Associate Bioinformatics Scientist at Flagship Pioneering, Inc.

Company Summary:

Who Are We?

Founded by Flagship Pioneering, Empress pioneers the future of small molecule drugs through the discovery of pharmacologic loci. The company’s product platform leverages AI and multi’omic data from thousands of humans around the globe to discover novel, important small molecules inside of humans and their cognate mechanisms in health or disease. Empress uses this platform to improve the speed to and success rate of drug programs, by starting with human-experienced molecules and real-world evidence of their benefit.

Position Summary:

We are seeking an Associate Bioinformatics Scientist to join our Computational Discovery team to execute on data infrastructure and pipeline projects.  The ideal candidate will have a background in data lake and database development, as well as in bioinformatics.  The candidate should be comfortable in Linux/Unix high-performance computing environment, including AWS technologies.  S/he will work under the supervision of a member of the research team.

Key Responsibilities:

  • Improve our cloud data infrastructure
  • Facilitate access to model-ready data frames
  • Improve integration between raw data, model results, and the company ELN
  • Work on online visualization tools (Tableau, Shiny, etc)
  • Work on bioinformatics pipelines, e.g. RNA sequencing pipeline
  • Assist in execution of research projects


  • BS or MS. in Computational Biology, Machine Learning, Bioinformatics, Genomics, Systems Biology, or a related field
  • Proficiency in Python or R, Unix command-line environment
  • Experience in genomics and bioinformatics (microbial genomics, metagenomics, meta-transcriptomics, and/or metabolomics is a plus)
  • Familiarity with visualization tools a plus (e.g. Quicksight, Tableau, etc)
  • Experience with workflow management tools a plus (Nextflow, snakemake, etc)
  • Foundational knowledge of statistics and computer science necessary
  • Familiarity with AWS, GCP, or similar cloud-computing services
  • Excellent communication and presentation skills – ability to convey technical information in a clear and thorough manner
  • Intellectual curiosity and proclivity for a fast-paced, entrepreneurial, and technical environment


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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