Lead Bioinformatics Engineer
Flagship Pioneering · Cambridge, MA USA
About this role
**Lead Bioinformatics Engineer** **About Flagship Pioneering** Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since 2000, Flagship has originated 100+ ventures (including Moderna) and deployed $4B+ toward scientific discovery. The **Scientific Cloud** team powers data and technology infrastructure across Flagship’s portfolio. **About Scientific Cloud** Scientific Cloud is Flagship’s portfolio-facing IT organization responsible for cloud engineering, data & informatics engineering, research systems, lab systems, and vendor management—focused on building durable, shared infrastructure that ventures can rely on at every stage. --- ## 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**. You will **own and operate Flagship’s bioinformatics platform stack**, build **reusable pipeline frameworks** that portfolio companies can deploy independently, and serve as the bridge between **Pioneering Intelligence’s open-source bioinformatics library** and scientific teams across the portfolio. This role is designed around **platform ownership and enablement** (not bespoke consulting). You’ll coach teams to use the platform effectively and help ensure compliant, timely access to high-quality biological datasets. --- ## Core Responsibilities ### Bioinformatics Platform Engineering & Enablement - Own and operate the portfolio bioinformatics platform stack, including **CodeOcean**, **Sequera (Nextflow Tower)**, **Tamarind.bio**, and adjacent tools (primary administrator/configurator/escalation point). - Build and maintain a library of **reusable, production-quality pipeline templates** and starter deployments. - Translate contributed open-source code into **deployable, documented workflows** that scientists and informatics teams can run independently. - Establish standards for **data formats**, **pipeline documentation**, and **code contribution guidelines** to ensure reproducibility and portability. - Guide portfolio teams in building/adapting pipelines within the platform framework to achieve **scientific self-sufficiency**. - Partner with Scientific Cloud Engineering to align platform infrastructure with enterprise cloud standards (identity, security, cost governance). ### Consortium & Institutional Data Partnerships - Serve as Flagship’s primary point of contact with external genomic/biomedical data consortia and repositories (e.g., **UK Biobank**, **Francis Crick Institute**, **dbGaP**, **GTEx**, **ENCODE**, and others). - Manage the full lifecycle of data access agreements (e.g., **DAC applications**, **DUAs**, renewals, compliance reporting) in coordination with legal/compliance. - Monitor consortium roadmaps and emerging datasets; surface new access opportunities aligned to portfolio needs. - Coordinate onboarding of new consortium datasets into Flagship’s data environment (ingestion, governance metadata, access controls). - Build relationships with data operations and scientific leads at partner institutions. ### Cross-Functional Collaboration - Work with Data & Informatics Engineering (data architects, data engineers, software engineers) to integrate bioinformatics workloads into shared platforms, pipelines, and catalogs. - Collaborate with Research Systems, Lab Systems, and informatic
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