Lead Bioinformatics Engineer

The role

The Bioinformatics Engineer will own and operate the bioinformatics platform stack and build reusable pipeline frameworks. They will serve as a bridge between open-source libraries and scientific teams while managing external genomic data partnerships.

What you will do

• Own and operate Flagship's portfolio bioinformatics platform stack
• Build and maintain a library of reusable, production-quality pipeline templates
• Serve as the technical bridge between open-source bioinformatics libraries and end users
• Establish and maintain standards for bioinformatics data formats and pipeline documentation
• Guide portfolio company scientists in building and adapting pipelines
• Partner with Scientific Cloud Engineering on cloud architecture standards
• Serve as the primary contact with external genomic and biomedical data consortia
• Manage the full lifecycle of data access agreements
• Coordinate onboarding of new consortium-sourced datasets
• Act as an internal subject matter expert on genomics, transcriptomics, and multi-omics data ecosystems

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.)
• Experience building and operating cloud-native bioinformatics workflows using workflow managers such as Nextflow, Snakemake, or WDL
• Strong programming proficiency in Python and/or R
• Experience in shell scripting for pipeline automation
• Familiarity with public genomic data repositories and access/compliance frameworks
• Proven ability to manage complex external relationships and data access processes

Nice to have

• Experience administering or deploying managed bioinformatics platforms such as CodeOcean, Sequera / Nextflow Tower, Tamarind.bio, or similar
• Experience working in a multi-company or portfolio environment
• Familiarity with single-cell omics platforms (10x Genomics, Seurat, Scanpy, scVelo) and spatial transcriptomics workflows
• Experience with containerization (Docker, Singularity) and container orchestration
• Knowledge of data governance frameworks, catalog tools, and lineage tracking
• Experience contributing to or maintaining open-source bioinformatics libraries or shared code repositories
• Prior experience in a biotechnology, pharmaceutical, or life sciences technology organization

Benefits

• Healthcare coverage
• Annual incentive program
• Retirement benefits
• Broad range of other benefits

About the company

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.