(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 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

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.

The salary range for this role is $115,000 - $184,300. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Fathem currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Fathem's good faith estimate as of the date of publication and may be modified in the future.

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