Director - Automation Engineering

Lilly • Boston, MA

12d

About The Position

Lilly is seeking an accomplished automation leader to head the Automation Engineering team within its RNA Therapeutics group. The role leads a team of automation experts and oversees the RNA automation strategy from vision through design, build, and deployment. The team develops walk-up and fully integrated automation systems and supports pipeline-facing processes in chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology across multiple sites.

The Director will work closely with scientists to understand experimental workflows, weigh scientific tradeoffs and priorities, and ensure automated processes meet scientific intent. The role builds trusted partnerships and encourages adoption by delivering reliable, user-centered systems. It also advances harmonized automation platforms that strengthen reproducibility and generate large-scale datasets for AI/ML modeling and pre-clinical drug development. The leader will advance the use of LLM-based tools and agentic systems, coordinate standards and delivery across sites, and lead lab orchestration and integrations with core scientific software such as Benchling.

Requirements

• Bachelor's degree in engineering, computer science, biological sciences, or a related engineering field.
• 10 or more years of relevant experience in laboratory automation, including experience leading teams.

Nice To Haves

• Demonstrated experience leading and developing automation engineering teams.
• Exceptional interpersonal skills and a proven ability to build trust and drive adoption among scientific users, including those with limited automation experience.
• Experience working directly with scientists to validate scientific workflows and weigh scientific tradeoffs and priorities.
• Deep familiarity with cell culture automation and genomics automation.
• Experience delivering pipeline-facing automation across chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology.
• Experience designing, building, and validating custom automation work cells.
• Hands-on expertise with the Hamilton automation ecosystem and familiarity with vendors such as Beckman, Dynamic Devices, and Agilent.
• Experience with schedulers and end-to-end lab orchestration.
• Experience integrating automation with ELN/LIMS, such as Benchling.
• Experience supporting in vivo sample preparation workflows.
• Experience using LLM-based coding tools or agentic assistants to accelerate method development, scripting, or systems integration.
• Experience designing automation platforms that generate large-scale, structured datasets suitable for AI/ML applications.
• Experience with automated sample management systems.
• Advanced degree in a relevant engineering or scientific field.
• Ability to travel up to 20% across sites.

Responsibilities

• Lead, mentor, and grow a team of automation experts, setting technical direction and developing talent.
• Partner with scientific users across RNA Therapeutics, building trust and driving adoption of automation solutions.
• Work directly with scientists to understand workflows, weigh scientific tradeoffs and priorities, and validate that automated processes meet scientific intent.
• Develop and implement the RNA automation strategy, aligning platform investments with scientific priorities.
• Design and deliver automation systems spanning walk-up instruments and fully integrated end-to-end workflows.
• Lead deployment of custom work cells tailored to pipeline processes and throughput needs.
• Deliver pipeline-facing automation across chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology.
• Strengthen reproducibility by establishing standards, controls, and validation practices for automated processes.
• Adopt and scale LLM-based tools to accelerate automation enablement and programming, reduce time from concept to deployed method, and lower barriers to onboarding instruments and workflows.
• Partner with AI/ML colleagues to implement agentic tools and workflows across automation platforms.
• Build integrated automation platforms that generate large-scale datasets designed for AI/ML modeling.
• Coordinate automation delivery and standards across multiple sites.
• Advance cell culture automation, genomics automation, agentic laboratory systems, and tissue sample preparation workflows.
• Lead lab orchestration efforts and integrations with core scientific software, including Benchling.
• Represent the team's work to internal and external partners and contribute to a culture of reliable, user-centered automation.

Benefits

• Company bonus, depending in part on company and individual performance.
• Company-sponsored 401(k).
• Pension.
• Vacation benefits.
• Medical, dental, vision, and prescription drug benefits.
• Flexible benefits, including healthcare and/or dependent day care flexible spending accounts.
• Life insurance and death benefits.
• Certain time off and leave of absence benefits.
• Well-being benefits, including an employee assistance program, fitness benefits, and employee clubs and activities.

What This Job Offers

• Job Type: Full-time
• Career Level: Director