Jobs at Flagship Pioneering

The Director of Sales will drive customer acquisition and revenue growth, build partnerships, and shape FL109's market development strategies. Responsibilities include managing sales targets, strategic planning, and overseeing external engagement activities.

The Sr. Director, HRBP will drive people strategy for Pioneering Business Units, influencing talent management, leadership, organizational design, employee engagement, and change management, while collaborating with senior management and HR leaders.

Lead execution and analysis of histology and bio-analytics to assess efficacy, safety, and biodistribution of nucleic acid therapeutics. Support in‑vivo studies, develop in‑house CRO capabilities, communicate results, and collaborate in a multidisciplinary team.

Lead month-, quarter-, and year-end close for multiple portfolio companies; prepare journal entries, reconciliations, cash forecasts, and accruals; support audits, funding, equity programs, lease and fixed-asset accounting, system reconciliations and integrations, and cross-functional finance operations.

Perform day-to-day accounting for multiple portfolio companies including reconciliations, AR, and month/quarter/year-end closes. Manage fixed assets, leases, payroll reconciliations, forecasts, and variance analysis. Support audits, statutory filings, tax and investor reporting, system integrations (NetSuite, NSPB, Expensify, Coupa, LeaseQuery), and cross-functional collaboration to improve accounting processes and support company transitions and mergers.

Lead strategy and investment decisions for a BioMedicines R&D portfolio from preclinical through development. Build new R&D programs, create investment cases, run portfolio reviews and scenario planning, evaluate opportunities and risks, and produce executive-level decision materials while collaborating across R&D, Clinical, Regulatory, Finance, Commercial, and venture teams.

Lead DMPK strategy for biologics across discovery and development. Design and interpret PK/BA/immunogenicity studies, support PK/PD modeling, toxicokinetic planning, IND-enabling regulatory submissions, and oversee CRO interactions to advance candidate selection and regulatory readiness.

Lead design, build, and execution of complex DNA libraries and high-throughput screens to enable protein engineering and CAR optimization. Combine in silico protein modeling with wet-lab validation, NGS-based variant tracking, plasmid design, automation of assays, and mentorship of junior scientists while collaborating across R&D and CMC teams.

Lead design, synthesis, purification, and analytical characterization of oligonucleotide-conjugates on antibodies and other modalities. Develop and optimize conjugation protocols, collaborate with assay and cross-functional teams, manage project timelines, maintain lab records, and present results to internal and external stakeholders to advance discovery toward pre-clinical development.

Lead a Protein & Cell Sciences team to deliver high-throughput expression, purification, and biophysical characterization of antibodies. Establish best practices, data management (ELN/LIMS), and automation-enabled workflows; manage CRO/CDMO partnerships, enable CMC handoffs, recruit and mentor staff, and contribute to program strategy and platform optimization to progress discovery candidates toward development.

Develop and apply advanced machine learning models that link chemoproteomics, quantum chemistry, and electronic structure to drive generative molecular design for covalent drug discovery. Build featurization and modeling pipelines, perform data curation and QC, design rigorous benchmarks, partner with medicinal chemistry and engineering teams to productionize workflows, and communicate results across cross-functional teams to support compound design and experimental iteration.

The Principal Scientist/Associate Director will lead analytical development, QC oversight, and ensure compliance across multiple CMC programs, influencing strategy and organizational growth.

This job is an opportunity to submit your resume for future positions at Flagship Pioneering, a leading biotechnology company focused on innovative health solutions.

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.

Manage the lifecycle of commercial agreements, including drafting, negotiating, and executing contracts, while ensuring compliance and streamlining processes across various teams.

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.

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.