Senior Scientist II/Principal Scientist, Bioprocess Development

THE ROLE

We are seeking a Principal Scientist or Senior Scientist II to build and lead bioprocess development and microbial production for a high impact, novel biological platform. This role will focus primarily on fermentation process development, scale-up strategy, and production robustness, translating early-stage biological systems into scalable and manufacturable processes. The successful candidate will work at the interface of microbial engineering and bioprocess optimization, guiding both process development and targeted strain improvements that enable industrial production. This individual will serve as a technical leader within a multidisciplinary team and help establish foundational capabilities in microbial manufacturing as the company grows.

KEY RESPONSIBILITIES

• Lead development and optimization of microbial fermentation processes from laboratory scale through pilot-scale production
• Design scalable fermentation strategies including media development, feeding regimes, oxygen transfer optimization, and process control
• Translate biological discoveries into robust production systems by improving yield, productivity, and process reproducibility
• Establish experimental frameworks for systematic process improvement, including DOE-based optimization and fermentation analytics
• Develop and execute scale-up strategies and support technology transfer to external CROs, CMOs, or manufacturing partners
• Contribute to long-term manufacturing strategy and help build the company’s microbial production platform

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• PhD in biochemical engineering, microbiology, chemical engineering, or a related discipline
  • Scientist II: At least 8 years of professional experience, including 3+ years developing microbial fermentation processes in an industrial or translational setting
  • Principal Scientist: At least 12 years of professional experience, including 5+ years developing microbial fermentation processes in an industrial or translational setting
• Demonstrated expertise in fermentation scale-up, optimizing parameters such as oxygen transfer, feeding regimes, media composition, etc.
• Hands-on experience developing and optimizing microbial fermentation across scales (e.g., 250 mL bench reactors through 50 L pilot-scale systems)
• Experience designing and executing fermentation experiments using systematic optimization approaches, such as DOE or structured process screening
• Experience working with external partners (CROs, CMOs, or manufacturing facilities) to develop or transfer fermentation processes, including preparation of process documentation and technical oversight
• Experience operating as a technical leader, either through mentoring scientists, guiding cross-functional collaborators, establishing technical best practices, or contributing to strategic scientific planning in an industry environment

PREFERRED EXPERIENCE

• Experience developing fed-batch fermentation processes across a range of industrial microbial hosts, including bacteria, yeast, and filamentous fungi
• Experience optimizing high-cell-density microbial fermentations
• Experience building fermentation or bioprocess development capabilities and facilities within a start-up environment
• Experience improving production performance through close collaboration or co-ownership of targeted strain engineering activities

LOCATION:  Cambridge, MA

 

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

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.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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The salary range for this role is $143,000 - $214,500. 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.