---
title: 'Sr. Scientist, Protein & Cell Sciences at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/sr-scientist-protein-cell-sciences-flagship-pioneering-inc-somerville-ma-qpeg3dfcafh3'
type: 'job'
last_seen: '2026-11-06'
---

# Sr. Scientist, Protein & Cell Sciences at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Somerville MA, United States
- **Posted:** 2026-11-04
- **Last confirmed live:** 2026-11-06
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8924950002?gh_jid=8924950002

## Job description

Sr. Scientist, Protein & Cell Sciences

Metaphore Bio is a generative AI drug design company creating a new class of functional antibodies. We are seeking an accomplished protein scientist and leader to run and continually optimize the engine that turns computationally designed antibodies into well-characterized, developable therapeutic proteins. This is a rare opportunity to pair deep protein biochemistry and antibody purification expertise with a first-in-class AI platform — and to shape how a new modality moves from sequence to drug candidate.

Position Summary:

Metaphore Biotechnologies is seeking a highly motivated Sr. Scientist to join our Protein Sciences team within Research and Discovery. This role will focus on protein expression, purification, and analytical characterization in support of platform development and therapeutic discovery programs. The ideal candidate will bring strong hands-on experience with mammalian expression systems, protein biochemistry, and assay development, along with the ability to work independently and collaborate effectively across a multidisciplinary team.

Key Responsibilities:

- Design and execute workflows for recombinant protein production, including transient mammalian expression, purification, and quality assessment.
- Contribute to the design, execution, and troubleshooting of experiments that improve throughput, reproducibility, and data quality.
- Partner closely with Antibody Discovery, Antibody Engineering, Computational Biology, and other cross-functional teams to support integrated project execution.
- Serve as a mentor to junior team members and a subject matter expert within the company in the areas of recombinant production and protein stability metrics.
- Establish and maintain strong documentation practices, experimental rigor, and reproducible workflows.
- Prepare study reports, summarize data, and present results clearly to internal stakeholders.
- Support continuous improvement of lab operations, including the adoption of new methods, tools, and workflows as needed.

Required Qualifications:

- PhD (or BS/MS degree with equivalent level of experience) in protein biochemistry, molecular biology, chemical engineering, structural biology, analytical chemistry, or a related field with 5+ years of industry experience.
- Experience in protein production, purification, and analytical characterization in a biotechnology or pharmaceutical setting responsible for regular production of milligram to grams of material on a reoccurring weekly basis.
- Strong hands-on experience with mammalian cell culture and transient transfection.
- Proficiency with protein purification systems (FPLCs and Autosamplers) and analytical systems (UHPLCs) used to assess protein quality and function.
- Experience with biophysical characterization methods such as BLI, SPR, DSF, DLS, or related approaches.
- Demonstrated ability to design, troubleshoot, and optimize experiments independently.
- Strong organizational skills, scientific rigor, and written and verbal communication skills and a record of establishing robust systems
- Ability to work effectively in a fast-paced, collaborative, cross-functional environment.

Preferred Qualifications:

- Experience with antibody discovery workflows and biologics development.
- Experience with automated multi-step midscale purification.
- Experience with production from linear DNA templates.
- Experience with bi and multi specific antibody formats.
- Experience managing direct reports or mentoring junior scientists.
- Familiarity with data capture systems and structured documentation practices.
- Exposure to assay development and validation for discovery or translational applications.

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. Metaphore Biotechnologies, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Metaphore Biotechnologies, Inc.'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)

## Other roles at Flagship Pioneering, Inc.

- [Senior Research Associate / Associate Scientist, Nonclinical](https://feeny.ai/job/senior-research-associate-associate-scientist-nonclinical-flagship-pioneering-kpyk97evc5j0) — Cambridge, MA
- [Senior Analog/Mixed-Signal Hardware Engineer, Single-Molecule Sensing Instrumentation](https://feeny.ai/job/senior-analog-mixed-signal-hardware-engineer-single-molecule-sensing-jngdq7cygjxb) — Cambridge, MA
- [FL114: Senior Research Associate, Genomics](https://feeny.ai/job/fl114-senior-research-associate-genomics-flagship-pioneering-inc-cambridge-0q5q7ej897wv) — Cambridge, MA
- [FL114: Scientist, Genomics](https://feeny.ai/job/fl114-scientist-genomics-flagship-pioneering-inc-cambridge-7y7dcef63454) — Cambridge, MA
- [Senior Director, Platform Experience](https://feeny.ai/job/senior-director-platform-experience-flagship-pioneering-inc-cambridge-cqx7ym4352dv) — Cambridge, MA
- [Principal Scientist, Structural Biology / Protein Biophysics](https://feeny.ai/job/principal-scientist-structural-biology-protein-biophysics-flagship-pioneering-hmdq4s5y31f7) — Cambridge, MA
- [Senior Scientist, LNP Formulations](https://feeny.ai/job/senior-scientist-lnp-formulations-flagship-pioneering-inc-cambridge-ztwykh5vnq98) — Cambridge, MA
- [Flagship Pioneering ML Internship](https://feeny.ai/job/flagship-pioneering-ml-internship-flagship-pioneering-inc-cambridge-dsf2d8q572m7) — Cambridge, MA
- [Research Associate II/Senior Research Associate, LNP Production](https://feeny.ai/job/research-associate-ii-senior-research-associate-lnp-production-flagship-bwk9zn8pyhy8) — Cambridge, MA
- [Senior ML Engineer](https://feeny.ai/job/senior-ml-engineer-flagship-pioneering-inc-cambridge-aexf2nmm2e1x) — Cambridge, MA