---
title: 'Sr. Director, Clinical Operations at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/sr-director-clinical-operations-flagship-pioneering-inc-somerville-ma-enbcsd3aqgxk'
type: 'job'
last_seen: '2026-09-25'
---

# Sr. Director, Clinical Operations at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Somerville MA, United States
- **Posted:** 2026-09-24
- **Last confirmed live:** 2026-09-25
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8830615002?gh_jid=8830615002

## Job description

Company Summary

Metaphore Biotechnologies, Inc. is a privately held biotechnology company building the next generation of biological therapeutics. Inspired by nature, our mission is to transform patient lives by unlocking the power of biological therapeutics with a new proprietary discovery platform. Metaphore’s platform brings together live-cell experimentation and AI/ML to understand how biological mechanisms drive functional outcomes in living systems. By capturing these mechanism-function relationships, Metaphore aims to design antibody medicines with intended activity from the start.

Position Summary

Metaphore Biotechnologies is seeking a Senior Director of Clinical Operations to lead the hands-on execution of early clinical development activities for the company’s first-in-human program. Reporting to the Chief Medical Officer, this is a senior individual-contributor role with broad ownership and visibility across the organization.

This individual will own clinical operational planning and study execution encompassing CROs and vendor management, site strategy, protocol feasibility, regulatory coordination, and global study start-up, with particular focus on Phase 1 readiness and execution. The successful candidate will be highly operational, able to ramp quickly, and comfortable establishing fit-for-purpose capabilities while working across internal teams, external partners, and consultants to move studies forward with urgency and rigor.

## Key Responsibilities

- Lead clinical operations planning and execution for early development programs, with primary accountability for first-in-human study readiness, global start-up, and delivery against key milestones.
- Develop and maintain integrated study plans, timelines, budgets, forecasts, resource requirements, and risk-mitigation strategies aligned with clinical and corporate objectives.
- Lead CRO and vendor selection and oversight, including requests for proposals, bid evaluations, scope-of-work development, budget negotiations, change-order management, performance monitoring, and issue escalation.
- Partner with Clinical Development and Medical leadership to evaluate protocols, study designs, operational feasibility, and start-up requirements.
- Represent Clinical Operations on cross-functional study and program teams, partnering with other relevant functions internally and externally (e.g., Clinical Development, Regulatory, Safety, Clinical Pharmacology, Data Management, Biostatistics, Bioanalytical, CMC, Quality, and clinical supply colleagues).
- Develop and execute the Phase 1 site strategy, including the identification, qualification, activation, and ongoing management of sites with appropriate participant access, clinical pharmacology capabilities, bioanalytical infrastructure, and operational experience.
- Lead global clinical operations activities across the U.S., Europe, Australia, and other ex-U.S. regions, accounting for applicable regulatory, ethics, site, laboratory, vendor, and country-specific start-up requirements.
- Contribute to operational planning for potential studies in China and coordinate with internal and external experts to support regional requirements.
- Establish an effective operating cadence with CROs, sites, vendors, consultants, and functional partners to track deliverables, timelines, budgets, quality metrics, risks, and escalation paths.
- Oversee the development and maintenance of study-level operational documentation, including monitoring, communication, enrollment, vendor-oversight, and risk-management plans.
- Partner with CMC and clinical supply stakeholders to support investigational product packaging, labeling, distribution, accountability, and site readiness.
- Ensure clinical studies are conducted in accordance with the protocol, ICH-GCP, applicable regulatory requirements, internal procedures, and established quality standards.
- Maintain inspection-ready clinical trial documentation and oversee the completeness, quality, and timeliness of the Trial Master File.
- Identify operational risks early and implement mitigation and contingency plans related to timelines, sites, enrollment, vendors, clinical supply, and data delivery.
- Establish scalable, fit-for-purpose clinical operations processes, systems, SOPs, and governance practices appropriate for a growing biotechnology company.
- Provide clear and timely updates on study status, timelines, budgets, risks, and mitigation plans to the CMO, clinical leadership, and other key stakeholders.

Required Qualifications

- BS/MS/PhD degree in a scientific, healthcare, or related discipline; an advanced degree is preferred.
- 10+ years of progressive clinical operations experience in the biotechnology or pharmaceutical industry.
- Direct experience leading first-in-human or Phase 1 studies from operational planning and vendor selection through regulatory and ethics submissions, site activation, first-participant-in, and ongoing execution.
- Strong working knowledge of CRO and vendor selection and oversight, site strategy, global study start-up, and operational planning.
- Demonstrated experience managing study budgets, vendor contracts, scopes of work, change orders, timelines, and forecasts.
- Experience reviewing clinical protocols and translating study designs into executable operational plans.
- Experience supporting clinical pharmacology/DMPK, including dose-escalation, SAD/MAD, biomarker, or other early-phase study designs, as applicable.
- Experience conducting studies involving [healthy volunteers/specific patient population-to be completed based on the planned first-in-human study].
- Broad understanding of FDA, EU, and other ex-U.S. clinical trial requirements.
- Strong knowledge of ICH-GCP, sponsor oversight responsibilities, TMF requirements, clinical quality standards, and inspection readiness.
- Ability to operate independently and influence without direct authority in a fast-paced environment with limited infrastructure and high levels of ambiguity.
- Strong communication and cross-functional collaboration skills, with the ability to manage internal stakeholders, external vendors, and consultants effectively.
- Ability and willingness to travel domestically and internationally, as needed.

## Preferred Qualifications

- Experience in both biotechnology and pharmaceutical company environments, with exposure to the broader clinical development lifecycle.
- Direct experience initiating and executing early-phase studies in Australia, including familiarity with local regulatory, ethics, site, and vendor pathways.
- Experience with China regulatory and clinical operations pathways.
- Experience in antibody therapeutics, biologics, or other advanced therapeutic development programs.
- Experience operationalizing biomarker, immunogenicity, pharmacokinetic, pharmacodynamic, or other specialized sample-collection and bioanalytical strategies within early-phase studies.
- Experience establishing clinical operations infrastructure, processes, systems, and external partnerships within an organization entering the clinic for the first time.

Values and Behaviors

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort 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 candidate.

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.

The salary range for this role is $213,000 - $280,000. 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)

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