Senior Automation Engineer, Platform Biology

What if you could join a rapidly growing company and play a critical role in bringing new medicines to patients by helping scale the programmable infrastructure behind a new human cellular biology platform?

About Vesalius

Vesalius Therapeutics is pioneering a new platform to generate breakthrough treatments for common diseases. Our platform combines large-scale human genetics, genomics, stem cell studies, high-dimensional cellular phenotyping, and artificial intelligence to uncover causal biology and identify optimal intervention points for new therapies. Vesalius was founded in 2019 by Flagship Pioneering.

Role Overview

Vesalius is seeking a highly motivated Automation Engineer to help scale our automated biology platform. This early-career role sits at the intersection of biology, robotics, software, and data systems, with a focus on programming, data handling, systems integration, and workflow automation. You will partner with scientists, automation operators, IT, and data science teams to translate biological workflows into robust automated workcells and ensure experiments generate reliable, traceable, analysis-ready data. This role goes beyond operating instruments—it is focused on making automation programmable, integrated, scalable, and reliable.

Key Responsibilities

• Develop and optimize high-throughput automated protocols that translate biological workflows from the bench to integrated workcells.
• Partner with scientific teams to design automation solutions that balance biological fidelity, throughput, cost, reliability, and lead time.
• Collaborate with scientists and automation operators on workflow execution, troubleshooting, training, and continuous improvement.
• Develop and maintain automation scripts, scheduling workflows, error handling, monitoring, and instrument-control methods using tools such as Python, C#, JSON, platform APIs, and vendor-specific languages.
• Validate automated workflows against benchtop methods, assessing precision, accuracy, reproducibility, and data quality.
• Build integrations between automation platforms, instruments, LIMS/ELN, imaging systems, databases, and downstream data pipelines, including structured metadata capture and data handoff.
• Integrate and troubleshoot new instruments and workcell components, including instrument interfaces or drivers where needed.
• Apply sound software engineering practices including version control, testing, debugging, modular design, and documentation.
• Program liquid-handling and robotic workflows across platforms such as Hamilton STAR, Dynamic Devices Lynx, HighRes Biosolutions/Cellario, and similar systems.
• Develop barcode to workflow mapping to enable batch and sample tracking.
• Create and maintain SOPs, method documentation, validation reports, troubleshooting guides, and other technical documentation.

Qualifications

• Bachelor's or master's degree in computer science, engineering, bioengineering, automation, robotics, biomedical engineering, computational biology, or related field.
• Early career experience in laboratory automation, scientific software, robotics, biotech automation, or a related environment.
• Experience with biological workflows such as mammalian cell culture, cell-based assays, high-content imaging, high-throughput screening, NGS, or iPSC systems is strongly preferred.
• Hands-on experience with automated liquid handlers, robotic systems, integrated workcells, laboratory scheduling software, or instrument-control methods.
• Experience developing and troubleshooting automated biological workflows, liquid-handling methods, instrument workflows, software tools, or systems integrations.
• Ability to troubleshoot across software, hardware, liquid handling, instrument communication, data, and sample-tracking workflows.
• Programming experience in Python and/or C#, or comparable languages, with familiarity with Git/version control, testing, debugging, and code documentation.
• Strong communication and documentation skills with the ability to work effectively across scientific, automation, IT, and data teams.

Preferred Experience

• Exposure to cloud infrastructure such as AWS, event-driven integrations, or data pipelines supporting automated laboratory environments.
• Experience with Hamilton STAR, Dynamic Devices Lynx, HighRes Biosolutions/Cellario, Beckman Biomek, Tecan, Biosero, Celltrio, Ginkgo Automation RAC systems, or similar platforms.
• Experience with platform APIs, instrument drivers, SQL/databases, LIMS/ELN, automated metadata capture, or laboratory scheduling software.
• Experience building tools for sample tracking, run monitoring, QC reporting, workflow validation, or automated data handoff.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $108,000 - $170,700. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Vesalius Therapeutics currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Vesalius Therapeutics's good faith estimate as of the date of publication and may be modified in the future.