Senior Scientist I/II, Bioprocess Development at Flagship Pioneering, Inc.

About the role Flagship Pioneering is seeking a Senior Scientist I/II with expertise in bioprocess development and microbial production. This position will act as the technical lead in a laboratory setting, focusing on the innovative biological platform that emphasizes the development of fermentation processes suitable for scaling up to manufacturing levels. The ideal candidate will work in close collaboration with teams dedicated to microbial engineering and the optimization of bioprocesses.

Key facts

Location: Cambridge, MA

Engagement: Full-time

Team: Bioprocess Development

What you’ll do

- Design and execute bioprocess experiments aimed at improving fermentation processes, partnering with the Strain Development team to enhance strain performance, optimize media formulations, and refine feeding strategies while ensuring robust process control.
- Convert biological insights into practical production systems, focusing on increasing yield, productivity, and consistency of fermentation processes.
- Play a key role in establishing experimental frameworks that facilitate systematic improvements in processes, including the development of optimization methodologies and fermentation analytics.
- Act as a subject matter expert during technology transfer initiatives to external contract research organizations (CROs), contract manufacturing organizations (CMOs), or other manufacturing partners, ensuring smooth transitions and effective communication.
- Collaborate with cross-functional teams to integrate findings from bioprocess experiments into broader project goals, ensuring alignment with organizational objectives.




- Analyze data from fermentation experiments to identify trends and areas for improvement, applying statistical tools and methodologies to support decision-making.
- Mentor junior scientists and provide guidance on best practices in bioprocess development, fostering a culture of innovation and continuous improvement within the team.
- Stay updated on industry trends and advancements in bioprocessing and fermentation technologies, contributing to the strategic direction of the bioprocess development team.

Requirements

- A PhD in biochemical engineering, microbiology, chemical engineering, or a closely related discipline is required.
- For Scientist I: A minimum of 5-7 years of relevant experience, including at least 1 year of direct involvement in microbial fermentation process development in an industrial or translational setting.
- For Scientist II: A minimum of 8-11 years of relevant experience, with at least 3 years dedicated to hands‑on work in microbial fermentation process development in an industrial or translational context.
- Demonstrated expertise in fermentation process development and scale‑up, with a focus on optimizing key parameters such as oxygen transfer rates and media composition.
- Experience in high‑cell‑density microbial fermentations and a proven track record of developing fermentation processes across various scales,



from small bench reactors (250 mL) to larger pilot systems (50 L).
- Knowledge of systematic optimization techniques, including Design of Experiments (DOE) or structured process screening methodologies.

Nice to have

- Experience in collaborating with external partners, such as CROs, CMOs, or manufacturing facilities, to develop or transfer fermentation processes, including the creation of comprehensive process documentation and providing technical oversight.
- A background in developing fed‑batch fermentation processes utilizing a range of industrial microbial hosts, including bacteria, yeast, and filamentous fungi.
- Experience in driving production performance improvements through collaboration or co‑ownership of targeted strain engineering initiatives, demonstrating a proactive approach to problem‑solving.

Skills & tools

- Solid proficiency in fermentation process development and optimization techniques.
- Familiarity with statistical analysis and experimental design methodologies to support process improvements.
- Excellent communication skills, enabling effective collaboration with cross‑functional teams and stakeholders.
- Ability to analyze complex data sets and translate findings into actionable insights for process enhancement.

Practical notes

The salary range for this position is between $126,000 and $181,500, with compensation determined by qualifications, skills, competencies, and experience.

- healthcare coverage
- an annual incentive program
- retirement benefits
- a wide array of additional perks to support employee well‑being and professional growth

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📌 Senior Scientist I/II, Bioprocess Development (Cambridge)
🏢 Flagship Pioneering
📍 Cambridge