Senior Backend & Data Engineer — EHR, AWS & AI Ops

Flagship Pioneering; Cambridge (MA); On-site; USD 108,000 - 186,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering is seeking a Senior Software Engineer, Backend & Data, to own backend systems that transform EHR data into trusted, model-ready outputs. You will work on AWS-based pipelines, partner integrations, and collaborate with data scientists on data mapping and model packaging.

A strong emphasis on security and PHI handling under HIPAA shapes daily work. You will contribute to infrastructure, MLOps, and product engineering as the company grows, while helping shape the architectural

Qualifications

• BS in Computer Science or a related field and practical software engineering experience.
• Hands-on healthcare data experience, including EHR data, FHIR or HL7, and PHI handling under HIPAA.
• Production AWS experience and proficiency in Python and SQL.
• Experience running AI/ML systems in production and collaborating with data scientists.
• Comfort using AI coding agents and maintaining security and privacy.

Responsibilities

• Design, build, and operate secure, auditable pipelines on AWS processing EHR data.
• Extend EHR integrations (Athenahealth FHIR APIs) across new systems.
• Develop AI-assisted tooling with data scientists for faster onboarding of data sources.
• Lead technical go-lives with partner IT and data teams; resolve issues end-to-end.

Skills

Backend engineering

Data pipelines

AWS

Python

SQL

EHR data experience

Communication with teams

Education

BS in Computer Science or related field

Tools

Athenahealth FHIR APIs

CDK / Terraform

CI/CD

AWS tooling

React

Job description

Flagship Pioneering is seeking a Senior Software Engineer, Backend & Data, to own backend systems that transform EHR data into trusted, model-ready outputs. You will work on AWS-based pipelines, partner integrations, and collaborate with data scientists on data mapping and model packaging.

A strong emphasis on security and PHI handling under HIPAA shapes daily work. You will contribute to infrastructure, MLOps, and product engineering as the company grows, while helping shape the architectural