Director - Automation Engineering

Eli Lilly and Company; Boston (MA); On-site; USD 180,000 - 240,000; Full time

Benefits offered by this job

Company bonus

401(k) plan

Vacation benefits

Well-being benefits

Job summary

Lilly seeks an accomplished automation leader to head the RNA Therapeutics automation engineering team. You will shepherd end-to-end automation strategy, guiding the design, build, and deployment of integrated systems used by chemistry, biology, genomics, and pharmacology groups.

You will mentor a team of automation experts, partner with scientists to translate workflows into scalable workflows, and explore emerging tools including LLMs to accelerate development and data quality at scale.

Qualifications

• Bachelor's degree in engineering, computer science, biological sciences, or related field.
• 10+ years of experience in laboratory automation, with prior leadership roles.
• Proven ability to design, build, validate, and deploy pipeline-facing automation systems.

Responsibilities

• Lead, mentor, and grow an automation team across RNA Therapeutics.
• Partner with scientists to understand workflows and validate automated processes.
• Develop and implement the RNA automation strategy aligned with scientific priorities.
• Design and deploy automation systems spanning walk-up instruments and end-to-end workflows.
• Lead cross-site delivery and standards across geographies.

Skills

Automation leadership

Team mentoring

RNA automation

LLM tooling

Cross-functional collaboration

Education

Bachelor's degree in engineering, CS, or biological sciences

Tools

Benchling

LLM-based coding

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.

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 to validate scientific workflows and weigh scientific tradeoffs and priorities.
• Deep familiarity of cell culture automation and genomics automation.
• Experience delivering pipeline-facing automation across chemistry, biology, genomics, in vivo sample preparation workflows.
• Experience designing & ... lots more
• 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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