Senior Scientist, Agentic Systems Pipeline Strategy

Principal Scientist, Agentic Systems for Pipeline Strategy

Cambridge, MA USA

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 ultimately 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…