Company Summary:

Empress Therapeutics is an early stage biotechnology company founded by Flagship Pioneering.  Empress is pursuing medicines based on a novel category of molecules that play a fundamental role in host-microbe communication.

Empress Therapeutics originated in Flagship’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), and Editas Medicines (NASDAQ: EDIT) were also conceived and launched.  Since Flagship’s founding in 2000, the firm has originated and fostered the development of nearly 100 scientific ventures resulting in $19+ billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents.  

Position Summary:

We are looking for a talented scientist to join our computational discovery team.  An ideal candidate would have a strong background in machine learning and computational biology to help develop and drive the core informatics platform and apply both in-house and off-the-shelf tools to discovery efforts in various therapeutic areas.  S/he should possess a foundation in math relevant to ML/statistics, and have a strong record of original research.  Expect to interact with bench scientists within the company, with members of our world-class scientific advisory board, and with stakeholders at Flagship.  Bring willingness to think outside of the box, and a hunger to leave a mark.

Key Responsibilities:

  • Contribute to building our computational platform with the aim of identifying and characterizing host-microbiome interactions and advancing our therapeutic programs
  • Develop and apply novel computational methods to assemble, annotate, and mine pathways from genomic, metagenomic, and other complex multi-dimensional data.
  • Contribute creatively and strategically to the company’s research strategy, helping drive actionable biological hypotheses from the data
  • Identify emerging methods and tools in computational approaches to multi-omic data analysis, and lead prototyping and implementation when applicable.  Examples include network and causal methods, predictive modeling, deep learning
  • Lead and collaborate closely with other scientists and research associates
  • Manage research relationships with external parties, including academic collaborators
  • Report results to scientific team and management

Key Requirements:

  • Ph.D. in Computational Biology, Bioinformatics, Genomics, Systems Biology, Biophysics, or a related field, or an MS degree with an exceptional record of achievement
  • Proficiency in Python or R.  Experience in genomics and bioinformatics (microbial genomics, metagenomics, meta-transcriptomics, and/or metabolomics is a strong plus)
  • Strong background in statistics or machine learning – beyond-API understanding of tools used
  • Familiarity with the HPC stack, from cluster computing to cloud-computing services
  • Able to work both independently and as part of a team, manage multiple projects concurrently, and collaborate across teams
  • Excellent communication and presentation skills, capable of conveying 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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