Senior Platform Bioinformatics Engineer

Pioneering Medicines; Cambridge (MA); On-site; USD 128,000 - 176,000; Full time

Job summary

Flagship Pioneering seeks a Bioinformatics Engineer to own the bioinformatics platform stack and enable portfolio teams. You will build reusable pipelines, bridge open-source libraries and end users, and ensure reproducibility and portability across data resources.

The role emphasizes platform ownership, collaboration with engineering, and coaching scientific teams to operate independently within Flagship's Scientific Cloud framework.

Qualifications

• 7+ years of hands-on bioinformatics engineering experience.
• Experience building/operating cloud-native bioinformatics workflows.
• Strong programming in Python and/or R; shell scripting helpful.
• Familiarity with dbGaP, UK Biobank, TCGA and data access rules.
• Ability to manage external relationships and DUAs/DACs.
• Excellent communication and collaboration skills.

Responsibilities

• Own and operate Flagship's bioinformatics platform stack as
• Build reusable, production-grade pipeline templates for teams.
• Bridge between open-source library and portfolio company users.
• Establish standards for data formats, docs, and code contribs.
• Guide scientists in building pipelines within the platform.
• Partner with engineering to align infra with cloud standards.

Skills

Bioinformatics engineering

Nextflow/Snakemake/WDL

Python

R

Cloud computing (AWS)

Genomics data formats

Communication skills

Education

M.S./Ph.D. in Bioinformatics or related field

Tools

CodeOcean

Sequera / Nextflow Tower

Tamarind.bio

Docker

Kubernetes

Job description

Flagship Pioneering seeks a Bioinformatics Engineer to own the bioinformatics platform stack and enable portfolio teams. You will build reusable pipelines, bridge open-source libraries and end users, and ensure reproducibility and portability across data resources.

The role emphasizes platform ownership, collaboration with engineering, and coaching scientific teams to operate independently within Flagship's Scientific Cloud framework.