Bioinformatics Engineer

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies.

About Scientific Cloud: Scientific Cloud is Flagship Pioneering's portfolio-facing IT organization, responsible for the cloud engineering, data and informatics engineering, research systems, lab systems, and vendor management capabilities that power Flagship's emerging companies. The team operates with a portfolio-first orientation — building durable, shared infrastructure that individual ventures can rely on at every stage of company formation and growth.

THE POSITION

Flagship Pioneering is seeking a Bioinformatics Engineer to join the Scientific Cloud team within Flagship IT. This is a high-impact individual contributor role reporting into the Director, Scientific Cloud Engineering, embedded within the sub-team.

The Bioinformatics Engineer will own and operate Flagship's bioinformatics platform stack, build reusable pipeline frameworks that portfolio companies can deploy on their own, and serve as the critical bridge between Pioneering Intelligence's open-source bioinformatics library and the scientific teams across Flagship's portfolio who need to put that code to work. Equally important, t— including UK Biobank, the Francis Crick Institute, dbGaP, and similar curated dataset providers — ensuring that Flagship scientists and portfolio companies have timely, compliant access to the world's highest-quality biological data resources.

This role is designed around platform ownership and enablement, not bespoke consulting. The ideal candidate is technically deep, organizationally savvy, and equally comfortable building production-grade infrastructure and coaching scientific teams to use it independently.

CORE RESPONSIBILITIES

Bioinformatics Platform Engineering & Enablement

• Own and operate Flagship's portfolio bioinformatics platform stack — including CodeOcean, Sequera (Nextflow Tower), Tamarind.bio, and adjacent tools — serving as the primary administrator, configurator, and first point of escalation for platform-level issues.
• Build and maintain a library of reusable, production-quality pipeline templates and starter deployments that portfolio companies and Pioneering Medicines teams can adopt without requiring bespoke engineering for each use case.
• Serve as the technical bridge between Pioneering Intelligence's open-source bioinformatics library and portfolio company end users — translating contributed code into deployable, documented workflows that scientists and informatics teams can operate independently.