Principal Scientist, AI-Driven Pipeline Strategy

Flagship Pioneering; Cambridge (MA); On-site; USD 179,000 - 236,000; Full time

Job summary

Flagship Pioneering in Cambridge, MA seeks a Principal Scientist to lead agentic, AI/ML‑powered pipeline strategy for transformative life‑science applications. You will codify strategy into autonomous systems that translate expert judgment into scalable opportunities, working with PI and Flagship engineers to scale capabilities.

The ideal candidate combines deep clinical/commercial pipeline expertise with hands‑on AI and prototyping experience, guiding strategy across ecosystem partners while

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.
• Significant translational medicine experience with IND and Phase 1 exposure; collaboration across late‑stage preclinical, CMC, regulatory, and clinical functions.
• Strong judgment distinguishing legitimate patient need from commercially convenient framing.
• Familiarity with industry databases (Clarivate Cortellis, EvaluatePharma, Citeline, GlobalData).
• Meaningful use of frontier LLMs in passing from chat into structured prompting and tool use.
• Comfort reading/writing code to prototype agentic workflows; production-grade engineering not required.
• Principal‑level operating style with high autonomy and clear outcomes.

Responsibilities

• Serve as PI's in‑house expert on clinical and commercial pipeline strategy, embedding judgment into AI capabilities.
• Codify pipeline strategy into agentic systems and autonomous workflows.
• Own the legitimate patient need problem end‑to‑end and define product concepts for agentic tools.
• Prototype agentic capabilities: prompts, tools, orchestration logic; partner with engineers for production readiness.
• Set technical and strategic direction for agentic capabilities across Flagship and ecosystem companies.
• Collaborate with analysts to translate strategic questions into agent specs and return insights to leadership.
• Present progress and findings in research and product development forums.

Skills

Pipeline strategy

Translational medicine

AI/ML in life sciences

Prototyping agentic workflows

Cross-disciplinary collaboration

Senior leadership communication

Analytical problem-solving

Education

PhD or MD (or equivalent)

Tools

Clarivate Cortellis

EvaluatePharma

Citeline

GlobalData

Python

Git

AWS

Job description

Flagship Pioneering in Cambridge, MA seeks a Principal Scientist to lead agentic, AI/ML‑powered pipeline strategy for transformative life‑science applications. You will codify strategy into autonomous systems that translate expert judgment into scalable opportunities, working with PI and Flagship engineers to scale capabilities.

The ideal candidate combines deep clinical/commercial pipeline expertise with hands‑on AI and prototyping experience, guiding strategy across ecosystem partners while