Flagship Pioneering hiring Bioinformatics Scientist, Next Generation Sequencing (NGS) in Cambridge, Massachusetts, United States

Who We AreGenerate Biomedicines, Inc. is a Flagship backed, privately-held biotechnology company on a mission to reimagine the drug discovery process through the use of cutting-edge machine learning techniques. Core to Generate’s approach is the development and application of novel machine learning algorithms to solve foundational problems in molecular and protein biology. Generate’s unique platform seeks to drive innovation at the intersection of machine learning and biology through deep collaborations between wet lab and dry lab scientists and engineers. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Since its inception in 2018, Generate has received over $50 million in venture funding and its board of directors includes scientific and entrepreneurial luminaries such as Frances Arnlold (Nobel prize in chemistry, 2018), Stéphane Bancel (CEO, Moderna), and Noubar Afeyan (Founder and CEO, Flagship Pioneering). Generate was founded by Flagship Pioneering, a venture creation firm based in Cambridge, MA that conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since Flagship’s launch in 2000, the firm has applied a unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, including: Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Indigo Agriculture, and Sana Biotechnology.

Position Summary

Generate’s deep learning technology is built to constantly improve with more data, therefore high-throughput experimentation is critical to our platform. We use creative, highly customized application of next generation sequencing technology to precisely couple full-length protein sequences to quantitative measurements in novel assays.

We are seeking a self-motivated Bioinformatics Scientist (NGS) to develop novel processing and analysis techniques across multiple sequencing platforms, and then to build them into production pipelines. She/he will work with experimental scientists from Protein Sciences and Medicines groups to guide assay design, select key technologies, and devise sequencing prep protocols. The successful candidate will be comfortable iterating rapidly in development phase, while building robust and reliable pipelines in production, in order to gather massive volumes of training data for generative protein models. Finally, this role will work with the Medicines group to build NGS pipelines and carry out target-specific genomics and transcriptomics analyses in support of ongoing drug development programs.

Key Responsibilities

  • Design and implement custom NGS processing pipelines, statistical models, and analysis methods for high-throughput protein function assays.
  • Act as internal expert and thought leader for NGS computational methodology.
  • Interface NGS pipelines with in-house data platform and computational cluster via programmatic APIs and web apps.
  • Work with Protein Sciences and Medicines groups to process and analyze genomic and transcriptomic data.
  • Develop production-quality code and scalable, reproducible, shared workflows in a team setting.
  • Present progress from scientific work in regular research meetings.


  • MS with 3+ years experience or PhD in Computational Biology, Computer Science or a related field
  • Demonstrated experience applying NGS computational techniques to a variety of biological applications, preferable in the biotech industry.
  • Experience developing, debugging, and applying custom software for processing raw reads and alignments.
  • Proficiency in Python and experience analyzing data with Numpy/Scipy, R, or similar.
  • Deep expertise in managing Linux environments using Docker, as well as package management using conda, pip, apt/yum or other package management tools.
  • Experience deploying robust, automated workflows using workflow management tools such as Prefect, Luigi, Cromwell, or similar, and compute cluster infrastructures such as AWS ECS, Kubernetes, LSF, or similar.

Nice To Have

  • Experience designing and optimizing NGS experiments
  • Demonstrated experience developing software in a team setting.
  • Experience with optimizing performant code.

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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