Senior Research Associate, Chemical Biology at Flagshippioneeringinc

What if… you could pioneer a new approach to designing life’s most essential molecules? FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to transform how critical research, diagnostic, and therapeutic molecules are manufactured. We are seeking passionate problem solvers ready to make a profound impact on biotechnology and therapeutic innovation. Position Summary We are seeking a motivated, detail-oriented, and intellectually curious Research Associate or Senior Research Associate to join our Chemical Biology team. This role is centered on applying chemistry to solve complex biological problems, interrogating and controlling enzyme-driven biomolecular synthesis through a mechanistic and molecular lens. You will execute high-throughput experiments to probe enzyme–substrate interactions, characterize biomolecule products, and contribute to the development of robust, scalable assays that power our platform. The ideal candidate appreciates the dynamic chemical nature of biological systems and is excited to manipulate and measure biology at the molecular level. This is an exciting opportunity to build deep expertise at the interface of chemistry and biology within a fast-paced, collaborative startup environment. You are a hands-on experimentalist who thrives in execution-focused, pipeline-driven work and is eager to grow alongside a rapidly evolving technology platform. Key Responsibilities • Execute high-throughput experiments to characterize enzyme–substrate and enzyme–product interactions, with a focus on understanding underlying chemical mechanisms • Apply chemical principles to modulate and interrogate protein function, reactivity, and biomolecular synthesis pathways • Perform biomolecular product characterization using analytical and separation techniques (e.g., gel electrophoresis, TapeStation, HPLC, plate-based assays) • Support the development, optimization, and scaling of biochemical and enzymatic assays with an emphasis on quantitative, reproducible readouts • Generate, analyze, and interpret experimental datasets to extract mechanistic insight and inform pipeline progression • Collaborate closely with cross-functional teams, including Enzyme Science and Assay Development, to integrate chemical insight into broader platform workflows • Maintain rigorous experimental documentation and contribute to protocol development and knowledge sharing across the team Qualifications • B.S. or M.S. in Chemistry, Chemical Biology, Biochemistry, Biotechnology, or a related discipline with a strong foundation in chemical principles applied to biological systems • 2+ years of relevant laboratory experience (industry or academic) • Hands-on experience applying chemistry to biological systems, including enzymatic assays, biomolecule manipulation, or reaction-based workflows • Strong foundation in protein chemistry, enzymology, or biomolecular interactions • Proficiency in core laboratory techniques including pipetting, gel electrophoresis, and quantitative assay execution • Demonstrated ability to generate high-quality, reproducible data and perform rigorous data analysis • Experience working in fast-paced, collaborative laboratory environments Preferred Qualifications • Experience with analytical and separation techniques such as HPLC, capillary electrophoresis, TLC, or plate-based detection systems • Exposure to bioorthogonal chemistry, chemical modification of biomolecules, or mechanistic enzymology • Familiarity with nucleic acid or protein characterization platforms (e.g., TapeStation or similar technologies) • Experience contributing to assay development, optimization, or high-throughput workflows Who You Are Innovative Pioneer: You are excited by the opportunity to explore new scientific frontiers and apply chemical thinking to unlock biological complexity. Collaborative Contributor: You work effectively across teams, communicate clearly, and value shared success in a highly interdisciplinary environment. Inventive Problem Solver: You approach challenges with curiosity and creativity, using first-principles thinking to develop elegant experimental solutions. Mission-Driven Individual: You are motivated by the opportunity to fundamentally change how biomolecules are synthesized and to impact human health and biotechnology. Motivated Learner & Emerging Professional: You are eager to deepen your expertise in chemical biology, take ownership of your work, and grow into a highly capable scientist within a startup environment. Values and Behaviors: Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, we encourage you to apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background. The level of the role will be commensurate with the education and years of experience of the identified candidates. Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. 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. The salary range for this role is $81,000 - $107,250. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL116 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL116's good faith estimate as of the date of publication and may be modified in the future.