Senior Research Associate, Fermentation Development

THE ROLE

We are seeking a highly motivated Senior Research Associate to support the development and optimization of microbial fermentation processes for recombinant protein production. Reporting to the Principal Scientist, Bioprocess Development, this individual will play a key role in executing and scaling aerobic microbial fermentation workflows 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 bench‑scale bioreactors, microbial culture techniques, fermentation analytics, and laboratory operations.

Fermentation Operations

• Operate, monitor, and troubleshoot bench‑scale aerobic microbial fermentation systems with minimal supervision
• Execute batch and fed‑batch fermentation experiments to support process development objectives
• Prepare media, inoculum, feeds, and process solutions for fermentation campaigns
• Perform reactor setup, sterilization, calibration, and post‑run cleaning/maintenance

Sampling & Analytical Support

• Collect and process fermentation samples throughout cultivation runs
• Perform routine analytical assays including OD measurements, metabolite analysis, and sample preparation for HPLC or related analytical platforms
• Track fermentation performance metrics including biomass, substrate consumption, and product formation

Strain Evaluation & Process Development

• Support screening and characterization of microbial strains in shake flask and bench scale bioreactors
• Assist in process optimization studies, including media development and fermentation parameter evaluation
• Maintain accurate and well‑organized experimental records and documentation

Laboratory Operations

• Generate and maintain microbial cell banks and inventory records
• Coordinate ordering and tracking of fermentation consumables and raw materials
• Support routine laboratory maintenance, equipment upkeep, and troubleshooting
• Contribute to safe laboratory operations and maintain a strong culture of safety and operational rigor

Cross‑Functional Collaboration

• Collaborate with strain engineering, downstream, and analytical teams to support integrated process development activities
• Assist with scaling workflows and implementing improved operational practices as the platform grows

• 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, Chemical Engineering, Microbiology, Biotechnology, or related discipline.
• Hands‑on experience in microbial fermentation, microbiology, bioprocess development, or related laboratory environments
• Experience in operating and maintaining bench‑scale bioreactors
• Strong understanding of aseptic technique and microbial culture handling
• Experience with aerobic microbial fermentation workflows
• Strong organizational and documentation skills
• Ability to independently execute experiments and troubleshoot routine process issues

• Experience with fed‑batch fermentation processes
• Familiarity with HPLC‑based analysis of sugars, organic acids, or fermentation metabolites
• Experience with recombinant protein expression systems
• Experience supporting process optimization or scale‑up activities
• Familiarity with fermentation data analysis and process monitoring tools

Cambridge, MA

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

The salary range for this role is $81,000 - $107,300. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos’s good faith estimate as of the date of publication and may be modified in the future.