Flagship Pioneering
Lead Bioinformatics Engineer
$128K–$176K
Cambridge, MA USA +1 · Full-time · Posted Sep 25, 2026
- Location
- Cambridge, MA USA
Cambridge, Massachusetts, United States - Experience
- 7+ years of hands-on bioinformatics engineering experience.
- Education
- M.S. or Ph.D. in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field.
About the job
Own Flagship’s bioinformatics platform and reusable workflows, enable portfolio scientists to use them independently, and manage access to external genomic and biomedical datasets.
What you'll do
- Administer bioinformatics platforms and build reusable, production-quality pipeline templates and documented workflows.
- Manage consortium data access agreements, applications, renewals, compliance reporting, and dataset onboarding.
- Advise scientific teams and collaborate across engineering and data science to support platform standards and downstream analytical workflows.
What they ask for
- 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.
- Experience building and operating cloud-native bioinformatics workflows using workflow managers such as Nextflow, Snakemake, or WDL; AWS preferred, Azure or GCP acceptable.
- Proficiency in Python and/or R and shell scripting; genomic data-format expertise and experience with public repository access/compliance processes.
Nice to have
- Experience administering CodeOcean, Sequera / Nextflow Tower, Tamarind.bio, or similar platforms.
- Experience with single-cell or spatial transcriptomics, containers, data governance, open-source bioinformatics, or life sciences organizations.
Pay
$128,000 - $176,000 (base salary)
Tools
CodeOcean, Sequera (Nextflow Tower), Tamarind.bio, AWS, Azure, GCP, Nextflow, Snakemake
AI focus
Enable processed omics datasets for downstream analytical and AI workflows; the posting also states applications may be reviewed using AI-assisted screening tools.
Model-written summary · the original posting is authoritative