Automation Engineer

The Bowdoin Group; San Francisco (CA); On-site; USD 125,000 - 185,000; Full time

Job summary

The Bowdoin Group is representing a women's health diagnostics company hiring an Automation Development Engineer in San Francisco, CA. You will join an engineer building Hamilton-based automation from the ground up, focusing on development and future transfer to CLIA lab.

You will work closely with R&D to expand automated workflows, set validation, and contribute to scalable SOPs and playbooks as the program grows toward commercial launch.

Qualifications

• 5+ years of experience developing and deploying laboratory automation for molecular workflows.
• Hands-on Hamilton programming fluency (VENUS) and a degree in Engineering, Life Sciences, or related discipline.
• Experience transferring workflows into regulated environments such as CLIA, CAP, or NYSDOH.
• Strong cross-functional instincts and startup fluency; collaboration across scientist, engineer, and operations.
• Interest in AI-enabled tools, computer vision, or machine learning applied to lab automation.

Responsibilities

• Design, build, and continuously improve Hamilton-based workflows for RNA-based assays.
• Collaborate with R&D to optimize automation and transfer workflows into the CLIA lab with validation and change control.
• Grow the automation playbook, SOPs, training materials, and institutional knowledge.
• Work with Lab Ops as workflows move from development into daily clinical use.
• Grow with the program as automation complexity expands toward commercial launch.

Skills

Hamilton VENUS

Laboratory automation

RNA-based assays

Data analytics

Cross-functional collaboration

Education

Engineering, Life Sciences, or related discipline

Tools

VENUS programming

Job description

Our client, a women's health Dx company, is hiring an Automation Development Engineer. In this role, you'll join an existing Automation Development Engineer who has been building out our Hamilton-based infrastructure from the ground up. This isn't a "maintain the existing protocol" role. Our client is pre-launch, standing up the CLIA laboratory that will run their first test commercially, and there's meaningful new development work ahead with the opportunity to build automation in from the start. You'll help expand and mature the platforms, automation strategies, and the best practices the organization will rely on for years. The successful candidate will join at a pivotal point as the company prepares its first assay for CLIA deployment and commercial launch. You'll be close to the science, close to the clinical stakes, and close to the team making it happen.

What You’ll Be Building

• Design, build, and continuously improve Hamilton-based liquid handling workflows supporting our RNA-based molecular diagnostic assay, including nucleic acid extraction, library preparation, normalization, and sequencing setup. Partner with R&D scientists to optimize and extend current automated workflows while helping ensure future programs are developed with automation in mind from the outset. Support the transfer of automated workflows into our CLIA laboratory, with all the documentation, validation, and change control rigor that entails. You'll work across the R&D/CLIA boundary and need to be fluent in what it means to move from development into a regulated environment.
• Dig into failures together. When a workflow misbehaves, you and your teammate figure out why, whether it's a reagent interaction, a tip geometry mismatch, a timing issue, or a bug in the method. The team doesn't move on until it's understood. Evaluate and introduce emerging automation technologies, including advanced analytics, computer vision, and AI-enabled process control, where they can meaningfully improve throughput, reproducibility, or reliability. We're not chasing trends; we want tools that actually move the needle.
• Help build and expand the automation playbook, including SOPs, best practices, training materials, and institutional knowledge that make the program scalable beyond any one individual. The company is growing fast and the infrastructure you document today will help onboard the automation engineers who join after you. Contribute to measurable improvements in workflow performance, including throughput, reproducibility, failure rate, and hands-on time. Set baselines, track metrics, and demonstrate impact. In a regulated lab, "it seems better" isn't good enough.
• Work shoulder-to-shoulder with Lab Ops as workflows move from development into daily clinical use. The team cares about what happens after transfer, not just at it. Bring a fresh perspective. The best engineers in roles like this see around corners. They identify the bottleneck before it becomes the crisis and the integration risk before it becomes the delay. We want that instinct.
• Grow with the program. As the organization scales toward commercial launch and new development work comes online, automation complexity grows with it. We expect this role to evolve, and we're looking for someone who wants to grow into that expanded scope.

The Person

• You bring 5+ years of experience developing and deploying laboratory automation for molecular workflows, including RNA-based assays, nucleic acid extraction, NGS library preparation, or equivalent applications. Hands-on Hamilton programming fluency is required (VENUS or equivalent), and a degree in Engineering, Life Sciences, or a related discipline is expected. What matters most is what you've actually built and fixed.
• You have demonstrated success solving complex automation challenges and troubleshooting workflows in development or production environments. Experience working within, or transferring workflows into, a regulated environment such as CLIA, CAP, or NYSDOH is important. You understand why documentation and change control exist, not just that they do.
• You bring strong cross-functional instincts and startup fluency. You can translate across scientist, engineer, and operations vocabularies, collaborate effectively without heavy infrastructure, and help teams stay focused when everything feels urgent. You also have a genuine curiosity about the science behind the workflow. You don't need to be a molecular biologist, but you care about why the RNA is sensitive, why the extraction chemistry matters, and why a 2µL dead volume might matter more than it appears.
• Experience with, or a genuine interest in, AI-enabled tools, computer vision, advanced analytics, or machine learning applied to laboratory automation is highly valued. The field is moving quickly, and we're looking for someone who is paying attention. Most importantly, you want to build something that matters. We are working to provide women with faster, less invasive answers about endometrial cancer, and automation is a critical part of how we get there.

This is a full-time position offering a base salary between $125K-185K annually.