Research Associate II, Protein Sciences

Flagship Pioneering•Cambridge, MA

11d•Onsite

About The Position

Flagship Pioneering is seeking a highly motivated Research Associate II to join their Protein Sciences team. This role will support the discovery, engineering, and characterization of proteins, playing a central role in molecular biology, protein expression, and functional screening. The ideal candidate is hands-on, technically rigorous, comfortable operating independently in a fast-paced startup environment, and takes pride in generating clean, reproducible data. They should communicate results clearly and thrive in collaborative, high-performing teams. This position requires strong practical experience with core microbiology operations, molecular cloning, and protein analysis techniques, along with the flexibility to work across multiple host organisms as the platform scales and a drive to advance solutions to critical global environmental challenges.

Requirements

Bachelor’s degree (with 2-5 years of relevant research experience) in Bioengineering, Biochemistry, Microbiology, Biotechnology, or related discipline.
Hands-on experience with core microbiology operations: media prep, agar plate prep, aseptic technique, and general GLP.
Strong hands-on experience with molecular cloning: design, PCR, gel electrophoresis and analysis, isolation, Golden Gate, Gibson assembly, and related techniques.
Experience with protein analysis techniques including SDS-PAGE and Western blot.
Strong communication, organizational and documentation skills.
Ability to independently execute experiments and troubleshoot routine issues.

Nice To Haves

Exposure to high-throughput screening workflows.
Experience working across multiple host organisms, such as E. coli, Saccharomyces cerevisiae, Pichia pastoris, Bacillus, Pseudomonas putida, or Aspergillus niger.
Familiarity with bioinformatics/ELN tools such as Benchling and Geneious.
Experience with protein purification and chromatography techniques.
Experience supporting protein engineering or functional screening campaigns.

Responsibilities

Perform routine microbiology operations including media preparation, agar plate preparation, and aseptic technique.
Maintain rigorous good laboratory practices (GLP) and contribute to a strong culture of safety and operational excellence.
Generate and maintain microbial cell banks and inventory records.
Support routine laboratory maintenance, equipment upkeep, and troubleshooting.
Design and execute PCR for cloning, mutagenesis, and genotyping applications.
Perform DNA assembly using Golden Gate, Gibson, and other modern cloning techniques.
Run and analyze agarose gels; perform plasmid preparation (mini-prep, maxi-prep) and nucleic acid quantification.
Perform sequencing analysis using state-of-the-art NGS technologies and software.
Maintain accurate construct and strain records in Benchling.
Express engineered protein constructs across bacterial, yeast, and/or fungal expression systems.
Analyze protein expression, purity, and integrity via SDS-PAGE and/or Western blot.
Support protein purification workflows using standard chromatography and related techniques.
Support high-throughput screening workflows for functional characterization of protein variants, including assay setup, execution, and data capture.
Contribute to optimizing screening conditions for reproducibility and throughput.
Collaborate closely with the Protein Sciences team members and cross-functional partners.
Maintain clear, well-organized experimental records and communicate results effectively to the team.