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About the role
<p><strong>ABOUT PIONEERING INTELLIGENCE </strong></p>
<p>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.</p>
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<p><strong><span data-contrast="none"><span data-ccp-parastyle="heading 2">The Role</span></span><span data-ccp-props="{"134245418":true,"134245529":true,"335559738":160,"335559739":80}"> </span></strong></p>
<p><span data-contrast="auto"><span data-ccp-parastyle="Normal (Web)">The Pioneering Intelligence group at Flagship Pioneering is building intel</span><span data-ccp-parastyle="Normal (Web)">ligent s</span><span data-ccp-parastyle="Normal (Web)">oftware 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.</span></span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></p>
<p><span data-contrast="auto"><span data-ccp-parastyle="Normal (Web)">We are seeking a Principal Software Engineer to own the </span><span data-ccp-parastyle="Normal (Web)">underlying </span><span data-ccp-parastyle="Normal (Web)">agentic platform: the durable</span><span data-ccp-parastyle="Normal (Web)"> </span><span data-ccp-parastyle="Normal (Web)">orchestration layer on which long-running, multi-agent, multi-model scientific workflows run reliably.</span></span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></p>
<p><span data-contrast="auto"><span data-ccp-parastyle="Normal (Web)">This is a hands-on architect role for a senior engineer who has built and operated distributed systems at scale and wants to t</span><span data-ccp-parastyle="Normal (Web)">ake age</span><span data-ccp-parastyle="Normal (Web)">ntic 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.</span></span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></p>
<p><strong><span data-contrast="none"><span data-ccp-parastyle="heading 2">Key Responsibilities</span></span><span data-ccp-props="{"134245418":true,"134245529":true,"335559738":160,"335559739":80}"> </span></strong></p>
<p><span data-contrast="auto"><span data-ccp-parastyle="Normal (Web)">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 </span><span data-ccp-parastyle="Normal (Web)">w</span><span data-ccp-parastyle="Normal (Web)">orkflow orchestration, evaluation frameworks, and event-driven distributed systems that deliver scale, resilience, and reliability.</span></span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></p>
<ul>
<li><span data-contrast="auto">Define SDK abstractions and API contracts between model and agent outputs and downstream consumers, decoupling rapid model iteration from product stability and reducing integration friction across teams.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Deliver infrastructure-as-code reference implementations (AWS CDK, Terraform, containerized services) and transform exploratory AI proof-of-concepts into hardened, reusable patterns adopted across product domains.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Own platform cost-efficiency and scalability while preserving the performance and accuracy that our experiments and end users require.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Explore and template agent design and deployment patterns, and set technical standards, code quality, and architectural direction for the platform.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Partner across teams (modeling and agent teams, product) to align on integration points, dependency timelines, and delivery, and mentor engineers and scientists.</span><span data-ccp-props="{}"> </span></li>
</ul>
<p><strong><span data-contrast="none"><span data-ccp-parastyle="heading 2">Professional Experience & Qualifications</span></span><span data-ccp-props="{"134245418":true,"134245529":true,"335559738":160,"335559739":80}"> </span></strong></p>
<ul>
<li><span data-contrast="auto">B.S. or M.S. in Computer Science, Engineering, or a related field, with 10+ years of professional software development experience.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Demonstrated track record architecting and maintaining large-scale distributed systems in production at technology companies.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Deep expertise in workflow orchestration and event-driven architecture, including stateful execution, idempotency, durable retries, and replay.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Strong cloud-native engineering on AWS with infrastructure-as-code, containerization, and autoscaling.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Proven ability to take systems from prototype to hardened, observable, operationally excellent production.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Experience designing SDKs, APIs, and data contracts that serve multiple downstream teams.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Excellent communication skills and the ability to build organizational consensus around platform decisions.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Collaborative and empathetic working style: listens to understand the needs of scientists, engineers, and downstream teams, and leads through influence.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Proven track record setting technical strategy and direction for a growing engineering organization, and mentoring engineers in a fast-moving environment.</span><span data-ccp-props="{}"> </span></li>
</ul>
<p><strong><span data-contrast="none"><span data-ccp-parastyle="heading 2">Preferred Qualifications</span></span><span data-ccp-props="{"134245418":true,"134245529":true,"335559738":160,"335559739":80}"> </span></strong></p>
<ul>
<li><span data-contrast="auto">Hands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen).</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Experience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Familiarity with sandboxed code execution and agent harness development.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Experience with LLM observability and monitoring tooling and cost-governance / FinOps for AI infrastructure.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Background in scientific domains such as biology, chemistry, or complex systems (a plus, not required).</span><span data-ccp-props="{}"> </span></li>
</ul>
<p><strong><span data-contrast="none"><span data-ccp-parastyle="heading 2">Why Join Us</span></span><span data-ccp-props="{"134245418":true,"134245529":true,"335559738":160,"335559739":80}"> </span></strong></p>
<p><span data-contrast="auto"><span data-ccp-parastyle="Normal (Web)">By joining the Agentic AI team within Flagship’s Pioneering Intelligence group, you will:</span></span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></p>
<ul>
<li><span data-contrast="auto">Own the platform foundation for a category-defining autonomous scientific reasoning engine.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Take frontier agentic AI from research to dependable production at scale.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Collaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Set the technical standards that the broader platform and product teams build on.</span><span data-ccp-props="{}"> </span></li>
<li><span data-contrast="auto">Shape the future of AI-powered discovery in a role that combines deep engineering excellence with direct human-health impact.</span><span data-ccp-props="{}"> </span></li>
</ul>
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<p><strong>ABOUT FLAGSHIP PIONEERING</strong></p>
<p>Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. </p>
<p>Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at <a href="https://www.flagshippioneering.com">www.flagshippioneering.com</a>.</p>
<p>At Flagship, we accept impossible missions to enable bigger leaps. Our <a href="https://www.flagshippioneering.com/values">core values</a> guide us through uncertainty and toward lasting impact.</p>
<p><strong>We are an equal opportunity employer</strong>. 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.</p>
<p>We recognize that great candidates often bring unique strengths <strong>without fulfilling every qualification</strong>. 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<strong> and interest in Flagship.</strong></p>
<p><strong><em>Recruitment & Staffing Agencies</em></strong><em>: 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.</em></p>
<p>#LI-MB1</p><div class="content-conclusion"><p> </p>
<p style="text-align: left;"><strong>Privacy Notice for Applicants: </strong>When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com. </p></div><p id="pay-transparency" style="margin: 0 !important; padding: 0 !important; float: none !important; clear: both !important; display: block;">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.</p><div class="content-conclusion"><p> </p>
<p style="text-align: left;"><strong>Privacy Notice for Applicants: </strong>When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com. </p></div>
Perks & benefits
- Medical Insurance
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