Senior Scientist II/Principal Scientist, Microbial Protein Sciences

COMPANY DESCRIPTION

Flagship Pioneering is a bioplatform 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. 

THE ROLE

This role will be the first hire on the Protein Sciences team of a startup that is focused on environmental and planetary health. This role will serve as both a technical leader and foundational builder of the function. The individual will own the strategy, design, and execution of protein construct development and production across multiple expression systems and scales, working in close partnership with discovery research. They will determine the feasibility and application of advanced protein science approaches, translating scientific objectives into robust, scalable workflows aligned with company priorities. In addition to hands-on technical leadership, this role will guide external CRO partnerships, contribute to strategic planning, and help establish processes, standards, and capabilities that support long-term growth. Depending on experience, this role may expand to include team leadership and broader organizational influence.

KEY RESPONSIBILITIES

• Lead the design, development, and implementation of protein expression and production strategies, determining the feasibility and optimal application of scientific approaches across targets;
• Own protein production workflows across multiple hosts and scales (e.g., coli, B. subtilis, Pichia pastoris, cell-free systems; deep-well plates and shake flasks), ensuring rigor, reproducibility, and alignment with scientific and company objectives;
• Provide high-level technical expertise in protein quantification and validation, establishing fit-for-purpose analytical strategies (e.g., HiBit, Western analysis, related methods) to support decision-making;
• Manage and direct external CRO relationships, including protocol development, tech transfer, timelines, and budget considerations, while ensuring quality and strategic alignment;
• Contribute to the development of the Protein Sciences team by establishing best practices, documentation standards, and collaboration; support strategic planning and, with team growth, mentor or manage additional scientists.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• PhD (or equivalent industry experience) in protein science, biochemistry, molecular biology, bioengineering, or a related discipline, with 8-12 years (at least 3 in industry with 5+ strongly preferred) of deep hands-on experience in protein expression and production
• Demonstrated ownership of protein construct design and production across multiple expression systems and scales, including microbial and/or cell-free platforms, with a track record of delivering reproducible, decision-enabling data
• Experience determining the feasibility and application of advanced protein science approaches to support scientific programs, including selecting hosts, formats, and analytical strategies aligned with program objectives
• Proven ability to lead complex technical work with minimal oversight, including managing external CRO relationships, protocol development or transfer, timelines, and resource considerations (e.g., budgets, trade-offs)
• Experience operating as a technical leader-either through mentoring scientists, guiding cross-functional collaborators, establishing best practices, or contributing to strategic scientific planning in an industry setting (startup experience strongly preferred)

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.