Senior Scientist II/Principal Scientist, Protein Sciences

Flagship Pioneering, Inc.•Cambridge, MA

3h•Onsite

About The Position

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. This role will be the first hire on the Protein Sciences team and 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.

Requirements

PhD (or equivalent industry experience) in protein science, biochemistry, molecular biology, bioengineering, or a related discipline, with 8-12 years (at least 5 in industry) 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

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.