---
title: 'Senior Scientist, Protein Engineering at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/senior-scientist-protein-engineering-flagship-pioneering-inc-cambridge-emxcvtea75rw'
type: 'job'
last_seen: '2026-09-11'
---

# Senior Scientist, Protein Engineering at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-09-08
- **Last confirmed live:** 2026-09-11
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8784082002?gh_jid=8784082002

## Job description

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering. This is a hands-on role with substantial ownership for a scientist who is excited to set technical direction from day one and, over time, help build the team.

Position Summary:

We are seeking a motivated and highly collaborative Senior Scientist to join FL129’s growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have a strong track record of scientific and technical innovation in the design, construction, and functional interrogation of large protein variant libraries, including deep mutational scanning and related library-scale methods. Deep experience with protein display systems, high-throughput sorting, and sequencing-based readouts is essential, and familiarity with bioinformatic analysis of variant-level data is strongly desired. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment.

Key Responsibilities:

- Technology development, aligned with FL129’s core strategic goals. This role is among the first hires, and we’re looking for someone who thinks critically and will influence the company’s scientific direction.
- Design, construction, and experimental testing of large-scale protein variant libraries, including deep mutational scanning and related saturation mutagenesis approaches
- Establish and optimize display, selection, and sorting workflows that link protein genotype to measured phenotype
- Assess library quality and variant coverage, and validate library outputs by biochemical and biophysical characterization of purified proteins
- Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
- Ensuring rapid and accurate turnaround of data to drive achievement of key project goals.
- Translate experimental data into meaningful insights and present results at team meetings.

Preferred Qualifications:

- Ph.D. in molecular biology, biochemistry, protein engineering, or a similar field with 5+ years of industry or postdoctoral experience.
- End-to-end experience with deep mutational scanning or related library-scale mutagenesis methods, from variant library design and construction through selection, sequencing, and variant-level data analysis.
- Hands-on expertise in library-scale molecular cloning, including site-saturation or degenerate-codon mutagenesis, high-efficiency transformation, and managing library complexity, variant coverage, and bottlenecking.
- Experience with protein display systems that link genotype to phenotype, such as yeast surface display (YSD), mammalian display, or phage display.
- Experience with fluorescence-activated cell sorting (FACS), including selection strategy and sort-gate design for quantitative variant enrichment.
- Experience with next-generation sequencing (NGS) technologies (Illumina and PacBio), including amplicon sequencing and long-read approaches for variant–barcode linkage, and ideally single-cell sequencing technologies.
- Experience with protein expression and purification, and with biochemical/biophysical assay development to quality-control library inputs and quantitate the bioactivity of library outputs.
- Nice to have: experience with machine learning methods for protein engineering, or with statistical analysis of variant fitness landscapes.
- Motivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills.

What we can offer you:

- Opportunity to lay the scientific foundation of a transformative platform company as an early employee.
- Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
- Weekly lunches, monthly social events, and community lunchroom with free snacks, coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.

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. 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

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.

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL129 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL129's 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)

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