---
title: 'VP, Program Management & Business Operations at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/vp-program-management-business-operations-flagship-pioneering-inc-cambridge-emajvwk90431'
type: 'job'
last_seen: '2026-10-16'
---

# VP, Program Management & Business Operations at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-05-05
- **Last confirmed live:** 2026-10-16
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8520490002?gh_jid=8520490002

## Job description

## About Alltrna

Alltrna is the first clinical-stage biotech company advancing tRNA medicines to address shared disease-causing mutations across many indications. The company’s initial therapeutic programs are designed to restore full-length protein production in diseases caused by premature termination codons (PTCs), collectively referred to as Stop Codon Disease, which affect approximately 10% of people with a rare genetic disease.

Alltrna’s lead program, AP003, is a chemically modified, engineered tRNA oligonucleotide encapsulated in a clinically validated, liver-directed lipid nanoparticle. AP003 is being developed for the arginine-to-TGA (Arg-TGA) PTC in patients with liver Stop Codon Disease, including phenylketonuria, organic acidemias, and urea cycle disorders. Founded in 2018 by Flagship Pioneering, Alltrna has built an integrated platform to design, optimize, and deliver engineered tRNA therapeutics.

For more information, visithttps://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.alltrna.com%2F&data=05%7C02%7Csmendoza%40fsplabs.com%7Cdc3e9b7de1f74107ed9108dea14e646f%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C639125555247974459%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=JTaLIUO3RToNNIjhBkjAenPZ1SawJ6aftwUTzBBTr6I%3D&reserved=0[www.alltrna.com](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.alltrna.com%2F&data=05%7C02%7Csmendoza%40fsplabs.com%7Cdc3e9b7de1f74107ed9108dea14e646f%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C639125555248012066%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7Lv0pX7IYbl58Qj5Tp19fbuvjze03N6QD9CxAjQweug%3D&reserved=0)

VP, Director Program Management & Business Operations

Position Summary:

Alltrna is seeking a talented and highly motivated VP, Director Program Management and Business Operations, reporting to the President & CFO.  The successful candidate is a proven leader with extensive experience in leading research and early drug development program teams from research through the clinic with a particular initial focus on IND enabling and early/mid-stage clinical development. The candidate will be a member of the Company’s Leadership Team and will serve as Chief of Staff to the team to drive collaboration, cross-functional clarity, alignment and execution on key priorities and initiatives required to meet the goals of the organization.

Key Responsibilities:

Program Management:

- Work closely with the Chief Medical Officer to lead the program team for the Company’s lead program, AP003, and future programs instilling a culture of scientific rigor, open debate, collaborative teamwork, sense of urgency and accountability
- Possess a comprehensive understanding of the drug discovery process to guide program teams to define the key scientific questions, program strategy and objectives, translating these into optimal deliverables, cross-functional plans, timelines and budgets
- Identify bottlenecks, risks, issues and proactively develop appropriate mitigation proposals with input from team members
- Ensure all key decisions are identified and properly assessed as to their impact and alternative scenarios developed and evaluated, where appropriate
- Work closely with finance and functional teams to develop the operational plans to support program activities with realistic timelines, budget, and resource planning and monitor performance against plans
- Interface with and drive collaboration between the various functional teams and with the Leadership Team on program-related matters.
- Be the key accountable person for communicating matters related to the programs to management including strategy, work product, updates and issues; producing the one “source of truth” for program-related topics and timelines
- Point person for alliance management and coordination, as needed
- Lead and/or manage strategic or platform development projects as required and collaborate with Chief Scientific Officer and Research Leadership Team to coordinate relevant content for quarterly business review meetings

Operations:

- Collaborate with Leadership Team in development of strategic plans, company goals, long-range planning assumptions, portfolio-level reports and analyses to support business processes and strategic discussions
- Develop and deliver impactful presentations that effectively distill complex issues to the critical points and lead to increased understanding and optimized strategic planning & decision-making
- Prepare strategic communications utilizing a clear understanding of the business strategy and issues; develop and maintain consistent, relevant content for use in executive-level communications and to further organizational and business goals
- Lead the Scientific Communications process, working with the Scientific Communications Committee
- Manage schedule, agenda, and content for Leadership Team, Board of Directors and Town Hall meetings
- Proactively seek opportunities for organizational improvements (e.g. team structure, processes, communication, etc.)

Other:

- Support CEO / LT with partnership discussions and negotiations, including background research, preparation of presentation materials, supporting diligence activities, participating in analysis of terms, etc.
- Assist in mapping competitive landscape and proactively identify potential and emerging competitive threats and opportunities
- Promote strategic discussions on external trends, competitor strategies, and potential disruptors, and translate these into strategic choices/ recommendations
- Collect insights and intelligence from a variety of sources including literature searches, reviewing analyst research, KOL and patient group interactions, etc.

Key Competencies:

- This is a highly visible leadership role that requires exceptional interpersonal and communication skills, creative thinking, and early drug development experience that allows one to recognize opportunities/challenges and modify strategy accordingly
- The individual will need to have self-confidence and poise to manage complicated programs and projects with multiple stakeholders
- The individual will need a sense of urgency and can-do attitude to develop therapies for patients with significant unmet medical needs

Minimum Qualifications:

- BS/MS Degree in a scientific discipline, ideally life science or chemistry.
- At least 15 years relevant experience in pharma or biotech drug discovery and development, as well as a comprehensive understanding of drug discovery (preclinical and clinical).
- 10+ years of Program Management experience, preferably in early-stage drug discovery and development.
- Experience in the development of advanced therapies to treat rare genetic disease is a plus
- Demonstrated experience leading cross-functional teams; strong interpersonal and communication skills
- Scientific curiosity and passion for discovering new, innovative medicines.
- Openness to embrace new technologies and digital approaches in drug discovery
- Proven track record in driving successful, collaborative drug discovery teams.

The salary range for this role is $250,000 - $330,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Alltrna currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Alltrna'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.

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- [Research Associate II, Protein Sciences](https://feeny.ai/job/research-associate-ii-protein-sciences-flagship-pioneering-inc-cambridge-zeexx76bhczw) — 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
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