Senior / Principal Architect

Flagship Pioneering; Cambridge (MA); On-site; USD 120,000 - 180,000; Full time

Job summary

Join a pioneering company at the forefront of scientific innovation, where you will lead the development of a groundbreaking cryoEM platform. This role offers a unique opportunity to shape the future of biological discovery through hands-on prototyping and collaboration across diverse scientific domains. You will not only design and implement cutting-edge workflows but also contribute to a mission-driven team dedicated to transforming human health and sustainability. If you are excited about blending deep scientific knowledge with practical execution in a dynamic environment, this is the perfect opportunity for you.

Qualifications

• Hands-on experience with cryoEM workflows and data processing.
• Strong systems integration mindset connecting wet lab and imaging.

Responsibilities

• Architect integrated workflows across sample prep and imaging.
• Collaborate with teams to define platform architecture.

Skills

cryoEM workflow

systems integration

prototyping scientific systems

data processing

Education

PhD in a relevant scientific field

Master's degree in Biology or related discipline

Tools

imaging hardware

data capture systems

Job description

Company overview:

Flagship Labs 109, Inc. (FL109) is a privately held, early-stage technology company pioneering the use of artificial intelligence, physics and hardware to transform the way we see biology. FL109 was conceived by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. Become part of our mission-driven team and help envision the future of science.

Position Summary

FL109 is building a platform that redefines cryoEM discovery — from sample preparation through imaging acquisition, data capture, and AI/ML integration. We are seeking a Senior/Principal Architect to shape, build, and anchor the scientific and technical foundation of the platform. This is a platform-first leadership role for a deeply technical, execution-driven architect who is excited to create systems that compound insight and enable discovery at scale.

Environment

• Early-stage, venture-backed platform company.
• Senior leaders are expected to contribute hands-on from Day 1.
• Highly collaborative across science, product, AI/ML, and infrastructure.
• Rapid prototyping and structured learning prioritized over polished perfection.
• Multiple hats worn — leaders flex between domains and workflows.
• Balancing scientific exploration with operational platform building is critical.

Key Responsibilities

• Architect integrated workflows across sample prep, imaging, data capture, and AI/ML linkages.
• Collaborate with AI/ML leadership, product leadership, and infrastructure teams to define platform architecture.
• Hands-on prototyping and execution of cryoEM workflows and technical experiments.
• Design early platform modules that move beyond traditional cryoEM practices.
• Step in hands-on across cryoEM workflows and enabling technologies (such as sample preparation and vitrification) to advance platform development as needed.
• Document technical learnings to inform future scaling.
• Serve as technical conscience for first-principles thinking across platform development.

Key Requirements

• Direct, hands-on experience with the full cryoEM workflow: molecular expression, purification, vitrification, imaging acquisition, and data processing.
• Strong systems integration mindset — able to connect wet lab, imaging hardware, and data domains.
• Demonstrated ability to build and prototype scientific systems from first principles.
• Willingness to operate in a dynamic, ambiguous environment and take direct ownership of execution.
• Flexibility to pinch-hit across scientific modalities where needed.
• Comfort balancing deep scientific rigor with platform scalability requirements.
• Excitement to help define the early DNA of a next-generation discovery platform.
• Based in Boston, MA — in-person collaboration required.

About Flagship

Flagship Pioneering is a bioplatform innovation companythat 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 generation of over 500 patents, initiation of over 50 clinical trials for novel therapeutic agents and an aggregate value of more than $90 billion. 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 atwww.flagshippioneering.com.

Flagship Pioneering is committed toequal employment opportunityregardless 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.