Fermentation Engineer Jobs in Boston, MA (NOW HIRING)

The Role
Moderna is seeking an Associate Director, Process Development to lead upstream/fermentation process development for E. coli-based production of recombinant enzymes, plasmids, and related biological starting materials critical to Moderna's technology platforms and pipeline programs.
This role translates strain, vector, and expression-screening outputs into robust, scalable, and manufacturable processes, with responsibility for microbial fermentation, cell banking strategy, scale-up/scale-down, process characterization, technology transfer, and CMC support.
The successful candidate will bring strong technical judgment in E. coli physiology and fermentation engineering and will partner closely with strain and expression screening, downstream purification, analytical development, quality, manufacturing, and CMC teams.
Here's What You'll Do

• Lead upstream/fermentation process development for E. coli-based production of recombinant enzymes, plasmids, and related biological materials.
• Manage a team and translate strain, vector, and screening outputs into scalable fermentation processes with clear development strategies, success criteria, and manufacturing-readiness plans.
• Develop and optimize high-cell-density fed-batch fermentation processes, including media/feed design, induction strategy, and key parameters such as temperature, pH, dissolved oxygen, agitation, aeration, backpressure, and harvest criteria.
• Apply DOE, scale-down models, and data-driven approaches to define operating ranges, improve robustness, reduce variability, and improve titer, yield, productivity, and quality.
• Lead microbial cell banking strategy, including research and development cell bank generation, characterization readiness, storage strategy, traceability, passage history, genetic stability considerations, and fit-for-purpose documentation.
• Partner with Quality, Manufacturing, and internal or external banking partners to ensure cell bank generation and handling align with intended use, process maturity, and CMC expectations.
• Use E. coli physiology and metabolism to manage growth/production tradeoffs, oxygen limitation, overflow metabolism, acetate formation, redox/energy balance, and carbon flux.
• Develop physiology-aware feeding and induction strategies that improve consistency, product quality, downstream processability, and scale translation.
• Establish and interpret inline, online, and at-line monitoring approaches, including off-gas analytics, OUR/CER, respiratory quotient, pH/DO behavior, biomass indicators, and other process-state measurements.
• Evaluate and deploy fit-for-purpose PAT tools and partner with automation, digital, and manufacturing teams to support reproducible execution and troubleshooting.
• Partner with downstream purification and analytical development to define upstream-to-downstream interfaces, including harvest timing, clarification strategy, impurity load, endotoxin/host-cell impurity burden, nucleic acid burden, and process economics.
• Lead or support technology transfer, root-cause investigations, process documentation, technical reports, process characterization summaries, and CMC/regulatory sections as needed.
• Serve as a technical leader and mentor for microbial process development, ensuring clear handoffs with the Strain & Expression Screening role and driving scientific rigor, documentation discipline, and fast-cycle learning.

Here's What You'll Need (Basic Qualifications)

• PhD in Chemical Engineering, Biochemical Engineering, or a related discipline with 5+ years of relevant industry experience; or MS with 10+ years; or BS with 12+ years of relevant industry experience.
• Substantial industry experience developing E. coli or other microbial upstream processes for recombinant protein, enzyme, plasmid, or related biological production.
• Hands-on expertise in high-cell-density microbial fermentation, especially fed-batch E. coli process development.
• Strong understanding of microbial physiology, metabolism, media/feed development, induction optimization, scale-up/scale-down, and process characterization.
• Experience with microbial cell banking strategy, generation, characterization support, documentation, and interface with process development or manufacturing.
• Experience implementing or interpreting online/inline measurements such as off-gas analytics, OUR/CER, pH/DO trends, biomass indicators, and related process-state measurements.
• Demonstrated ability to lead complex technical projects, influence cross-functional stakeholders, support manufacturing readiness, and communicate clearly through technical writing and presentations.

