Company Summary:

Empress Therapeutics is a biotechnology company founded by Flagship Pioneering.  Our product platform uses artificial intelligence and principles from co-evolution and pharmacology to harness human data and uncover novel drug candidates.  Our mission is to turn Co-Evolved MoleculesTM into innovative medicines for cancer, immunological, metabolic, and neurodegenerative diseases.

Empress Therapeutics was founded in Flagship’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), and Editas Medicines (NASDAQ: EDIT) were conceived and created.  Since Flagship’s founding in 2000, the firm has originated and fostered the development of more than 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents.  

Position Summary:

Empress Therapeutics is seeking a creative, motivated scientist to play a leading role in the Drug Discovery group’s efforts to identify microbial products of interest. The candidate will be responsible for employing untargeted metabolomics workflows based on UHPLC-HRMS/MS for elucidating microbial product structures. S/he will be an expert in mass spectrometry and will have strong expertise in sample extraction and preparation for metabolomic analysis, high throughput MS data analysis, and dereplication of MS data sets. The ideal candidate will also have knowledge of microbial natural product biosynthetic pathways. Familiarity with Compound Discoverer and/or the open-access GNPS metabolomics software is a plus. The ability to do in-depth analysis of biosynthetic gene clusters is a plus. The candidate will contribute critically to shaping the vision and strategy of the Drug Discovery group. S/he will bring a strong entrepreneurial orientation, demonstrate strong communication skills, and be comfortable working in and contributing to a very dynamic and cross-functional team environment.

Key Responsibilities:

  • Design and conduct end-to-end untargeted and targeted metabolomics workflows, including preparation of bacterial- and mammalian-sourced samples, full use of UHPLC-HRMS/MS instrument capabilities to separate metabolites of moderate to high structural complexity, and identification of chemical formulas and structural motifs to enable candidate structures to be proposed for synthesis
  • Develop analysis workflows for large MS data sets for use by the Drug Discovery team
  • Oversee in-house mass spec instruments, including maintenance, troubleshooting, and method development/optimization
  • Collaborate closely with other computational and wet lab scientists, including a team of synthetic biologists
  • Identify and lead external research relationships with academic and commercial partners
  • Report results to scientific team and management


  • Ph.D. focusing on Metabolomics, Analytical Chemistry, Natural Product Chemistry, Biochemistry, Biological Engineering and/or related field
  • Experience with metabolomic analysis of biological samples, including significant analysis of samples containing natural products or secondary metabolites
  • Experience with diverse analytical chemistry techniques, including HPLC, LC-MS/MS, etc.
  • Excellent communication and presentation skills, capable of conveying technical information in a clear and thorough manner
  • Self-driven and demonstrated ability in working with highly skilled teams in a fast-paced, entrepreneurial setting


More About Flagship Pioneering

We are creative optimists and we would love for you to consider joining our team!  See all our open opportunities across Flagship Pioneering’s Ecosystem!

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, the firm has applied a unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $34 billion in aggregate value. To date, Flagship is backed by more than $4.4 billion of aggregate capital commitments, of which over $1.9 billion has been deployed toward the founding and growth of its pioneering companies alongside more than $10 billion of follow-on investments from other institutions. The current Flagship ecosystem comprises 41 transformative companies, including:  Axcella Health (NASDAQ: AXLA), Denali Therapeutics (NASDAQ: DNLI), Evelo Biosciences (NASDAQ: EVLO),  Foghorn Therapeutics, Indigo Ag, Kaleido Biosciences (NASDAQ: KLDO), Moderna (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Sana Biotechnology, Seres Therapeutics (NASDAQ: MCRB), and Syros Pharmaceuticals (NASDAQ: SYRS).

We believe pioneering is best done by teams, and that it is a process that can be taught, learned, and replicated.  Learn more about our Company Creation Model.

Can Breakthrough Innovations Be Made Systematically? A Conversation With Noubar Afeyan, Flagship Pioneering’s CEO.

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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