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

Flagship Pioneering, Inc.•Cambridge, MA

About The Position

We are seeking a Cryo-EM Scientist to independently execute cryo-EM data processing across multiple programs. This role is responsible for delivering high-quality structural insights end-to-end and requires 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.

Requirements

Demonstrated ability to independently process cryo-EM data using RELION or cryoSPARC
Experience building and refining atomic models in Phenix, Coot, ChimeraX/Isolde, etc.
Sound 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
Ability to explain complex technical concepts clearly to both scientific and non-specialist audiences
Comfort onboarding into and operating within existing software tools and workflows without owning their development
Demonstrated experience presenting technical or scientific work and the ability to clearly articulate results, assumptions, and technical tradeoffs in discussions with clients, collaborators, and software partners
Strong working knowledge of UNIX/Linux environments and large-scale data handling
Experience with scripting and light debugging in support of cryo-EM data analysis
Experience using insights from cryo-EM data at multiple resolutions: complex formation, antibody mapping, high-resolution, etc.
Experience working with diverse project/sample types

Nice To Haves

Cryo-EM grid preparation and vitrification
Cryo-EM microscope operation or data acquisition

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
Identify data-quality and processing-related issues and clearly distinguish them from infrastructure or software issues, engaging platform or engineering teams as needed
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 next steps across programs