Senior Bioinformatics Platform Engineer (Genomics & Cloud)

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

Job summary

Flagship Pioneering seeks a Bioinformatics Engineer to own and operate its bioinformatics platform stack within the Scientific Cloud team. You will develop reusable pipeline templates and deployable workflows, bridging open-source libraries with portfolio scientists who need reliable, compliant data resources.

You will collaborate with data science and engineering to align platform infrastructure with enterprise cloud standards and data governance, enabling scientific teams to work independently

Qualifications

• MS or PhD in Bioinformatics, Computational Biology, Genomics, CS or related field.
• 7+ years hands-on bioinformatics engineering with production-grade pipelines.
• Deep expertise in genomic data types (FASTQ, BAM/CRAM, VCF, BED, HDF5, AnnData).
• Experience building/operating cloud-native workflows (AWS preferred).
• Strong programming in Python and/or R; shell scripting for automation.
• Familiarity with public genomic data repos and data access/compliance frameworks (dbGaP, UK Biobank).
• Ability to manage complex external relationships and data access processes (DUAs, DACs).
• Strong communication and collaboration across scientific and technical teams.

Responsibilities

• Own and operate Flagship’s bioinformatics platform stack (CodeOcean, Sequera, Tamarind.bio).
• Build reusable, production-grade pipeline templates and starter deployments.
• Bridge open-source bioinformatics library with portfolio company end users.
• Set standards for bioinformatics data formats, docs, and code contribution.
• Guide scientists to build and adapt pipelines within the platform framework.
• Coordinate with data science and engineering teams for platform integration.

Skills

Bioinformatics

Nextflow

Python

Cloud computing

Data governance

Communication

Education

MS/PhD in Bioinformatics or related

Tools

CodeOcean

Sequera

Tamarind.bio

Nextflow Tower

Docker

Job description

Flagship Pioneering seeks a Bioinformatics Engineer to own and operate its bioinformatics platform stack within the Scientific Cloud team. You will develop reusable pipeline templates and deployable workflows, bridging open-source libraries with portfolio scientists who need reliable, compliant data resources.

You will collaborate with data science and engineering to align platform infrastructure with enterprise cloud standards and data governance, enabling scientific teams to work independently