Director - Automation Engineering

BioSpace; Boston (MA); On-site; USD 180,000 - 240,000; Full time

Job summary

Lilly seeks an accomplished automation leader to head the Automation Engineering team in the RNA Therapeutics group. You will guide a team of automation experts, shaping end-to-end workflows and partnering with scientists to ensure automated processes meet experimental intent.

The ideal candidate combines deep automation expertise with strong people leadership, and leverages AI/LLM tooling to accelerate development across multiple sites while maintaining data quality and reproducibility.

Qualifications

• Demonstrated leadership of automation engineering teams.
• Experience applying automation to RNA/biotech workflows.
• Deep familiarity with cell culture and genomics automation.
• Experience delivering pipeline-facing automation across chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology.

Responsibilities

• Lead, mentor, and grow a team of automation experts.
• Partner with scientific users to drive adoption of automation solutions.
• Understand workflows and validate automated processes meet scientific intent.
• Develop and implement the RNA automation strategy and platform investments.
• Design and deploy automation systems for walk-up instruments and end-to-end workflows.
• Lead deployment of custom work cells tailored to pipeline processes.
• Strengthen data reproducibility and establish standards and validation practices.
• Adopt LLM-based tools to accelerate method development and integration.
• Collaborate with AI/ML teams to implement agentic workflows.
• Build integrated automation platforms for large-scale data generation.
• Coordinate multi-site delivery and standards across geographies.

Skills

Team leadership

User collaboration

Scientific workflow validation

Strategic thinking

Education

Bachelor's degree in engineering, computer science, biological sciences, or related field

PhD degree in engineering, computer science, biological sciences, or related field

Tools

Hamilton automation ecosystem

Beckman

Dynamic Devices

Agilent

Benchling

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work— but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

We are seeking an accomplished automation leader to head the Automation Engineering team within Lilly's RNA Therapeutics group. In this role, the successful candidate will lead a team of highly qualified automation experts and shepherd the RNA automation strategy end to end, from vision through design, build, and deployment. The team designs and delivers both walk-up and fully integrated automation systems, and supports pipeline-facing processes across chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology for users across RNA Therapeutics at multiple sites. This is an opportunity to build highly integrated automation platforms that strengthen data reproducibility and enable the creation of massively scaled datasets to feed AI/ML modeling and pre-clinical drug development efforts across the organization.

The ideal candidate is a seasoned automation engineer and people leader who pairs deep technical command with genuine emotional intelligence. Above all, they are an expert who scientists want to work with: they build trust quickly, drive adoption by meeting users where they are, and navigate complex partner relationships with ease. They work directly with scientists to understand experimental workflows, weigh scientific tradeoffs and priorities, and validate that automated processes faithfully serve scientific intent. They bring a strong technical foundation across the modern automation stack, a track record of delivering reliable, pipeline-facing systems that scientific teams depend on, and a forward-looking view on how emerging tools, including LLM-based coding and agentic assistants, can accelerate automation development. They will build upon a strong foundation of excellence in automation, and deliver a harmonized strategy that enables the reproducible generation of high-quality data at scale.

Key Responsibilities

• Lead, mentor, and grow a team of automation experts, setting technical direction and developing talent across the group
• Partner with scientific users across RNA Therapeutics, building trust and driving adoption by delivering automation solutions that teams genuinely want to work with
• Work directly with scientists to understand their 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 the scientific priorities of RNA Therapeutics
• Design and deliver automation systems spanning walk-up instruments and fully integrated end-to-end workflows
• Lead the deployment of custom work cells tailored to specific pipeline processes (e.g. NGS enablement) and throughput needs
• Deliver pipeline-facing automation across chemistry, biology, genomics, in vivo pharmacology, and in vitro pharmacology
• Strengthen data reproducibility across automated processes, establishing the standards, controls, and validation practices that make results consistent and reliable
• Adopt and scale LLM-based tools to accelerate automation enablement and programming, reducing the time from concept to deployed method and lowering the barrier to onboarding new instruments and workflows
• Partner with AI/ML colleagues to facilitate the implementation of agentic tools and workflows across automation platforms
• Build highly integrated automation platforms that enable the generation of massively scaled datasets purpose-designed for AI/ML modeling efforts
• Lead an automation team that spans multiple sites, coordinating delivery and standards across geographies
• Advance capabilities across 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

Basic Qualifications

• Bachelor's degree in engineering, computer science, biological sciences, or related engineering field, with 10+ years of relevant experience in laboratory automation, including experience leading teams OR
• PhD degree in engineering, computer science, biological sciences, or related engineering field with 5+ years experience in laboratory automation, including experience leading teams

Additional Skills/Preferences

• Demonstrated experience leading and developing automation engineering teams.
• Exceptional interpersonal skills, with a proven ability to build trust and drive adoption among scientific users, including those with limited prior 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 other major automation 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 is a plus.
• Ability to travel up to 20% across sites.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.

The anticipated wage for this position is

$ - $

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

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