Senior Research Associate, Protein Sciences

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

As a Senior Research Associate in Protein Sciences at one of our latest startup ventures, you will be an integral part of our protein R&D team, helping drive the discovery, optimization, and formulation of novel biologics for novel applications. This role is ideal for a detail-oriented and highly collaborative scientist who is excited to work across molecular biology, upstream production, downstream process development, and data organization. You’ll support both the design and execution of protein expression strategies, conduct hands-on bench work to optimize expression conditions and downstream formulations, and maintain rigorous experimental documentation. This position also emphasizes scientific communication and presentation within an industry setting, offering the opportunity to contribute to both foundational and applied research.

Key Responsibilities

• Molecular Biology
  
  
  
  • Perform traditional cloning techniques including Gibson Assembly, In-fusion, site-directed mutagenesis, etc.
  
  
  • Support in silico construct design and vector optimization
  
  
  • Maintain, transform, and prepare plasmids for various downstream workflows
  
  
  
  


• Protein Expression & Research-Scale Production
  
  
  
  • Screen and optimize expression conditions (e.g. temperature, induction system, media) in bacterial systems.
  
  
  • Conduct upstream research-scale fermentation to support recombinant protein production.
  
  
  • Collaborate in designing scale-up experiments and troubleshooting expression challenges
  
  
  
  


• Downstream Process Development
  
  
  
  • Test and optimize downstream processing methods
  
  
  • Optimize formulation conditions to enhance stability and activity across various storage and use environments.
  
  
  • Assess the functional performance of downstream materials through relevant stability and compatibility assays.
  
  
  
  


• Scientific Operations and Communication
  
  
  
  • Maintain detailed and organized electronic lab notebooks (ELN).
  
  
  • Support scientific presentations and internal knowledge sharing in team meetings.
  
  
  • Participate in experimental planning and note-taking for cross-functional projects
  
  
  
  

Who you are

• Entrepreneurial scientist: You are a visionary scientist with a passion for innovation and real-world impact. You thrive in fast-paced, dynamic environments where creativity and initiative are essential. You are not just a researcher—you are a builder, eager to pioneer novel scientific discoveries and transform them into practical solutions that address one of the world’s most pressing challenges: water scarcity. You excel at pushing boundaries, questioning conventional wisdom, and finding groundbreaking ways to apply science for meaningful change.


• Relentless Pioneer: You thrive in new and unknown territory – capable of charting comprehensive but actionable plans, executing rapidly and iteratively to make progress, and reliable in delivering decisive readouts on time.


• Team player: You flourish in collaborative work environments with other highly-skilled individuals. You readily celebrate your peers’ victories and support their challenges.


• Effective communicator: You not only understand the science but can convey technical information in a clear, concise, and decisive manner.

Basic Qualifications

• B.S. or M.S. in biochemistry, molecular biology, biological engineering, biotechnology, or related field and 3-5+ years of hands-on industry experience in a biotechnology or pharmaceutical setting.


• Proficiency in:
  
  
  
  • Basic molecular biology techniques: cloning, plasmid prep
  
  
  • Protein expression in bacteria with research-scale production experience
  
  
  • Analytical methods for protein quantification and characterization (e.g. SDS-PAGE, immunoblotting, UV-Vis)
  
  
  • Maintaining ELNs and summarizing experimental findings for technical and non-technical audiences.
  
  
  
  


• Ability to work full-time on-site in our Cambridge, MA labs.


• Strong organizational and communication skills in a fast-paced, team-oriented environment.

Preferred Qualifications

• Experience with downstream biologic formulation screening
  
  
  
  • Evaluating and optimizing buffer conditions or excipients to enhance stability and shelf-life
  
  
  • Perform basic stability testing (e.g. freeze-thaw, accelerated storage, or thermal stress)
  
  
  • Functional testing of biologics post-processing
  
  
  
  


• Prior experience with protein expression in diverse host systems (bacterial, fungal, mammalian)


• A strong understanding of codon optimization strategies and expression vector design.


• Prior experience with protein purification and solubility optimization.

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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please 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.

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.