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

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
We're looking for a Director (Principal) Lab Automation Engineer to lead the design, architecture, and software/usability layer of the automated systems that power our NY lab's discovery pipeline. As the senior-most individual contributor on automation, you'll work with the AVP to set technical direction and architecture, partner closely with scientists, software engineers, and platform leaders to translate scientific workflows into reliable, scalable automation — and you'll also get hands-on building the software, tools, and interfaces that make that automation genuinely easy for scientists to use day to day. This is a role for someone who's as comfortable in a scientist's workflow discussion as they are in a systems design review or writing the code themselves — someone who wants to help set the technical direction for automation and build the tools that make it usable.
This position reports to the AVP-Automation, Discovery Oncology and will be onsite in NYC.
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
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
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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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