Scientist, Computational Biology

Company Summary:

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Metaphore Biotechnologies is an early-stage biotechnology company with an ambitious and exciting mission: to reimagine drug discovery and vaccine design. The company is developing a first-in-class platform for the intelligent design of molecular mimicry. Our platform integrates massively parallel assays with machine-learning-guided protein engineering to navigate the combinatorial space of molecular interactions and design protein-protein interfaces with exquisite precision.

Metaphore Biotechnologies is a product of Flagship Pioneering's venture creation engine, which has also given rise to companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally on Fortune’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies.

Position Summary:

We are seeking a motivated Computational Immunologist to join our rapidly growing team. The successful candidate will conduct immune repertoire analysis with highly parallel assay data and computational modeling to support the discovery, engineering, and evaluation of novel therapeutic antibodies and vaccines. They will play a key role in our discovery through translational efforts, formulating and executing on a science & technology strategy that will allow the company to deliver against its goals. 

This position requires a strong foundation in the biology of the adaptive immune system and computational immune repertoire analysis, including interrogation of large in vitro and in vivo experiments to characterize determinants of immune receptor specificity and the response to candidate therapeutics and vaccination strategies.  The candidate will work closely with experimental and computational scientists to interpret results and design experiments.  This individual will join an interdisciplinary and collaborative team at the interface of computational immunology, functional genomics, and next-generation antibody design; they should be comfortable communicating and working with diverse backgrounds in a fast-paced startup environment.

The candidate will have an extraordinary opportunity to be part of the Flagship ecosystem of companies providing unique networking benefits through regular meetups, collaboration, and an environment of development and discussion around new ideas shaping the fields of computational biology and ML/AI.

In the interest of fostering collaboration, the candidate is expected to work on-site at our Kendall Square, Cambridge, MA location.

Key Responsibilities:

• Explore, design, and implement bioinformatic algorithms for immune repertoire analysis
• Assist the design of screening libraries and build NGS analysis pipelines for hit identification
• Formulate hypotheses, aid experimental design and perform analyses to evaluate novel immunization strategies
• Collaborate with team members to interpret immunogenicity
• Leverage internal and external datasets to further develop our ML-guided protein-interface engineering platform
• Collaborate with engineers, computation scientists, and experimentalists to execute on company goals
• Communicate insights and conclusions to colleagues in the scientific and leadership teams

Basic Qualifications:

• Ph.D. plus 2-5 years of experience in computational biology, bioinformatics, immunology, or a related field
• Strong skills in immune repertoire analysis, particularly as pertains to understanding antibody maturation and the repertoire response to vaccination
• Experience with NGS data pipelines and analysis
• Excellent understanding of statistics
• Strong programming skills in Python (preferably) or R and knowledge of software best practices

Preferred Qualifications:

• Experience with protein engineering or vaccine development
• Experience with machine learning, especially in the context of biomolecules
• Experience with publicly available data sources such as IMGT, OAS or ImmPort
• Experience with cloud and/or distributed computing
• Experience with single cell immune profiling
• Laboratory experience in molecular biology or immunology

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

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.