Research Associate, Protein Production

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, maintain, troubleshoot, and continuously improve liquid handlers, magnetic-bead purification platforms (e.g., KingFisher), automated purification systems, and associated analytical instrumentation.

• Run high-throughput protein analytics across many samples in parallel, including plate-based quantitation, capillary electrophoresis, analytical SEC/SEC-HPLC, and thermal stability or aggregation screening.

• Translate methods between scales — adapting preparative purifications into miniaturized high-throughput formats, and scaling promising hits back up for in-depth characterization.

Required Qualifications & Experience

• Bachelor’s degree in biochemistry, molecular biology, biotechnology, bioengineering, synthetic biology or a related scientific discipline with 1-4 years s of relevant academic and/or industry experience; or a master’s degree with 0-2 years of commercial experience.

• Hands-on experience with recombinant protein expression and production workflows in E. coli, including multi-liter culture growth and harvest.

• Direct, hands-on experience operating ÄKTA FPLC systems, including independently designing, executing, and troubleshooting purification methods in UNICORN — not solely running pre-established protocols.

• Demonstrated proficiency across multiple column purification modalities.

• Demonstrated experience working at both scales: preparative purification of individual targets to milligram-or-greater quantities, and parallel, plate-based production and analytics across large sample sets.

• Exceptional organization and record-keeping, with a proven ability to track samples, buffers, and method runs in parallel without loss of traceability.

• Core molecular biology skills, including plasmid preparation, cloning, and transformation.

• Ability to independently execute experiments, analyze data, troubleshoot technical problems, maintain accurate documentation, and advance assigned work.

• Ability to maintain flexibility in the face of evolving priorities and short timelines in a collaborative, matrixed research environment.

• Strong communication, collaboration, and problem-solving skills, with a clear commitment to laboratory safety and data integrity.

Preferred Qualifications

• Experience with magnetic-bead–based purification platforms such as the Thermo KingFisher.

• Familiarity with cell-free or yeast expression systems.

• Hands-on experience programming and operating liquid handlers and robotic workstations (e.g., Hamilton, Tecan, Opentrons, Bravo).

• Comfort organizing and analyzing experimental data in Excel, Python, or similar tools, and maintaining structured records in an ELN or LIMS.

Who You Are

Innovative Pioneer: You are excited to help build new production capabilities and continually look for better ways to make and characterize protein.

Collaborative Contributor: You work effectively across disciplines, partnering closely with scientists in protein engineering, assay development, automation, machine learning, and beyond.

Inventive Problem Solver: You proactively identify challenges and rapidly develop creative, practical solutions.

Comfortable at Any Scale: You move easily between a careful multi-step purification of a single important target and a plate of ninety-six variants, and you bring the same rigor to both.

Rigorously Organized: You keep meticulous records, design your workflows so results are reproducible months later, and are trusted by colleagues to know exactly where every sample stands.

Mission-Driven Individual: You are motivated by the opportunity to fundamentally transform how biomolecules are designed and synthesized, with meaningful impact on human health and biotechnology.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, generating billions in value. Flagship companies are known for addressing humanity’s most pressing challenges and advancing innovative solutions with global impact.

We are an equal opportunity employer and are dedicated to building diverse and inclusive teams. If you have some of the qualifications listed above but not all, we still encourage you to apply. We value passion, experience in many forms, and unique backgrounds.

Come pioneer the future with us.

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.

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.

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.