Location: Cambridge, MA 

Flagship Labs 104 (FL104) is a privately held, early-stage company leveraging artificial intelligence and large language models (LLMs) to transform how we reason about complex phenomena. This is a unique opportunity to be at the forefront of scientific innovation, as we leverage cutting-edge advancements in AI and ML to drive breakthroughs in drug discovery and fundamental science.

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.

Position Summary:

We're looking to welcome a dynamic Principal Software Engineer to our scientific team. The successful candidate will play a pivotal role in the design, development, and application of LLM-based software to support scientific reasoning. It's a unique opportunity to influence our team’s culture and tackle intricate technical challenges in an innovation-driven environment. This role is among the first hires, and we’re looking for someone who is excited to help drive the technical and scientific direction of the company.

Key responsibilities:

  • Lead the design and development of system architecture for an innovative SaaS application, focusing on scalability, reliability, and security.
  • Spearhead the design, implementation, and optimization of LLM systems through prompt engineering, fine-tuning, and multi-agent architectures.
  • Guide the design and deployment of cloud infrastructure to orchestrate an AI-enabled back-end stack.
  • Promote a collaborative software development environment by adopting Git, participating in code reviews, and delivering reliable software.
  • Streamline application deployment via Docker containerization and managing CI/CD pipelines.


  • Bachelor’s in computer science or a related field and 12+ years of industry experience, M.S. and 9+ years of experience, or Ph.D. in computer science and 5+ years of experience.
  • Proven experience in designing scalable and secure system architectures, preferably for SaaS or data-intensive applications.
  • Experience with AI-enabled technology integration within backend software stacks.
  • Comprehensive knowledge of AI/ML models (particularly LLMs) and their application in software solutions.
  • Proficiency in Python and exposure to other major programming languages.
  • Extensive experience managing AWS offerings including EC2, ECS, S3, Lambda, RDS, adhering to well-architected best practices.
  • Proficiency in workflow orchestration, containerization, and managing CI/CD pipelines.
  • Demonstrated experience in establishing rigorous testing frameworks.
  • Strong leadership skills in promoting code quality standards, conducting infrastructure improvements, and driving best practices in software engineering.
  • Energetic self-starter with the ability to work effectively in a startup environment.

Preferred Qualifications:

  • Experience in designing and implementing LLM agent-systems.
  • Software development experience in the pharmaceutical or biotech industry is a distinct advantage.

Why Join Us?

FL104 offers you a unique opportunity to:

  • Collaborate with highly talented, interdisciplinary team members.
  • Participate in the evolution of a pioneering early-stage company, with the immense potential to transform how much a single scientist can accomplish.
  • Contribute to a proactive work culture, with an emphasis on mutual learning and continuous improvement.

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering is 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.


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