Research Associate, Protein Production

The posting, as Flagship Pioneering, Inc. wrote it

What if… you could pioneer a new approach to designing life’s most essential molecules?

FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to redefine how critical research, diagnostic, and therapeutic molecules are designed and built. We are seeking passionate problem solvers ready to make a profound impact on biotechnology and therapeutic innovation.

Position Summary

We are seeking a highly motivated and exceptionally organized Research Associate II to expand our protein production capabilities across two complementary scales: bulk expression and purification of individual high-priority targets, and high-throughput parallel production of large variant panels. This hands-on, laboratory-facing role will execute and advance scalable protein expression, purification, normalization, and characterization workflows that feed the design–build–test cycles at the core of our platform.

The successful candidate will bring direct, practical experience in recombinant protein production and chromatographic purification at both preparative and high-throughput scale — together with the ability to execute experiments, run high-throughput analytics, troubleshoot workflows, and deliver well-characterized protein reagents on rapid timelines. This individual will work closely with Protein Engineering, Chemistry, and Assay Development team to align production activities with program priorities and experimental timelines. Meticulous record-keeping and sample traceability are essential to this role. Experience with liquid handlers, magnetic-bead purification platforms such as the KingFisher, cell-free expression, or workflow scripting is preferred.

The ideal candidate thrives in a fast-paced, collaborative environment, enjoys solving technical challenges, and is motivated to apply automation and emerging technologies to developing a synthetic biology platform.

Key Responsibilities

Bulk Expression & Purification

• Execute multi-liter recombinant expression campaigns in bacteria from construct transformation and culture growth through induction, harvest, and lysis.
• Design, build, and run preparative purification methods on ÄKTA FPLC systems using UNICORN, including affinity, ion exchange, size exclusion, and mixed-mode chromatography.
• Deliver milligram-to-gram quantities of highly pure, well-characterized protein.
• Troubleshoot expression and purification challenges such as low yield, insolubility, aggregation, and proteolysis, and drive protocol improvements that increase yield and purity.

High-Throughput Production & Analytics

• Bacterial library transformation, colony picking and sequencing
• Execute miniaturized, parallel protein expression and purification in plate-based formats
• Perform automated purification, sample normalization, and quality assessment to deliver fit-for-purpose protein reagents at scale.
• Operate, ma

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The salary range for this role is $65,000 - $93,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL116 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL116's good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.