Senior Automation Engineer, Platform Biology

The posting, as Flagship Pioneering, Inc. wrote it

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

• Implement Benchling as a data platform, not only as an ELN: entity schemas, the Postgres warehouse, Insights, the API, and the supporting integrations.
• Establish sample tracking end to end. Chain of custody from donor material through line, vial, thaw, run and instrument output, and the links that let a result be attached back to the sample that produced it.
• Deliver analysis-ready data to the data team, including structured metadata capture, stable identifiers, and documented schemas with reliable handoff.
• Identify gaps in commercial software and design, ship and operate REST APIs and internal web applications, for example a results parser, a scheduling interface, or an app to integrate Benchling.
• Build integrations between automation platforms, instruments, LIMS/ELN, imaging systems, databases and downstream data pipelines.
• Build tools scientists use independently: search interfaces, pull lists, capacity dashboards.
• Investigate and resolve discrepancies, such as inventory that does not reconcile after a migration, and build the checks that catch them earlier.
• Apply sound software engineering practice: version control, testing, debugging, modular design, and documentation that someone else can maintain.
• Partner across scientific, automation, IT and data teams, bridging experimental work and the systems that record it.
• Anticipate future data and integration needs, plan for them, and stay flexible about learning new systems as the platform evolves.

Qualifications

• Bachelor's or master's degree in computer science, engineering, bioengineering, biomedical engineering, computational biology or a related field, or a life science degree wit

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bout your background and interest in Flagship.

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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.

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