Jobs at Flagship Pioneering

Provide high-quality administrative and operational support to the Chief Scientific Officer and research leadership. Manage calendars, meetings, travel and expense reporting, prepare materials, plan events, coordinate visitors, troubleshoot minor IT issues, support office/lab moves, and assist with department communications and special projects.

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 Neuromorphic Systems Architect will design next-gen hardware architectures inspired by neuroscience, focusing on nonlinear dynamics and computational principles for intelligent systems.

Lead operational oversight and continuous improvement for enterprise applications and MSPs. Own incident/change management, SLAs, KPIs, runbooks, knowledge management, license governance, and application implementations. Partner with BRMs and IT leadership to standardize processes, automate routine operations (e.g., Workato), mentor junior staff, and mature application support, vendor governance, and service delivery frameworks.

Provide legal leadership on complex life-sciences transactions across licensing, collaborations, partnerships, joint ventures, M&A, and capital activities. Structure and negotiate deals, counsel senior stakeholders, manage external counsel, standardize playbooks and templates, and manage multiple concurrent transactions while monitoring industry and regulatory developments.

Provide transactional legal counsel across venture financings, capital markets, M&A, licensing, and corporate governance for Flagship and its portfolio. Draft, review, and negotiate financing and governance documents, manage external counsel, support finance and portfolio teams, conduct legal research, standardize processes, and drive deals to closure in a fast-paced, high-volume environment.

Lead ideation and vetting of novel life‑science venture hypotheses, design experiments, assess IP, recruit KOLs and early teams, develop company strategy and operations, and operationalize new company formation in partnership with Flagship stakeholders.

Lead end-to-end accounting and finance for early-stage biotech portfolio companies: manage monthly close, GAAP compliance, budgeting, cash runway forecasting, audits, controls, treasury, ERP systems, and board-level reporting while scaling finance functions.

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.

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 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 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 and build a computational sciences team to develop algorithms, ML models, and scalable data infrastructure for nanopore-based protein reading. Partner with experimental teams to design analyses, implement ML pipelines, manage cloud infrastructure, establish reproducible data practices, protect IP, and communicate progress to leadership and external partners.

Develop computational methods to process and interpret nanopore and electrophysiology data. Build event-detection, classification, and fingerprinting pipelines; create quantitative models linking signals to molecular identity; collaborate with experimental teams and ML, protein, and signal-processing groups; establish benchmarking and uncertainty quantification practices.

Lead design, fabrication, and optimization of MEMS sensor components and nanoscale structures. Develop cleanroom process flows (photolithography, PVD/CVD/ALD, RIE/DRIE), design masks, perform metrology and failure analysis, integrate devices with PCB, packaging and fluidic/bio-interfaces, transfer processes to foundries, and contribute to IP and technical strategy.

Lead and deliver AI/ML and computational projects that accelerate pharmaceutical R&D across preclinical-to-clinical stages. Build, scale, benchmark, and maintain agentic systems combining ML and computational biology tools; manage cross-functional teams; drive strategy, resourcing, best practices, and stakeholder communication across ventures and platform partners.

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.

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 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.