Senior) Scientist, Cryo-EM Data Processing & Computational Workflows

Company overview: Fathem Inc. is a privately held, early-stage technology company pioneering the use of artificial intelligence, physics and hardware to transform the way we see biology. Fathem 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.

Company overview: Fathem Inc. is a privately held, early-stage technology company pioneering the use of artificial intelligence, physics and hardware to transform the way we see biology. Fathem 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 the role: We are seeking a Cryo-EM (Senior) Scientist to independently execute cryo-EM data processing and interpretation across multiple programs. This role is responsible for delivering high-quality structural insights end-to-end. The ideal candidate will have deep hands‑on experience with cryo‑EM data processing platforms, a strong practical understanding of single‑particle cryo‑EM, comfort operating within established internal software environments, and the ability to communicate results clearly in collaborative and client‑facing settings.

• Independently process single-particle cryo-EM datasets from raw movies through validated reconstructions
• Build, refine and help interpret atomic models
• Apply, adapt, and troubleshoot established processing workflows
• Learn and efficiently use internally developed software tools and processing pipelines as a primary user
• Interpret results in the context of sample quality, data collection conditions, and experimental limitations; and communicate implications clearly
• Present results to internal stakeholders and external clients, fielding technical questions and defending conclusions in real time
• Collaborate with experimental, computational, and software teams to align on collective needs and directions across programs

• Demonstrated ability to independently process cryo-EM data using established tools (RELION, cryoSPARC, cisTEM, etc.)
• Demonstrated experience building and refining atomic models in Phenix, Coot, ChimeraX/Isolde, etc.
• Demonstrated ability to draw relevant technical and biological insights from processed datasets, and use those insights to suggest next steps
• Deep practical understanding of single-particle cryo-EM, including common failure modes and tradeoffs related to sample quality (e.g., heterogeneity, preferred orientation, ice quality, particle behavior) and how these factors affect processing strategies and results
• Experience using insights from cryo-EM data at multiple resolutions: complex formation, protein-protein interaction mapping, high-resolution, etc.
• Demonstrated experience presenting technical or scientific work and the ability to clearly articulate results, assumptions, and technical tradeoffs in discussions with internal and external stakeholders
• Strong background in biochemistry, biophysics, and/or cell biology; and an ability to communicate and collaborate with protein scientists to facilitate project success.
• Comfort onboarding into and operating within existing software tools and workflows without owning their development
• Experience working with diverse projects and samples, and operating in a dynamic environment
• Creativity and excitement to advance the frontiers of capability, throughput, and speed in structural biology.

• Experience with scripting (python, shell) in support of cryo-EM data analysis
• Strong working knowledge of UNIX/Linux environments…