Advisor, Automation Engineering

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 131,000 - 211,000; Full time

Job summary

Eli Lilly and Company in Indianapolis is seeking a senior automation engineer to design, deploy, and support laboratory automation for in vitro pharmacology and chemistry workflows. You will work closely with scientific users to understand needs, ensure reliable operation, and drive adoption of automation across pipeline processes.

The role emphasizes hands-on bench proximity, system integration, and building robust automated workflows with a focus on reproducibility and scalability.

Qualifications

• Bachelor's degree in engineering, computer science, biological sciences, or related field with 5+ years of hands-on laboratory automation experience.
• Experience with Hamilton automation and lab workflow integration.
• Experience automating in vitro pharmacology and chemistry workflows.
• Experience collaborating with scientific users to gather requirements and support adoption.
• Proficiency in scripting or programming for automation.
• Experience with ELN/LIMS integration (Benchling).

Responsibilities

• Build, program, deploy, and maintain laboratory automation systems for in vitro pharmacology, chemistry, and related pipeline workflows.
• Develop and validate automated methods, translating scientific protocols into robust, reproducible automated processes.
• Partner directly with scientific users to gather requirements and deliver automation solutions that meet their needs.
• Deploy and support automation systems tailored to specific pipeline processes and throughput needs.
• Provide ongoing support for deployed systems, responding to user needs and keeping automation running reliably day to day.
• Develop clear documentation, quick-reference guides, and ongoing support resources for teams.
• Plan and deliver hands-on training to local end users on new instrumentation, automated methods, and protocols.
• Resolve hardware, software, and integration issues to keep systems running reliably.
• Strengthen data reproducibility across automated processes through sound standards, controls, and qualification practices.
• Integrate automation with scheduling and lab orchestration software and with ELN/LIMS platforms such as Benchling.
• Apply LLM-based coding tools and agentic assistants to accelerate method development, scripting, and systems integration.
• Contribute to generation of large-scale, structured datasets for AI/ML applications.
• Build effective working relationships across scientific and engineering teams to ensure automation solutions fit real-world use

Skills

Lab automation

Scripting/Programming

Scientist collaboration

LLM tooling

Education

Bachelor's degree in engineering/CS/biological sciences

Tools

Hamilton automation ecosystem

Echo acoustic dispenser

Tecan instruments

Benchling ELN/LIMS

Lab schedulers/orchestration

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 Indianapolis‑based senior automation engineer to join the Automation Engineering team within Lilly's RNA Therapeutics group. In this role, the successful candidate will do the core technical work of building, deploying, and supporting laboratory automation that advances pipeline‑facing science, with a particular focus on in vitro pharmacology and chemistry workflows. Equally important is the partnership side of the role: working closely with scientific users to understand their needs, supporting the systems they depend on, and enabling teams to get the most out of automation. This is a builder's role for someone who wants to be close to the bench and the instruments, and who takes satisfaction in seeing their systems genuinely adopted.

Key Responsibilities

• Build, program, deploy, and maintain laboratory automation systems supporting in vitro pharmacology, chemistry, and related pipeline workflows
• Develop and validate automated methods, translating scientific protocols into robust, reproducible automated processes
• Partner directly with scientific users to gather requirements, understand their workflows, weigh practical tradeoffs, and deliver automation solutions that meet their needs
• Deploy and support automation systems tailored to specific pipeline processes and throughput needs
• Provide ongoing support for deployed systems, responding to user needs and keeping automation running reliably day to day
• Develop clear documentation, quick‑reference guides, and ongoing support resources that help teams operate automated workflows independently
• Plan and deliver hands‑on training to local end users on new instrumentation, automated methods, and protocols, tailoring instruction to varying levels of automation experience and ensuring users can operate systems confidently and independently
• Resolve hardware, software, and integration issues to keep systems running reliably
• Strengthen data reproducibility across automated processes through sound standards, controls, and qualification practices
• Integrate automation with scheduling and lab orchestration software and with ELN/LIMS platforms such as Benchling
• Apply LLM‑based coding tools and agentic assistants to accelerate method development, scripting, and systems integration
• Contribute to the generation of large‑scale, structured datasets suitable for AI/ML applications
• Build effective working relationships across scientific and engineering teams to ensure automation solutions fit real‑world use

Basic Qualifications

• Bachelor's degree in engineering, computer science, biological sciences, or related field with 5+ years of hands‑on laboratory automation experience.

Additional Skills/Preferences

• Hands‑on expertise with the Hamilton automation ecosystem and a track record of building and deploying integrated automation across other platforms (e.g. acoustic dispensers (e.g., Echo), oligonucleotide synthesizers, robotic arms, Tecan instruments)
• Experience automating in vitro pharmacology and chemistry workflows.
• Strong method development and qualification skills, with a focus on reproducibility.
• Demonstrated ability to work directly with scientific users to gather requirements and support adoption.
• Experience with schedulers and end‑to‑end lab orchestration.
• Experience integrating automation with ELN/LIMS, such as Benchling.
• Experience with automated sample management systems.
• Proficiency in scripting or programming for automation.
• Experience using LLM‑based coding tools or agentic assistants to accelerate method development, scripting, or systems integration.
• Strong interpersonal skills, with a proven ability to build durable working relationships with scientific users.

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 $130,500-$211,200 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).

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly