Senior Software Engineer (Backend)

Flagship Pioneering•Cambridge, MA

2d•$108,000 - $186,000

About The Position

FL113 is an AI diagnostics company developing products to uncover disease earlier and enable proactive care. It is part of the Flagship Pioneering ecosystem. The Senior Software Engineer, Backend & Data reports to the VP of Engineering and owns major parts of the system that transforms health-system partners’ EHR data into results partners can trust. The role focuses on backend, data, and EHR integration engineering on AWS. As the product evolves, the engineer will also contribute to MLOps, infrastructure, and product engineering, and help shape what the company builds. Engineering and Research work as one team, sharing code and pipelines from experimentation through deployment and accountability for model performance. The role does not require training AI/ML models, but involves collaborating with data scientists on data mapping, evaluation, and model packaging.

Requirements

Bachelor’s degree in Computer Science or a related field, or equivalent practical experience.
At least 7 years of professional software engineering experience building and operating production backend systems and data pipelines.
Hands-on healthcare data experience, including EHR data, FHIR or HL7, clinical vocabularies such as LOINC, SNOMED, ICD, and RxNorm, and systems that handle PHI under HIPAA.
Substantial production experience on AWS.
Proficiency in Python and SQL.
Experience running AI/ML systems in production and working in shared code and pipelines with data scientists or ML researchers.
Daily use of AI coding agents and agentic workflows, with review of their outputs and accountability for correctness, security, and privacy.
Experience in an early-stage startup or comparable zero-to-one environment, and willingness to work outside one’s core specialty as needed.
Experience debugging complex problems across system boundaries, from partner EHRs or data feeds through production.
Clear communication with engineers, data scientists, clinicians, and partner IT teams.

Nice To Haves

Experience building EHR integrations with athenahealth, Epic, or similar systems, including SMART on FHIR or bulk FHIR exports.
Experience with infrastructure as code such as CDK or Terraform, containers, and CI/CD, including AWS environments that isolate sensitive data.
Experience building software under HITRUST, SOC 2, or FDA quality-system expectations.
Frontend or full-stack experience, such as React and TypeScript.
Experience on integrated teams where engineers and data scientists share code, reviews, and responsibility for results.

Responsibilities

Design, build, and operate secure, auditable AWS pipelines that transform partner EHR data from ingestion into model-ready tables and evaluated results, handling PHI appropriately throughout.
Build and extend EHR integrations, beginning with athenahealth’s FHIR APIs, for additional EHRs, data formats, and partner environments.
Create AI-assisted tools with data scientists to make onboarding partners and data sources faster and more repeatable.
Lead technical go-lives with partner IT and data teams, and resolve issues through to completion.
Contribute to infrastructure, DevOps, and security, including infrastructure as code, CI/CD, monitoring, and HIPAA and HITRUST controls.
Package, run, and monitor production models in partnership with Research, sharing accountability for real-world performance.
Build reports, dashboards, and clinician- and patient-facing products as needed.
Establish engineering standards for a growing team, and help hire and mentor future engineers.
Use AI coding agents and automation effectively, exercising sound judgment when working near PHI.
Shape FL113’s product architecture and engineering practices as the company grows.