---
title: 'Research Associate II, Protein Sciences at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/research-associate-ii-protein-sciences-flagship-pioneering-inc-cambridge-zeexx76bhczw'
type: 'job'
last_seen: '2026-10-16'
---

# Research Associate II, Protein Sciences at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-10-12
- **Last confirmed live:** 2026-10-16
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8882558002?gh_jid=8882558002

## Job description

## COMPANY 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](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.flagshippioneering.com%2F&data=05%7C02%7Cemccurdy%40flagshippioneering.com%7C8e54295c994c4d440a7b08ddc94a4a72%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C638888043086011906%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=gknIK%2BmYfQpsSi0%2FyQmhzNBo4DurYfmbUQpruIKf6Mc%3D&reserved=0).

At Flagship, we accept impossible missions to enable bigger leaps. Our [core values](https://www.flagshippioneering.com/values) guide us through uncertainty and toward lasting impact.

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.

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.

## #LI-TL1

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.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.

## About Flagship Pioneering, Inc.

## Company Overview
- **One-liner**: Flagship Pioneering is a life sciences venture creation firm that conceives, creates, and capitalizes breakthrough bioplatform companies in biotechnology, health, and sustainability.
- **Entity Type**: Private (Venture Creation Firm)
- **Headquarters**: Cambridge, Massachusetts, United States
- **Founded**: 2000
- **Founders**: Noubar Afeyan (Co-Founder & CEO)

## Core Business
- **Primary industry/industries**: Biotechnology Research, Life Sciences Venture Creation, Company Incubation
- **Target customers**: B2B / B2G – partners with academic institutions, pharma companies, and investors; also acts as an employer for scientists, entrepreneurs, and corporate builders
- **Mission or purpose statement**: “To harness the 21st century's most powerful technological forces for good to deliver a better future for all.”

## Products & Services
Flagship does not sell products directly; its offerings are the companies it creates and the innovation platform it operates.
- **Innovation Platform**: A systematic, institutionalized process to identify “unreasonable” scientific questions, test them rigorously, and spin out independent companies that develop therapeutics, diagnostics, agricultural technologies, and more.
- **Portfolio Companies**: Over 120 companies founded, including Moderna, Generate:Biomedicines, Inari Agriculture, Tessera Therapeutics, Lila Sciences, and others. Each is a separate enterprise with its own products (e.g., mRNA vaccines, gene-editing tools, AI-driven drug discovery).

## Market Standing
- **Valuation/Market Cap**: Not publicly disclosed (privately held)
- **Key Metric**: Annual revenue of approximately $800 million (2025/2026 estimate) and 620 employees (+9.7% YoY growth)
- **Notable Investors/Partners**: Flagship is itself an investor and partner; key collaborations include AWS (to accelerate drug discovery), Harvard Medical School, Broad Institute, and multiple top-tier biopharma companies. Portfolio company Moderna is a publicly traded giant.
- **Growth Signals**: 78 active job postings (+50% quarterly), recent formation of Terion (digital agriculture infrastructure) and Serif Biomedicines (modified DNA platform), and expanded presence in Europe and Asia.

## Competitive Advantages
- **Unique Model**: Combines scientific exploration, company creation, and capital investment under one roof – “a way that is largely without precedent”
- **Deep Talent Pool**: Exceptional network of scientist-entrepreneurs and company builders; top hires from MIT, Harvard, Biogen, Novartis, and Pfizer
- **Track Record**: Over two decades of founding transformational companies (e.g., Moderna’s COVID‑19 vaccine), demonstrating repeatable innovation
- **Process-Driven**: Systematic methodology for turning “what‑if” questions into patentable bioplatforms, reducing risk compared to ad‑hoc startup creation

## Strategic Focus
- **Current priorities**: Expanding AI/machine learning integration across drug discovery and life sciences (highlighted by AWS collaboration); entering preemptive health and medicine; advancing sustainable agriculture and climate solutions; growing international operations (UK, Singapore, Canada, Switzerland, Japan)
- **Direction for growth**: Launching new platform companies at a steady cadence (e.g., Terion, Serif in 2026); deepening expertise in computational protein design, modified DNA, and gene editing

## Why Work Here
- **Culture**: “Brave and bold organization of creative-thinkers with insurgent mindsets” – emphasis on fearlessness, mentorship, and teamwork across science and business
- **Work Environment**: Headquarters in Cambridge, MA with 5 US offices; roles span research, strategy, finance, and operations; hybrid/remote flexibility varies by role
- **Notable Perks**: Opportunity to work on world-changing science (e.g., COVID‑19 vaccine, gene editing) alongside top scientists and company builders; strong compensation (salary range example: Sr. Associate ~$68K, ML Engineer ~$122K; overall comp rating 3.7/5)
- **Engineering/Science Culture**: Heavy investment in R&D (15% of workforce in research), cutting-edge tools (Cryo‑EM, AI/ML), and a process that encourages bold leaps

## Sources
1. [flagshippioneering.com](https://www.flagshippioneering.com/)
2. [flagshippioneering.com/about](https://www.flagshippioneering.com/about)
3. [flagshippioneering.com/join](https://www.flagshippioneering.com/join)
4. [flagshippioneering.com/join/roles](https://www.flagshippioneering.com/join/roles)
5. [linkedin.com/company/flagship-pioneering](https://www.linkedin.com/company/flagship-pioneering)

## Other roles at Flagship Pioneering, Inc.

- [Origination Associate](https://feeny.ai/job/origination-associate-flagship-pioneering-inc-cambridge-rezba4m39nft) — Cambridge, MA
- [Scientific Manager – High Throughput Laboratory](https://feeny.ai/job/scientific-manager-high-throughput-laboratory-flagship-pioneering-inc-cambridge-fy1vfg2prvq6) — Cambridge, MA
- [Senior / Principal Data Infrastructure Engineer](https://feeny.ai/job/senior-principal-data-infrastructure-engineer-flagship-pioneering-inc-cambridge-0cve2nw8geq3) — Cambridge, MA
- [Scientist I, In Vitro Pharmacology](https://feeny.ai/job/scientist-i-in-vitro-pharmacology-flagship-pioneering-inc-watertown-ma-0mkf7pjwbjfy) — Watertown MA, United States
- [Senior Scientist, Bioanalytical Sciences](https://feeny.ai/job/senior-scientist-bioanalytical-sciences-flagship-pioneering-inc-cambridge-y3z3svs22m0e) — Cambridge, MA
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- [Research Associate, Protein Production](https://feeny.ai/job/research-associate-protein-production-flagship-pioneering-inc-cambridge-73xj2rtm9ea7) — Cambridge, MA
- [Senior Associate, Origination - Agriculture and Sustainability](https://feeny.ai/job/senior-associate-origination-agriculture-and-sustainability-flagship-pioneering-ba5zat81r1rt) — Cambridge, MA
- [Product Concept Innovation Associate](https://feeny.ai/job/product-concept-innovation-associate-flagship-pioneering-inc-cambridge-a54bzmrcn4zt) — Cambridge, MA
- [Senior Machine Learning Scientist](https://feeny.ai/job/senior-machine-learning-scientist-flagship-pioneering-inc-cambridge-5dbcemqxg7pf) — Cambridge, MA