We are seeking an experienced Automation Engineer to design and implement robust automation platforms that integrate scientific instrumentation, robotic automation, and laboratory data management across Lilly's RNA Therapeutics portfolio. This role reports to the Automation Lead for RNA Therapeutics and works within a multidisciplinary automation team responsible for delivering high throughput automated systems that increase the efficiency, reproducibility, and scalability of RNA therapeutic discovery workflows. The focus of this position is the design and implementation of automation platforms and integrated workcells rather than support of individual instruments, ensuring solutions are scalable, standardized, and deployable across multiple sites.
A key objective of this role is enabling Design Make Test Learn (DMTL) discovery cycles by implementing automation platforms that generate consistent, high quality experimental data with structured metadata capture. These platforms serve as experimental data generation infrastructure supporting downstream analytics and AI and machine learning model development. Automation platforms developed in this role will act as the experimental backbone of the RNA discovery DMTL cycle, enabling the generation of large, high quality datasets required to train and continuously improve AI and machine learning models.
Automation platforms developed in this role will support the generation of high-quality, standardized experimental datasets with consistent metadata capture, enabling reliable downstream analytics and machine learning model training.
The role requires deep expertise in liquid handling automation and experience implementing complex scientific workflows including next generation sequencing (NGS) library preparation and high throughput RNA processing. These automated workflows form a critical part of the infrastructure required to generate clean, reproducible, and unbiased datasets used to train machine learning models.
The successful candidate will partner closely with scientific, AI and ML, informatics, and data engineering teams to translate biological workflows into reliable automated platforms that produce traceable, structured experimental datasets. The ability to work in a collaborative, fast moving environment and adapt to evolving scientific needs is critical.
Responsibilities- Partner with internal partners to understand scientific workflows and develop automation solutions that improve throughput, reproducibility, data quality, and the generation of structured experimental datasets.
- Design automation workflows that minimize experimental variability and bias while ensuring consistent metadata capture and traceability, enabling datasets suitable for downstream analytics and AI/ML model development.
- Design, implement, and support laboratory automation platforms including liquid handlers, robotics, and integrated workcells from requirements gathering through deployment and scale up.
- Lead implementation of complex automation platforms including RNA processing systems and next generation sequencing (NGS) library preparation workcells.
- Develop robust liquid handling methods on Hamilton STAR liquid handling platforms including liquid class optimization, assay miniaturization, and workflow standardization.
- Implement integrated automation workcells involving liquid handlers, plate handling robotics, and analytical instrumentation.
- Contribute to the automation strategy and evolve solutions with business needs.
- Find opportunities to improve reliability, efficiency, and scalability of existing automation platforms.
- Implement complex integrated projects while proactively identifying risks and mitigation strategies and communicating progress to partners.
- Work with Lab Operations and IT teams to plan space requirements, installation of automation hardware, and automation supply management.
- Translate biological workflows into automation requirements including data capture, metadata tracking, experiment lineage and integration with digital systems.
- Provide end user training and support for automation systems and digital laboratory platforms including ELN and LIMS systems such as Benchling to ensure consistent workflow execution and high quality experimental data capture.
- Collaborate with interdisciplinary teams including scientists, hardware engineers, software engineers, informatics teams, data engineers, and data scientists.
- Contribute to vendor selection and evaluation for automation hardware, software, and technology solutions.
Basic RequirementsBS in engineering or related field with 15+ years of pharma or biotech laboratory automation experience OR MS in engineering or related field with 10+ years of pharma or biotech laboratory automation experience, including demonstrated leadership in implementing complex automation platforms and delivering large scale automation systems.
Additional Skills/Preferences- Extensive experience designing and implementing laboratory automation solutions in an industry environment, including leading complex platform deployments and supporting production scale automation systems.
- Deep hands-on experience designing, developing, and optimizing methods on Hamilton STAR liquid handling platforms, including authoring STAR methods, developing and tuning liquid classes, solving complex liquid handling behavior issues, and standardizing workflows across multiple systems or sites.
- Experience implementing complex liquid handling methods including bead based workflows, assay miniaturization, and high precision pipetting.
- Experience automating next generation sequencing (NGS) library preparation workflows including bead cleanup, normalization, and indexing PCR.
- Experience implementing integrated automation workcells involving liquid handlers, robotics, and supporting analytical instrumentation.
- Experience integrating automation systems with scheduling software such as Biosero Green Button Go.
- Strong understanding of molecular biology workflows including RNA extraction, nucleic acid quantification, and sequencing workflows.
- Experience integrating automation workflows with digital laboratory systems such as Benchling or similar ELN/LIMS platforms.
- Experience developing automation requirements and documenting business processes.
- Experience writing technical documentation including SOPs and automation specifications.
- Fluency with Python or similar scripting languages.
- Strong communication skills for technical and non technical audiences.
- Demonstrated ability to manage multiple complex projects simultaneously in a collaborative environment.
Additional Information- This role may require up to 15 percent travel for training, conferences, or vendor visits.
- The position is located in Boston, Massachusetts at the Lilly Genetic Medicine site in the Seaport district.
- The role provides opportunities to mentor junior engineers and contribute to the evolution of the RNA automation platform across multiple sites.
Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$141,000 - $228,800
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.
#WeAreLilly
