(Senior) Scientist, Computational Cryo-EM

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.

About Us

FL109 is a pioneering structural biology company reimagining molecular discovery through cutting-edge technology. We leverage AI, software engineering, and experimental biology to create a scalable platform for understanding the molecular world.

As our (Sr.) Computational CryoEM Scientist, you will lead the processing of high-throughput cryo-EM experiments, ensuring seamless integration of computational methods into our cryo-EM pipeline. You will be the critical link between structural biology and informatics, enabling automated, scalable solutions that reduce manual decision-making. This is an exciting opportunity to help redefine structural biology by combining deep domain expertise with innovative tools and techniques.

The Role

We are seeking a skilled and driven computational cryo-EM scientist to manage and optimize our high-throughput cryo-EM processing pipelines. You’ll work closely with software engineers and machine learning scientists to automate workflows, eliminate manual bottlenecks, and integrate modern cryo-EM tools into our platform. You will stay at the forefront of cryo-EM research, testing new models and approaches to assess their potential for real-world impact, and leveraging your network to connect the team to cutting-edge knowledge and tools.

How You Will Contribute

• Pipeline Management: Lead the processing of high-throughput cryo-EM experiments, optimizing data workflows to support scaling.
• Automation: Collaborate with software engineers to develop solutions that eliminate manual decision-making in cryo-EM data processing, with a keen eye for identifying areas where automation and software can deliver outsized value.
• Tool Integration: Develop and integrate custom software solutions alongside open-source cryo-EM tools to create seamless, automated pipelines tailored to the platform’s needs.
• Stay Cutting-Edge: Stay informed on the latest cryo-EM research and advancements. Rapidly prototype and test new methods, tools, and models to evaluate their practical impact, distinguishing game-changing solutions from those that are simply novel or cool.
• Community Engagement: Leverage your network within the cryo-EM community to identify and access emerging technologies, methods, and collaborations. Act as a resource for the ML and software teams to get smart quickly on cryo-EM-specific challenges and opportunities.
• Value-Oriented Thinking: Bring a strategic mindset to evaluate new technologies and approaches, focusing on areas with the highest potential to streamline workflows, reduce bottlenecks, and enhance results.
• Cross-Functional Collaboration: Serve as the translator between structural biology, software engineering, and machine learning teams, ensuring computational solutions align with experimental and platform goals.
• Rapid Prototyping: Prototype and test new ideas to validate approaches quickly and iteratively.
• Data Analysis: Analyze cryo-EM datasets to troubleshoot, optimize, and provide insights that guide decision-making.

The Ideal Candidate Will Have:

• Cryo-EM Expertise: Deep knowledge of academic and industry-standard cryo-EM tools (e.g., RELION, cryoSPARC, Thermo EPU) and all processing steps (e.g., alignment, classification, refinement).
• Research Savvy: Demonstrated ability to stay informed on cutting-edge cryo-EM methods and research, with a passion for testing and validating their applicability in real-world workflows.
• Community Connections: A strong network within the cryo-EM or structural biology community to identify trends, access emerging tools, and facilitate collaborations.
• Automation Mindset: Experience in automating cryo-EM workflows to improve throughput and reduce manual steps.
• Technical Collaboration Skills: Ability to work closely with software engineers to integrate tools into broader computational pipelines.
• Programming Skills: Proficiency in scripting languages (e.g., Python, bash) for automating data processing workflows.
• Builder Mentality: A resourceful, iterative approach to solving problems, with a focus on rapid prototyping and shipping results.
• Communication Skills: Strong ability to communicate complex structural biology concepts to non-experts, bridging the gap between computational biology and informatics.

Preferred Qualifications:

• Experience in structural biology or biophysics, particularly in cryo-EM.
• Familiarity with high-performance computing (HPC) environments and cloud platforms for data processing.
• Experience with machine learning or AI applications in structural biology is a plus.
• Passion for reimagining traditional approaches in cryo-EM and structural biology workflows.

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 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 at www.flagshippioneering.com.

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.