Principal Engineer, Full Stack & LLM-Integrated Web Applications

The Pioneering Intelligence group at Flagship Pioneering is building intelligent software systems that integrate agentic AI with scientific reasoning to accelerate therapeutic discovery and decision-making. We are seeking a Lead/Principal Software Engineer to drive the design, integration, and deployment of web-based applications that enable seamless human-AI collaboration. This role is part of a bold, agentic initiative within the Pioneering Intelligence portfolio and offers the opportunity to help define the future of user-centric, LLM-enabled platforms.

About Flagship Pioneering
Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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. 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 www.flagshippioneering.com. 

Position Summary
As a key technical leader in this early-stage initiative, you will architect and implement the software backbone of a new platform that leverages large language models (LLMs) and AI agents to enhance high-stakes human workflows. This is a user-first, AI-augmented product—your work will translate abstract reasoning tasks into intuitive, high-performance tools that empower experts across therapeutic domains.

You will lead the integration of frontend and backend systems, build reliable deployment pipelines, and collaborate closely with engineers, AI scientists, product designers, and end users. This is a rare opportunity to shape a greenfield product at the intersection of usability, flexibility, and advanced reasoning.

Key Responsibilities

• Architect and implement a full-stack web application that integrates frontend components with LLM-powered backend agents, orchestration layers, and databases.
• Design data schemas and APIs for scalable, distributed systems.
• Collaborate with product and design teams to craft elegant and flexible ui/ux tailored to scientific and analytical workflows.
• Integrate core agentic capabilities via APIs and microservices that manage dynamic task decomposition, memory, and reasoning logic.
• Own the infrastructure and DevOps/GitOps lifecycle, including CI/CD pipelines, observability, and secure cloud deployment (AWS).
• Mentor other engineers, drive technical quality, and ensure extensibility and performance across rapidly evolving use cases.
• Champion workflow-centric development, ensuring every feature supports seamless user interaction with intelligent systems.

Qualifications

• B.S., M.S., or Ph.D. in Computer Science, Engineering, or related field with 7+ years of professional software development experience.
• Seasoned full-stack engineer with deep experience designing and deploying secure, scalable web and database applications in AWS.
• Mastery of modern frameworks such as React, FastAPI, and NodeJS.
• Detailed understanding of RESTful, GraphQL and other mechanisms to enable a distributed system architecture.
• Experience with containerized services (Docker, Kubernetes) and secure deployment at scale.
• Experience with core AWS services (e.g., EC2, S3, Lambda) and infrastructure-as-code using AWS CDK.
• Familiarity with integrating LLMs (e.g., OpenAI, Claude, Gemini) and vector databases into responsive applications.
• Experience with system design, performance optimization, observability, and operational excellence.
• Strong intuition for UX design and a demonstrated commitment to building delightful, workflow-first products.
• Excellent communication skills and collaborative mindset, especially in fast-moving, cross-functional environments.

Preferred Qualifications

• Experience with agentic AI frameworks (e.g., LangChain, CrewAI, AutoGen) and their orchestration models.
• Background in scientific domains such as biology, chemistry, or complex systems is a plus but not required.
• Familiarity with system evaluation and observability tools (e.g., Grafana, Langfuse, Kibana, Cloudwatch) and managing SLAs in production environments
• Professional-level AWS certification (e.g., Solutions Architect, DevOps Engineer) is a plus.
• A deep interest in augmenting human decision-making and intellectual workflows with AI.

Why Join Us

• Help define a new category of intelligent software tools that support real-time human-AI collaboration.
• Work on a greenfield product at the intersection of usability, reasoning, and scientific innovation.
• Collaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem.
• Build in a supportive, mission-driven culture with access to world-class technical and operational resources.
• Shape the future of AI-powered discovery in a role that combines engineering excellence with health impact.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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.  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 www.flagshippioneering.com.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.