Here's What You'll Bring to the Table (Preferred Qualifications)

• Direct experience developing and scaling E. coli processes for recombinant enzymes and/or plasmids.
• Experience supporting GMP or GMP-enabling microbial cell banking activities.
• Experience with defined or semi-defined media, advanced feeding strategies, model-based feed control, and PAT tools such as off-gas analytics, capacitance, Raman/NIR, soft sensors, or process dashboards.
• Working knowledge of downstream operations, including harvest/clarification, cell disruption where relevant, chromatography, UF/DF, impurity clearance, and endotoxin or host-cell impurity control.
• Experience supporting tech transfer, deviation investigations, CAPA, change control, CMC deliverables, and regulatory interactions.
• A desire to make an impact as part of a high-growth, transformational company that is Bold, Relentless, Curious, and Collaborative.

Pay & Benefits
At Moderna, we believe that when you feel your best, you can do your best work. That's why our benefits and well-being resources are designed to support you-at work, at home, and everywhere in between.

• Competitive healthcare, plus voluntary benefit programs to support your unique needs
• A holistic approach to well-being, with access to fitness, mindfulness, and mental health support
• Family planning benefits, including fertility, adoption, and surrogacy support
• Generous paid time off, including vacation, volunteer days, sabbatical, global recharge days, and a discretionary year-end shutdown
• Savings and investments to help you plan for the future
• Location-specific perks and extras

The salary range for this role is $142,500.00 - $256,500.00. This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An individual's position within the salary range will be based on several factors including, but not limited to, specific competencies, relevant education, qualifications, certifications, experience, skills, performance, and business or organizational needs.The successful candidate may be eligible for an annual discretionary bonus, other incentive compensation, or equity award, subject to company plan eligibility criteria and individual performance.
About Moderna
Since our founding in 2010, we have aspired to build the leading mRNA technology platform, the infrastructure to reimagine how medicines are created and delivered, and a world-class team. We believe in giving our people a platform to change medicine and an opportunity to change the world.
By living our mission, values, and mindsets every day, our people are the driving force behind our scientific progress and our culture. Together, we are creating a culture of belonging and building an organization that cares deeply for our patients, our employees, the environment, and our communities.
We are proud to have been recognized as a Science Magazine Top Biopharma Employer, a Fast Company Best Workplace for Innovators, and a Great Place to Work in the U.S.
If you want to make a difference and join a team that is changing the future of medicine, we invite you to visit modernatx.com/careers to learn more about our current opportunities.
Our Working Model
As we build our company, we have always believed an in-person culture is critical to our success. Moderna champions the significant benefits of in-office collaboration by embracing a 70/30 work model. This 70% in-office structure helps to foster a culture rich in innovation, teamwork, and direct mentorship. Join us in shaping a world where every interaction is an opportunity to learn, contribute, and make a meaningful impact.
Moderna is a smoke-free, alcohol-free, and drug-free work environment.
Equal Opportunities
Moderna is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry or citizenship, ethnicity, disability, military or protected veteran status, genetic information, sexual orientation, marital or familial status, or any other personal characteristic protected under applicable law. Moderna is a place where everyone can grow. If you meet the Basic Qualifications for the role and you would be excited to contribute to our mission every day, please apply!
Moderna is an E-Verify Employer in the United States. We consider qualified applicants regardless of criminal histories, consistent with legal requirements.
Accommodations
We're focused on attracting, retaining, developing, and advancing our employees. By cultivating a workplace that values diverse experiences, backgrounds, and ideas, we create an environment where every employee can contribute their best.
Moderna is committed to offering reasonable accommodations to qualified job applicants with disabilities. Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should contact the Accommodations team at leavesandaccommodations@modernatx.com.
Export Control NoticeThis position may involve access to technology or data that is subject to U.S. export control laws, including the Export Administration Regulations (EAR). As such, employment is contingent upon the applicant's ability to access export-controlled information in accordance with U.S. law. Due to the nature of the work and regulatory requirements, only individuals who qualify as U.S. persons (citizens, permanent residents, asylees, or refugees) are eligible for this position. For this role Moderna is unable to sponsor non-U.S. persons to apply for an export control license.#LI-TR2