Description
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.
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.
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. + 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.
- Consortium & Institutional Data Partnerships
+ Serve as Flagship's primary liaison with external genomic and biomedical data consortia and repositories. + Manage the full lifecycle of data access agreements , including Data Access Committee (DAC) applications, DUAs, renewals, and compliance reporting.
- Cross-Functional Collaboration
+ Work closely with Data & Informatics Engineering teammates , including data architects, data engineers, and software engineers. + Collaborate with Research Systems, Lab Systems, and informatics counterparts across Flagship and portfolio companies.
- Scientific & Technical Leadership
+ Act as an internal subject matter expert on genomics, transcriptomics, and multi-omics data ecosystems. + Evaluate and recommend appropriate computational resources (HPC, cloud batch, spot instances) for large-scale genomic workloads.
Required Qualifications:
- M.S. or Ph.D. in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field.
- 7+ years of hands-on bioinformatics engineering experience, including production-grade pipeline development and deployment.
- Deep expertise in genomic data types and file formats (FASTQ, BAM/CRAM, VCF, BED, HDF5, AnnData, etc.) and the computational tools used to process them.
The salary range for this role is $128,000 - $176,000. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.