Principal Scientist, Agentic Systems for Pipeline Strategy

About Pioneering Intelligence

Pioneering Intelligence builds on Flagship Pioneering's legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship's integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

Position Summary

We are seeking a Principal Scientist to join Pioneering Intelligence (PI), a Flagship initiative dedicated to developing AI/ML-powered platforms for transformative applications in life sciences. This role will serve as PI''s in-house expert in clinical and commercial strategy, and will lead the codification of therapeutic pipeline strategy as agentic capabilities: translating the judgment that today lives in the heads of senior strategic and translational leaders into autonomous systems that identify, evaluate, and prioritize opportunities to create new medicines at a level of scale and rigor that humans alone cannot achieve.

This is a senior, hands-on role for a therapeutic strategy or business development leader who has been seriously engaged with AI, using LLMs and agentic tools in their own work and building intuition for what these systems can and cannot do, and wants their next chapter to be one where AI is at the center, not the side. The successful candidate brings deep clinical and commercial pipeline strategy expertise and a real working relationship with frontier AI; PI brings the engineering depth and research environment to take that AI work to the next level.

Although the role sits within PI, the Principal will collaborate extensively with business and strategy analysts across the Flagship ecosystem, ensuring that agentic capabilities are grounded in the real strategic questions driving decisions across the enterprise. Their work will ultimatly impact the whole Flagship ecosystem.

Responsibilities

• Serve as PI''s in-house subject matter expert on clinical and commercial pipeline strategy, embedding domain judgment directly into the AI capabilities PI develops.
• Codify pipeline strategy into agentic systems: taking the implicit frameworks used by senior strategists (how unmet need is assessed, how patient populations are sized and stratified, how clinical and commercial landscapes are weighed) and turning them into agentic workflows that execute autonomously.
• Own the "legitimate patient need" problem end-to-end: define what it means for an agentic tool to identify and value a real, underserved patient need, what a product that addresses it looks like, and build the evaluations, ground-truth sets, and feedback loops that make agent outputs trustworthy enough to inform pipeline decisions.
• Prototype agentic capabilities directly: building prompts, tools, and orchestration logic, and partnering with engineering to harden systems for production use.
• Help set the technical and strategic direction for how agentic capabilities are developed and deployed across pipeline strategy at Flagship and its ecosystem companies.
• Collaborate closely with business and strategy analysts across the ecosystem translating their strategic questions into agent specifications and translating emerging agent capabilities back into strategic possibilities.
• Present progress and findings in research and product development forums.

Qualifications

• PhD or MD (or equivalent doctoral-level training) in a life science, medical, or related discipline.
• Deep domain expertise in clinical and commercial pipeline strategy, drug development, or therapeutic area strategy, with a track record of personally making or directly influencing portfolio and indication-selection decisions.
• Significant translational medicine experience, shepherding post-development candidate assets through IND and Phase 1, with routine engagement across late-stage preclinical, CMC, regulatory, and clinical functions.
• Strong intuition for what constitutes a legitimate patient need versus a commercially convenient framing, and a history of pushing organizations toward the former.
• Familiarity with industry pipeline and competitive intelligence databases (e.g., Clarivate Cortellis, EvaluatePharma, Citeline, GlobalData).
• Meaningful, sustained use of frontier LLMs (e.g., Claude) in your own work. You''ve moved well past casual chat into structured prompting, tool use, and decomposition of complex tasks, and you want your next role to push that practice further.
• Comfort reading and writing code well enough to prototype agentic workflows, working alongside PI''s engineers initially and growing toward independent prototyping. Production-grade engineering is not required.
• Principal-level operating style: high judgment, high autonomy, comfortable framing ambiguous problems and driving them to outcomes.
• Demonstrated ability to collaborate in interdisciplinary teams and communicate complex technical and strategic concepts effectively to senior leadership.
• Excellent analytical and problem-solving skills.

Preferred

• Background in computational biology, bioinformatics, or a quantitative discipline applied to drug development.
• Direct experience building, evaluating, or deploying LLM agents or agentic workflows.
• Fluency in a programming language (e.g., R, python) and experience with version control (e.g., Git) and cloud computing environments (e.g., AWS).
• Track record of translating strategic questions into therapeutic-area or program-level decisions in a biopharma or platform context.
• Middle-management+ experience preferred, including BD-adjacent exposure such as buy-side or sell-side asset evaluations.

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.

At Flagship, we accept impossible missions to enable bigger leaps. Our core 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.

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The salary range for this role is $179,000 - $236,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence''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.