# Lead Bioinformatics Engineer at Flagship Pioneering

- Company: Flagship Pioneering
- What the company does: Pioneering Partnerships Latest News.
- Company website: https://www.flagshippioneering.com
- Type: VC firms
- Level: Senior
- Location: Cambridge, MA USA
- Work setup: On-site
- Pay: $128K to $176K base salary per year (USD)
- Posted: 2026-09-25
- Apply by: 2026-11-09
- Apply: https://boards.greenhouse.io/flagshippioneeringinc/jobs/8844445002?gh_jid=8844445002
- Page: https://www.1752.vc/careers/jobs/flagship-pioneering-lead-bioinformatics-engineer/

## About the role

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.

## What they're looking 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
- 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
- Demonstrated experience building and operating cloud-native bioinformatics workflows (AWS preferred, Azure or GCP acceptable) using workflow managers such as Nextflow, Snakemake, or WDL
- Strong programming proficiency in Python and/or R, with experience in shell scripting for pipeline automation
- Familiarity with public genomic data repositories and the access/compliance frameworks that govern them (e.g., dbGaP, UK Biobank, TCGA)

Tags: IT