Senior Research Associate, Strain Engineering

About the role

Flagship Pioneering is a platform innovation company that invents and builds companies that change the world. We are seeking a highly motivated Senior Research Associate to support the development and optimization of microbial strain engineering for recombinant protein production. Reporting to the Senior Scientist, Microbial Strain Engineering, this individual will play a key role in genetic engineering of microbial strains in a fast-paced startup environment. The ideal candidate is highly hands-on, technically rigorous, and comfortable operating independently in a dynamic research setting. This role requires strong practical experience with DNA assembly strategies, microbial culture techniques, and laboratory operations. Location: Cambridge, MA.

Responsibilities

• Construct plasmids using modern molecular biology techniques (e.g., Golden Gate assembly, HiFi assembly, etc.)
• Perform sequencing analysis using state-of-the-art NGS technologies and software
• Prepare plasmid DNA through mini-preps, maxi-preps, etc.
• Prepare competent cells for transformation of microbial strains
• Execute PCR to both prepare substrates for genetic engineering and genotyping of candidate strains
• Perform agarose gel electrophoresis, nucleic acid quantification, and sample preparation for routine functional assays
• Support screening and characterization of microbial strains in shake flask and microtiter plates
• Track strain performance metrics including biomass production, functional assay readouts, and product formation
• Generate and maintain microbial cell banks and inventory records
• Prepare media for strain-building campaigns
• Support routine laboratory maintenance, equipment upkeep, and troubleshooting
• Contribute to safe laboratory operations and maintain a strong culture of safety and operational rigor
• Maintain accurate and well-organized experimental records and documentation
• Collaborate with discovery, bioprocess development, downstream, and analytical teams to support integrated process development activities
• Closely partner with bioprocess development to align on best practices for strain development and evaluation

Requirements

• Bachelor’s degree with 5‑7 years of relevant research experience, or Master’s degree with 3‑5 years of relevant research experience in Bioengineering, Biochemistry,