Protocos | Cambridge, MA Senior Research Associate, Fermentation Development

Senior Research Associate, Fermentation Development

Cambridge, MA USA

Flagship Pioneering is a platform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies.

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.

• 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

• 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

• 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

• 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

• 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…