What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Metaphore Biotechnologies is an early-stage biotechnology company with an ambitious and exciting mission: to reimagine drug discovery and vaccine design. The company is developing a first-in-class platform for the intelligent design of molecular mimicry. Our platform integrates massively parallel assays with machine-learning-guided protein engineering to navigate the combinatorial space of molecular interactions and design protein-protein interfaces with exquisite precision.

Metaphore Biotechnologies is a product of Flagship Pioneering's venture creation engine, which has also given rise to companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally 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.

Position Summary:

Metaphore Biotechnologies is seeking an enthusiastic Senior Scientist to join our Computational Biology team and accelerate the design of protein-protein interfaces.  In this role, you will collaborate closely with members of the Computational Biology and Protein Engineering teams to advance our use of next-generation sequencing-based mutational assays to characterize and engineer molecular interactions.  Your scientific-rigor and creativity will advance our platform, unlocking the potential of molecular mimicry for therapeutic development.  The ideal candidate will bring experience in mutational screening, bioinformatic pipelines design and analysis, and experience implementing robust data standards.  This individual will have the opportunity to join a dynamic interdisciplinary team working at the interface of computational biology, protein engineering, functional genomics and machine learning.

The candidate will also have an extraordinary opportunity to be part of the Flagship ecosystem of companies, providing unique networking benefits through regular meetups, collaboration, and an environment of development and discussion around new ideas shaping the fields of computational biology and ML/AI.

Key Responsibilities:

  • Provide scientific and technical expertise in the analysis and interpretation of NGS-based mutational screens.
  • Contribute to the continuous development of scientifically rigorous next-generation sequencing (NGS) pipelines.
  • Develop and implement computational frameworks to derive biological insights from data, such as mapping key residues for molecular interactions and estimating interaction kinetics.
  • Collaborate on experimental design to establish and maintain high data quality standards and confidence in results.
  • Leverage internal and external datasets to aid in interpretation and further develop our ML-guided protein engineering platform.
  • Collaborate with computational and experimental scientists and engineers to execute on company goals.
  • Communicate insights and conclusions to scientific colleagues and the leadership team.


  • PhD or equivalent, plus 3+ years of experience in computational biology, bioinformatics, or a related field.
  • Experience developing robust quantitative NGS-based pipelines in a cloud platform.  Familiarity with AWS, docker and snakemake is a plus.
  • Experience with screening or highly parallel protein engineering workflows is highly desired.
  • Prior experience in automated noise thresholding is a plus.
  • Very strong programming skills in python and knowledge of software development best practices.
  • Excellent communication skills and capable of clearly conveying technical information.
  • Experience collaborating with wet lab scientists to jointly execute on goals.
  • Strong organization and problem-solving skills.
  • Experience with machine learning of biomolecules is a plus.

Flagship Pioneering and our ecosystem companies are 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.

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.

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