Jobs at Flagship Pioneering

Design, build, fine-tune, deploy, and monitor production machine learning systems focused on LLMs, RAG, agentic orchestration, and multimodal data. Own the full ML lifecycle, establish MLOps practices, guide architecture and technical standards, and collaborate with data engineering, product, scientists, and domain experts. Translate scientific and product requirements into reliable, scalable ML solutions while communicating technical tradeoffs to diverse stakeholders.

Lead the experience vision and architecture for an AI-native platform serving scientists. Design and ship end-to-end scientific workflows, define interactions with AI agents, build a coded design system, and guide AI-assisted design and development practices. Partner with product managers, engineers, ML researchers, computational biologists, and scientific users while communicating strategy to leadership. The role combines design strategy, hands-on prototyping, production UI, research, implementation partnership, and QA ownership.

Collaborate with scientific teams to identify high-impact AI opportunities, define future-backward implementation plans, assess data needs, and build and evaluate machine learning solutions. The intern will use scalable GPU resources, develop benchmarks, iterate across model approaches and scientific domains, and produce comprehensive analyses supporting new company creation.

Manage international patent portfolios and dockets, coordinate patent filings and formalities, monitor deadlines and procedural requirements, maintain ownership and filing records, prepare reporting documentation, and communicate with attorneys, inventors, vendors, and foreign associates. The role also includes mentoring junior staff, supporting diligence and transactions, maintaining data quality, and improving IP operations and workflows.

Build and scale programmable data infrastructure supporting Vesalius Therapeutics’ human cellular biology platform. The role contributes to large-scale genetics, genomics, stem cell, cellular phenotyping, and artificial intelligence initiatives designed to uncover causal biology and identify therapeutic intervention points.

Owns FL113’s initial commercial and go-to-market motion, from prospecting and customer discovery through pilot scoping, negotiations, deployment, and conversion to enterprise agreements. Targets biopharma, health systems, ACOs, and payers; develops pricing, packaging, positioning, and partnership strategies; and builds repeatable sales infrastructure, including CRM, pipeline reporting, deal reviews, and playbooks. Partners with clinical, product, data science, security, privacy, legal, and finance stakeholders to translate customer needs into commercial growth.

Own and extend production automation for Microsoft 365 and Entra ID across a complex multi-company tenant. Maintain identity lifecycle processes, Exchange Online and SharePoint Online automation, integrations, access governance, authentication, monitoring, and CI/CD practices. Troubleshoot and refactor existing code, support organizational lifecycle events, improve security and reliability, document solutions, and serve as a senior escalation point while mentoring peers.

Build and operate secure AWS backend systems, healthcare data pipelines, and EHR integrations that transform partner data into model-ready results. Develop FHIR integrations, AI-assisted onboarding tools, infrastructure, CI/CD, monitoring, and production ML operations while supporting product and full-stack needs. Lead partner technical go-lives, establish engineering standards, mentor future engineers, and collaborate with data scientists, clinicians, and IT teams while protecting PHI.

The Associate Director, Accounting will build and lead ProFound Therapeutics’ accounting function, overseeing close, U.S. GAAP reporting, technical accounting, controls, audit readiness, NetSuite OneWorld, tax coordination, treasury support, and outsourced providers. The role will establish scalable policies, systems, and processes; manage collaboration, licensing, grant, equity, debt, and R&D accounting; support financing and board reporting; and develop the accounting team and automation roadmap.

Design, build, and own scalable data infrastructure for proteomics research and machine learning. Responsibilities include developing production data platforms and pipelines, integrating instruments and LIMS, creating cloud infrastructure with infrastructure-as-code and CI/CD, ensuring data integrity and lineage, and transforming raw experimental data into reliable ML-ready datasets. The role partners closely with scientific teams, establishes engineering standards, sets technical direction, and mentors colleagues.

Lead product strategy and execution for Iris Chat, an AI-powered psychological fitness product. Own product vision, customer journeys, activation, retention, conversion, subscription value, experimentation, and AI quality. Manage product, design, engineering, and AI research teams; hire and develop leaders; balance research and delivery; and establish standards for evaluation, privacy, safety, reliability, and user trust. Partner with leadership to build a focused roadmap and durable consumer business.

Develop evolutionary algorithms for autonomous scientific discovery, enabling populations of models, hypotheses, programs, and representations to evolve through iterative search, selection, evaluation, and recombination. Build Bayesian and probabilistic methods for candidate ranking, uncertainty estimation, diversity preservation, and quality measurement. Establish benchmarks, integrate algorithms into autonomous-science pipelines, publish research, guide technical direction, and mentor colleagues as a senior individual contributor.

Lead full‑stack development of customer‑facing features, own product lifecycle from design to release, build scalable AI‑enabled back‑end systems on AWS, improve CI/CD and testing, collaborate with product, design, and ML researchers, and ensure security and privacy best practices.

Own international accounting, compliance, financial close, statutory reporting, audits, tax filings, consolidations, and intercompany transactions for multiple subsidiaries. Manage outsourced providers, support UK equity compensation and international billing, coordinate new entity setup, and oversee financial reporting for a government contracting entity. Partner with Legal, HR, Treasury, Tax, Compensation, portfolio companies, auditors, and government-contracting advisors across jurisdictions.

Leads the design, implementation, and optimization of cloud-native data infrastructure, platforms, storage solutions, and complex data pipelines. Establishes engineering standards for testing, monitoring, releases, and reliability; troubleshoots cross-system failures and leads incident reviews. Partners with infrastructure, laboratory IT, data science, bioinformatics, and scientific teams to deliver secure, scalable solutions. Mentors engineers, guides technical initiatives, and uses generative AI to accelerate development and data transformation.

Build and operationalize Flagship Pioneering’s compliance program for government contracts, grants, fund operations, and international activities. Responsibilities include developing policies, controls, training, monitoring, reporting, remediation, regulatory assessments, investor and conflicts compliance, escalation processes, and global standards. The role partners with Finance, Contracts, outside advisors, and portfolio companies while transitioning compliance capabilities in-house and applying AI legal tools to improve efficiency.

Develop and execute internal communications strategies across Flagship’s ecosystem of 40+ companies. Create content for intranet, newsletters, email, messaging platforms, digital signage, executive communications, and events. Manage editorial calendars, campaigns, governance, and communication analytics while partnering with leadership, HR, and functional teams. Support employee engagement, onboarding, culture-building, change management, and crisis communications through clear, compelling storytelling and strategic guidance.

Transactions Counsel supporting venture financings, capital markets, M&A, corporate governance, equity issuances, partnerships, and other complex transactions across Flagship’s portfolio companies. Responsibilities include drafting and negotiating transaction documents, conducting legal research, advising finance and portfolio teams, managing outside counsel, supporting compliance, standardizing legal processes, and driving multiple high-volume deals to completion.

The Operating Principal will lead operations and strategy in biotech firms, focusing on corporate development, team management, and aligning scientific goals with business objectives.

Lead the scientific direction and machine learning development for climate modeling. Manage model training, evaluation, and collaboration across teams to develop predictive systems based on hydrology and climate data.