Company Summary:

Flagship VL55, Inc. is an early stage biotechnology company founded by Flagship Pioneering.  VL55 is pioneering medicines based on a novel category of molecules that play a fundamental role in human-microbe communication.

VL55, Inc. 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 nearly 100 scientific ventures resulting in $19+ billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents.  

We are seeking a (Sr.) Scientist to join the team and lead an ongoing collaboration with the Harvard T.H. Chan School of Public Health.  The ideal candidate will have a strong background in machine learning and computational biology to help develop and drive the core informatics platform, including the processing and analysis of multi’omics from population microbiome data.  S/he should be comfortable in Linux/Unix high-performance computing environments, and will bring a strong entrepreneurial orientation, communication skills, and be comfortable working in and contributing to a very dynamic and cross-functional team environment. 

Key Responsibilities:

  • Contribute to building our computational platform with the aim of identifying and characterizing host-microbe interactions, advancing our therapeutic programs, and developing new modalities
  • 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
  • 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, or a related field with 3+ years of post-graduate experience, or MS degree and an exceptional record of achievement
  • Proficiency in Python or R, Unix command-line environment
  • Experience in genomics and bioinformatics (microbial genomics, metagenomics, metatranscriptomics, and/or metabolomics is a plus)
  • Strong knowledge of applied statistics including machine learning
  • Familiarity with AWS, GCP, or similar cloud-computing services
  • Excellent communication and presentation skills, capable of conveying technical information in a clear and thorough manner; publication record a strong plus
  • 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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