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Flagship Pioneering, Inc. Logo

Senior Scientist, AI/ML Protein Design

Flagship Pioneering, Inc.

Salary not specified
Oct 14, 2025
Cambridge, MA, US
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Develop novel proteins with specific functionalities using state-of-the-art machine learning algorithms and computational methods.

Requirements

  • Ph.D. in Computational Biology, Computer Science, Mathematics, or related discipline.
  • 3+ years of experience (including PhD work) in applying deep learning methods to problems related to protein sequence-structure-function relationships.
  • Demonstrated ability to deliver deep learning models to production use.
  • Strong technical proficiency in coding (including ML frameworks), cloud computing, and dev ops.
  • Knowledge of protein biochemistry and structural biology
  • Working experience with design of multi-subunit complexes and membrane proteins
  • Experience with cloud computing platforms (e.g., AWS, Google Cloud) for large-scale data processing.

Responsibilities

  • Develop and apply protein modeling and design strategies to advance the company’s platform.
  • Devise, train, refine, and deploy deep neural network models using public and proprietary sequence, structure, and function data.
  • Collaborate closely with experimental scientists to close the model-test-learn loop.
  • Drive external collaborations where necessary to augment internal capabilities.
  • Create, maintain, and update documents for all aspects of the development process as well as contributing to generating intellectual property

Other

  • Outstanding written and verbal communication skills, ability to work with colleagues from diverse scientific backgrounds and cultures.
  • Preferably a track record of success working in a fast-paced, cross-functional, and rapidly growing biotech organization.
  • Ph.D. in Computational Biology, Computer Science, Mathematics, or related discipline.
  • Equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.