Jobs at Flagship Pioneering

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

The Senior Engineer, AI and Automation role involves designing AI-powered systems, maintaining infrastructure, building integrations, and establishing MLOps while collaborating with various teams on enterprise applications.

The Associate Director, AI Operations & Enablement leads AI strategy execution, education, and vendor management to enhance AI adoption and impact across the organization.

Develop and deploy LLM-powered ML applications for psychological wellbeing. Collaborate with psychologists to translate insights into computational systems, advance RLHF and agentic AI methods, build scalable data and training pipelines, integrate ML systems into real-world products, and communicate results to multidisciplinary teams.

The Senior Research Associate will perform histopathological assessments, manage tissue sample workflows, and collaborate on method development for somatic genomics.

The VP of Finance will advise portfolio companies on financial strategy, oversee day-to-day operations, manage cash flow, and prepare financial materials for governance meetings.

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.

The Director of Program Management will drive R&D and corporate initiatives, ensuring alignment with company goals, managing cross-functional projects, and fostering communication among stakeholders.

The Contracts Attorney will draft, negotiate, and manage various contracts, support training on contract processes, advise stakeholders, and coordinate with departments to enhance contract workflows.

Lead design and implementation of talent management, leadership development, and organizational change frameworks. Partner with senior leaders to drive change, build career pathways, and run high-impact OD programs using talent technologies and people analytics. Manage multiple strategic initiatives, communications, and stakeholder alignment to scale organizational capability across the enterprise and portfolio companies.

Lead complex, cross-functional IT initiatives from planning through implementation. Define scope and success metrics, manage schedules, budgets, risks, vendors, and governance. Drive stakeholder alignment, change management, delivery excellence, and mentor project leaders.

Lead ideation, research, and validation of novel venture hypotheses; design experiments, assess IP, recruit KOLs and early teams, and build initial company strategy and operations. Drive lab setup, partnerships, and business development while translating scientific insight into executable plans and transitioning pressure-tested ideas into NewCos alongside senior venture leaders.

The Senior Accountant will manage month-end closes, develop accounting policies, conduct reconciliations, assist with budgets, and ensure compliance with GAAP, providing financial insights and reports.

The Associate Director, Finance will support financial planning, reporting, accounting, and operational finance for Pioneering Medicines, partnering with leadership and teams to provide insights and improve finance processes.

Build and fine-tune deep learning and foundation models for genomics and single-cell/perturbation data, create agentic AI workflows and LLM-assisted tools, model genotype–phenotype and causal relationships, collaborate with scientists and engineers, and communicate model results and limitations.

Supports executive search and talent acquisition operations across Flagship Pioneering and its portfolio companies. Responsibilities include coordinating searches, maintaining candidate data in Greenhouse, creating recruiting templates and documentation, preparing reports and dashboards, using AI-enabled tools to improve workflows, and providing timely stakeholder support. The role requires strong organization, communication, discretion, data accuracy, and the ability to manage multiple priorities in a fast-paced environment.

Lead the architecture and operation of AWS-based cloud, scientific data, and AI/ML infrastructure. Build reusable infrastructure-as-code, CI/CD, security, networking, observability, and environment-management patterns. Partner with cloud and data engineers, scientists, and computational biologists to enable reproducible workloads and scalable platforms. Diagnose complex cross-system failures, lead incident reviews, establish engineering standards, shape the infrastructure roadmap, and mentor engineers as a senior individual contributor.

Leads early research project management for a somatic genomics drug discovery platform. Establishes governance, integrated planning, reporting, budgeting, risk management, and portfolio visibility while coordinating cross-functional scientific and operational teams from disease ideation through target assessment and downstream development. Partners with research leadership, finance, and drug discovery teams to improve execution, resource planning, prioritization, and operational excellence in a growing biotech organization.

Lead development and deployment of AI/ML solutions for target discovery, translational research, biomarker identification, and scientific decision-making. Partner with scientists and engineering teams to build scalable workflows for complex biological and multimodal data, promote best practices, mentor colleagues, and recommend emerging AI technologies to accelerate research.

Lead development and scaling of cloning and construct generation capabilities, define cloning strategy, implement high-throughput DNA assembly and automation workflows, improve throughput and quality, partner cross-functionally, mentor scientists, and represent cloning capabilities externally to accelerate RNA-based agricultural product development.