Research Associate, Protein Production

Flagship Pioneering, Inc.•Cambridge, MA

1d•$65,000 - $93,500•Onsite

About The Position

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. 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.

Requirements

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.

Nice To Haves

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.

Responsibilities

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.
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.