Research Associate II, Protein Sciences

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 74,000 - 94,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering in Cambridge, MA is seeking a Research Associate II to join the Protein Sciences team. You will support molecular biology, protein expression, and functional screening, working closely with the Principal Scientist in a fast-paced startup environment.

The ideal candidate has hands-on experience with microbiology, cloning, and protein analysis, with a proactive, data-driven approach and strong collaboration skills.

Qualifications

• Bachelor's degree required with 2–5 years of relevant research experience.
• Hands-on microbiology operations: media prep, aseptic technique, GLP.
• Experience with cloning techniques: PCR, Golden Gate, Gibson.
• Protein analysis: SDS-PAGE, Western blot.

Responsibilities

• Perform routine microbiology operations with aseptic technique.
• Design and execute cloning, genotyping and DNA assembly.
• Express and analyze proteins across hosts; purify and assess quality.
• Support high-throughput screening and data capture.
• Collaborate with Protein Sciences team and maintain records.

Skills

Microbiology operations

Molecular cloning

Protein analysis

Documentation & communication

Independent troubleshooting

Education

Bachelor’s degree in Bioengineering, Biochemistry, Microbiology, Biotechnology

Tools

Benchling

Geneious

Job description

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 www.flagshippioneering.com.

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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