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

Position: (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.

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.

Responsibilities:

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

Qualifications

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.

Additional Strengths (at least one preferred)

Experience with scripting (python, shell) in support of cryo-EM data analysis

Strong working knowledge of UNIX/Linux environments and large-scale data handling

Cryo-EM grid preparation and vitrification

Cryo-EM microscope operation or data acquisition

Deep understanding of complementary structure determination methods such as X-ray crystallography or NMR spectroscopy

Experience with cryo-ET, milling, and tomographic reconstruction methods

About Flagship Flagship Pioneering is a bioplatform innovation company that invents and builds…