Dir/Sr. Dir - Lab Automation Engineer, Discovery Oncology

100 Eli Lilly and Company; New York (NY); On-site; USD 160,000 - 230,000; Full time

Benefits offered by this job

401(k)

Pension

Vacation benefits

Health benefits

Flexible benefits

Life insurance

Time off and leave

Job summary

Lilly is hiring a Dir/Sr. Dir - Lab Automation Engineer in New York. The role leads software/control architecture for automated lab systems in Discovery Oncology, partnering with scientists and engineers to advance platform scale, reliability, and data integration.

You will mentor engineers and drive end-to-end automation initiatives. The position requires a strong software engineering foundation, familiarity with lab data pipelines, and experience in vendor evaluation and system integration.

Qualifications

• Bachelor's or advanced degree in Engineering, Robotics, Computer Science, Biology or related field.
• 10+ years hands-on experience in laboratory automation, robotics integration, or related engineering discipline.
• Experience mentoring other engineers.

Responsibilities

• Set technical implementation and architecture for software/control layer across automated lab systems.
• Own future workcell design and platform maturation.
• Set technical standards and review designs; mentor engineers.
• Partner with AVP on requirements and vendor evaluation; own installation, validation, and performance.
• Lead root-cause investigations and drive reliability improvements.

Skills

Python

SQL

C#

Data pipelines

UI tools

Education

Bachelor's or advanced degree in Engineering/Robotics/CS/Biology

Tools

Cellario

Momentum

VWorks

Green Button Go

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.

Dir/Sr. Dir - Lab Automation Engineer, Discovery Oncology Summary

Responsibilities

• Set technical implementation and architecture for the software/control layer spanning liquid handling protocols and integrated hardware/software systems across the site
• Own future workcell design as the platform matures beyond its initial build-out, building on the architecture and standards established during early platform development
• Set technical standards and review designs across the automation team, provide hands‑on technical mentorship to other engineers without owning their formal management or career development
• Partner with the AVP on requirements gathering and vendor evaluation for the most complex automated systems; own installation, validation, and ongoing performance optimization
• Lead root‑cause investigations for the most complex hardware/software integration failures; drive corrective actions and systemic reliability improvements across the platform
• Serve as the primary technical bridge between software engineering, hardware/controls, data teams, and bench scientists to ensure automation and data systems integrate seamlessly
• Design and build user‑facing tools — UIs, dashboards, CLIs, or AI‑assisted interfaces — that let scientists configure, launch, monitor, and troubleshoot automated runs without needing to understand the underlying instrument control code
• Build and maintain data capture, upload, and validation pipelines that move experimental data cleanly from automated systems into downstream data processing pipelines and analysis tools
• Build monitoring, alerting, and self‑diagnostic tooling that surfaces instrument and workflow errors clearly, so scientists and engineers can resolve issues faster and with less escalation
• Write and maintain automation scripts, APIs, and configuration templates that standardize how new workflows get deployed onto existing hardware
• Advise on vendor relationships and evaluate new instrumentation, technologies, and partnerships to keep the automation platform state‑of‑the‑art

About you

• You enjoy working with both scientists and engineers, and can move fluidly between a wet‑lab workflow conversation and a systems architecture discussion
• You have a solid understanding of data processing pipelines and how automation systems fit into the broader flow of experimental data
• You’ve built tools — using standard programming or AI‑assisted harnesses — that make lab automation easier to use, whether that’s a UI layer, an instrument control abstraction, or automated data upload/ingestion
• You influence through technical credibility and clear communication, not formal authority
• You default to designing for the end user (the scientist at the bench) rather than just for the instrument or the codebase; you’re a strong software engineer at heart, with enough working knowledge of physical systems to design good interfaces to them

Basic Qualifications

• Bachelor's or advanced degree in Engineering, Robotics, Computer Science, Biology, or related field with 10+ years of hands‑on experience in laboratory automation, robotics integration, or a closely related engineering discipline, including experience providing technical mentorship to other engineers

Preferred Qualifications

• Working familiarity with liquid handling platforms (Tecan, Beckman Coulter/Labcyte, Agilent, Hamilton, etc) and automated imaging/detection systems
• Strong programming skills (Python, SQL, and/or C#) with demonstrated ability to build production‑quality software, not just scripts; experience with scheduling/control software (e.g. Cellario, Momentum, VWorks, Green Button Go, or custom ACS)
• Demonstrated experience designing and qualifying the software/control layer of new automated systems from concept through production
• Experience designing user‑facing tools (UIs, APIs, CLIs) for non‑software‑engineer end users
• Working knowledge of data processing pipelines and how lab systems integrate with downstream data infrastructure, including experience building or maintaining data pipelines that move data from instruments into analysis/storage infrastructure
• Experience building tooling (traditional or AI‑assisted) that lowers the barrier for scientists and engineers to use, configure, or troubleshoot automation
• Strong cross‑functional collaboration skills; able to communicate technical trade‑offs to non‑technical and senior audiences
• Experience partnering on vendor relationships or providing input on project resourcing and trade‑offs
• Experience applying LLMs/AI agents to instrument control, troubleshooting, or lab software workflows
• Experience with Cellario and Cellario integrations
• Some background in oncology, mammalian cell biology, or related scientific field
• Experience with driver design and implementation
• Experience with observability/monitoring tooling (dashboards, alerting, logging pipelines) applied to lab or industrial systems
• Understanding of PLCs, safety circuits, and power electronics

Additional Information

This is an onsite position (5 days) in New York, NY

Compensation

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).

Benefits

• 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
• 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.

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).

#WeAreLilly At Lilly we strive to be 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!