Research Associate II, Protein Sciences

Flagship Pioneering is a platform 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 We are seeking a highly motivated Research Associate II to join our Protein Sciences team, supporting the discovery, engineering, and characterization of proteins. Reporting to the Principal Scientist, Protein Sciences, this individual will play a central role in the molecular biology, protein expression, and functional screening work that underpins our programs. The ideal candidate is hands‑on, technically rigorous, and comfortable operating independently in a fast‑paced startup environment. They take pride in generating clean, reproducible data, communicate results clearly, and thrive in collaborative, high‑performing teams. This role requires strong practical experience with core microbiology operations, molecular cloning, and protein analysis techniques, along with the flexibility to work across multiple host organisms as the platform scales and a drive to advance solutions to critical global environmental challenges. KEY RESPONSIBILITIES Microbiology & Laboratory Operations Perform routine microbiology operations including media preparation, agar plate preparation, and aseptic technique Maintain rigorous good laboratory practices (GLP) and contribute to a strong culture of safety and operational excellence Generate and maintain microbial cell banks and inventory records Support routine laboratory maintenance, equipment upkeep, and troubleshooting Molecular Cloning & DNA Assembly Design and execute PCR for cloning, mutagenesis, and genotyping applications Perform DNA assembly using Golden Gate, Gibson, and other modern cloning techniques Run and analyze agarose gels; perform plasmid preparation (mini-prep, maxi-prep) and nucleic acid quantification Perform sequencing analysis using state‑of‑the‑art NGS technologies and software Maintain accurate construct and strain records in Benchling Protein Expression, Purification & Analysis Express engineered protein constructs across bacterial, yeast, and/or fungal expression systems Analyze protein expression, purity, and integrity via SDS-PAGE and/or Western blot Support protein purification workflows using standard chromatography and related techniques High-Throughput Screening Support high-throughput screening workflows for functional characterization of protein variants, including assay setup, execution, and data capture Contribute to optimizing screening conditions for reproducibility and throughput Cross-Functional Collaboration & Documentation Collaborate closely with the Protein Sciences team members and cross‑functional partners Maintain clear, well‑organized experimental records and communicate results effectively to the team PROFESSIONAL EXPERIENCE & QUALIFICATIONS Bachelor’s degree (with 2-5 years of relevant research experience) in Bioengineering, Biochemistry, Microbiology, Biotechnology, or related discipline. Hands‑on experience with core microbiology operations: media prep, agar plate prep, aseptic technique, and general GLP Strong hands‑on experience with molecular cloning: design, PCR, gel electrophoresis and analysis, isolation, Golden Gate, Gibson assembly, and related techniques Experience with protein analysis techniques including SDS‑PAGE and Western blot Strong communication, organizational and documentation skills Ability to independently execute experiments and troubleshoot routine issues Preferred Experience Exposure to high‑throughput screening workflows Experience working across multiple host organisms, such as E. coli, Saccharomyces cerevisiae, Pichia pastoris, Bacillus, Pseudomonas putida, or Aspergillus niger Familiarity with bioinformatics/ELN tools such as Benchling and Geneious Experience with protein purification and chromatography techniques Experience supporting protein engineering or functional screening campaigns 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 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. The salary range for this role is $74,000 - $93,500. 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' good faith estimate as of the date of publication and may be modified in the future. 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