. This role is eligible for an annual bonus and annual equity awards. Some roles may also be eligible for overtime pay, in accordance with federal and state requirements. Actual base salary pay will be based on a number of factors, including skills, competencies, experience, and other job-related factors permitted by law.

At Vertex, our Total Rewards offerings also include inclusive market-leading benefits to meet our employees wherever they are in their career, financial, family and wellbeing journey while providing flexibility and resources to support their growth and aspirations. From medical, dental and vision benefits to generous paid time off (including a week-long company shutdown in the Summer and the Winter), educational assistance programs including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more.

Flex Designation:
On-Site Designated

Flex Eligibility Status:

In this On-Site designated role, you will work five days per week on-site with ad hoc flexibility.


Note: The Flex status for this position is subject to Vertex's Policy on Flex @ Vertex Program and may be changed at any time.

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Company Information

Vertex is a global biotechnology company that invests in scientific innovation.


Vertex is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E-Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law.


Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at View email address on click.appcast.io