Jobs at Flagship Pioneering

Lead and define antibody discovery strategy, translate somatic genomics outputs into drug discovery programs, drive sequence and format optimization using structure-based and AI approaches, lead cross-functional teams through lead generation to IND nomination, manage external CROs/collaborators, and contribute to corporate strategy and BD.

Lead and define antibody discovery strategy, convert genomics targets into drug discovery programs, direct cross-functional teams through lead generation to IND, design and optimize antibody therapeutics using structure-based and AI/ML approaches, manage external CROs and collaborators, and contribute to corporate strategy and platform build.

Lead business development strategy and deal execution for Flagship portfolio companies. Partner with CEOs and cross-functional teams to identify partners, design partnership concepts and term sheets, conduct outreach, diligence, and structure transactions with pharma, and integrate BD strategy into R&D and corporate planning.

Provide high-level executive support to the Chief Business Development Officer and leadership team: manage complex calendars, coordinate domestic and international travel and expenses, organize meetings and communications with external partners, collaborate with other administrative staff, provide backup EA coverage, run departmental projects, and perform front-office administrative tasks while maintaining discretion and professionalism.

The role involves preparing cryo-EM grids, generating datasets, optimizing workflows, supporting clients, collaborating cross-functionally, and maintaining documentation for molecular structure studies.

The Business Systems Analyst focuses on SharePoint administration, collaboration platform management, workflow automation, user enablement, and continuous improvement to optimize knowledge management processes.

The Senior Analyst, People Analytics will enhance data accuracy and usability across HR processes, manage audits, and deliver operational reporting.

Lead codification of therapeutic pipeline strategy into agentic AI systems, define and validate legitimate patient needs, prototype prompts/tools, collaborate with engineers and strategy teams, and guide deployment of agentic capabilities across Flagship's ecosystem to prioritize and evaluate new medicine opportunities.

Lead translational decision-support using mechanistic models and quantitative analysis across a portfolio. Produce probabilistic predictions with transparent uncertainty, prioritize cross-program insights, prototype modeling approaches, validate AI outputs, and communicate findings to inform high-consequence investment and development decisions.

Lead DMPK and bioanalytical strategy across nonclinical and clinical programs, design and oversee PK/PK-PD studies, and develop/validate bioanalytical assays. Manage CROs and external labs, support toxicology programs, author regulatory nonclinical sections, present data to stakeholders, and lead a team within cross-functional research leadership.

Provide high-level administrative support to a Flagship executive: manage complex calendars, coordinate meetings and communications, organize worldwide travel and expenses, support projects that advance departmental priorities, collaborate with other administrative staff, and provide backup coverage as needed. Maintain discretion, strong organization, and effective written and verbal communication.

Lead FL110's scientific strategy and multidisciplinary teams to develop a nanopore-based protein reading platform. Define roadmaps, set technical milestones, manage cross-functional integration, mitigate technical risks, build external partnerships, contribute to IP strategy, and recruit and develop scientific talent to translate research into scalable products.

Support commercial assessments and competitive intelligence for biotech pipeline engagements. Build models, conduct competitive landscape analyses, develop reusable frameworks and AI-enabled tools, present findings to senior leadership, and manage end-to-end workstreams to inform investment-grade recommendations.

Lead design and ownership of an agentic orchestration platform for long-running, multi-agent scientific workflows. Architect durable, event-driven, cloud-native systems, define SDKs/APIs, deliver IaC reference implementations, optimize cost and scalability, set platform standards, and partner across modeling and product teams while mentoring engineers.

Lead creative direction and produce ready-to-run advertising assets across formats and audiences. Translate science into compelling messaging and visuals, iterate on A/B test variations, and prioritize concepts for market testing while partnering with the team. Part-time, remote contractor role (~10 hours/week).

The Senior Counsel will manage structuring and negotiating complex pharmaceutical licensing agreements, providing strategic legal support across various teams, and staying informed on industry trends. This includes leading negotiations and advising on legal compliance, while managing outside counsel.

Join our team to develop and deploy AI solutions that integrate AI, physics, and hardware for molecular biology advancements.

Lead the company's finance function—oversee accounting, GAAP financial reporting, audits, budgeting, cash management, R&D expense tracking, and compliance. Drive long-range planning, scenario modeling, fundraising support, implementation of scalable finance systems, manage external vendors, and deploy AI/automation to improve finance operations.

Serve as VP HR Business Partner for Flagship Labs (≈110 people). Lead HRBP team, shape talent strategy, org design, change management, performance, development, employee engagement, and partnering with TA and Talent Development to align HR solutions with business goals.

Lead and scale Metaphore's AI/ML platform for de novo protein and therapeutic design. Define strategy, build and mentor a computational team, deploy generative models and ML‑ops at scale, integrate high‑throughput assay data into the LDBT loop, and drive candidate discovery and external collaborations to advance programs to nomination.