Principal Software Engineer - Agentic Platform

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

The Pioneering Intelligence group at Flagship Pioneering is building intelligent software systems that integrate agentic AI with scientific reasoning to accelerate discovery and decision-making. At the center of this effort is a new autonomous research platform. It supports autonomous AI systems that reason over complex biological problems.

We are seeking a Principal Software Engineer to own the underlying agentic platform: the durable orchestration layer on which long-running, multi-agent, multi-model scientific workflows run reliably.

This is a hands-on architect role for a senior engineer who has built and operated distributed systems at scale and wants to take agentic AI from research to production. You will set the technical foundation and standards for the platform, work shoulder-to-shoulder with AI scientists, engineers, and domain experts, and turn frontier agent patterns into reusable, dependable infrastructure.

Own the agentic platform end to end, from research prototype to production, building the durable orchestration layer for long-running, multi-stage scientific workflows. Architect workflow orchestration, evaluation frameworks, and event-driven distributed systems that deliver scale, resilience, and reliability.

By joining the Agentic AI team within Flagship’s Pioneering Intelligence group, you will:

• Own the platform foundation for a category-defining autonomous scientific reasoning engine.

• Take frontier agentic AI from research to dependable production at scale.

• Collaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem.

• Set the technical standards that the broader platform and product teams build on.

• Shape the future of AI-powered discovery in a role that combines deep engineering excellence with direct human-health impact.

The salary range for this role is $188,000 - $257,500.

Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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