Flagship Pioneering · 9 hours ago
(Senior) Scientist, Cryo-EM Data Processing & Computational Workflows
Cambridge, MA USA
Full-time
Onsite
Mid, Senior Level
$115K/yr - $184K/yrFlagship Labs 109, Inc. (FL109) is an early-stage technology company pioneering the use of artificial intelligence and hardware to transform biology. The Cryo-EM Scientist will independently execute cryo-EM data processing, delivering high-quality structural insights and collaborating with various teams to align on project next steps.
FinanceFinancial ServicesVenture Capital
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
Qualification
Required
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
Preferred
Cryo-EM grid preparation and vitrification
Cryo-EM microscope operation or data acquisition
Benefits
Healthcare coverage
Annual incentive program
Retirement benefits
Broad range of other benefits
Company
Flagship Pioneering
Flagship Pioneering is a venture capital firm that invests in life sciences and healthcare companies.
Founded in 2000
501-1000 employees
H1B Sponsorship
Flagship Pioneering has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (8)
2024 (4)
2023 (4)
2022 (4)
2021 (1)
Funding
Current Stage
Late StageLeadership Team
Noubar Afeyan
Founder and CEO
Chuck Carelli
Chief Financial Officer
Recent News
2026-01-16
2026-01-16
Company data provided by crunchbase