Senior Software Engineer (Backend)

Flagship Pioneering, Inc.•Cambridge, MA

3d•$108,000 - $186,000

About The Position

FL113 is a fast-moving AI diagnostics company building products to detect disease earlier and support proactive care. As Senior Software Engineer, Backend & Data, you will report to the VP of Engineering and own major parts of the system that transforms health-system partners’ EHR data into reliable results. The role centers on backend, data, and EHR integration engineering on AWS, with flexibility to contribute to MLOps, infrastructure, security, and product engineering as company needs evolve. Engineering and Research operate as one team, sharing code and pipelines from experimentation through deployment and accountability for model performance. You will collaborate with data scientists on data mapping, evaluation, and model packaging; training AI/ML models is not expected. You will help shape the company’s architecture and engineering practices, establish standards for a growing team, and help hire and mentor future engineers. The position emphasizes initiative, evidence-based decisions, candid communication, and balancing ambitious work with relationships and recovery.

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 handling PHI under HIPAA.
Substantial production experience on AWS and 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 responsibility for reviewing outputs and ensuring 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 into model-ready tables and evaluated results, handling PHI appropriately throughout.
Build and extend EHR integrations, beginning with athenahealth FHIR APIs, across additional EHRs, data formats, and partner environments.
Develop AI-assisted tooling 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.
Contribute to infrastructure, DevOps, and security, including infrastructure as code, CI/CD, monitoring, and HIPAA and HITRUST controls.
Package, run, and monitor production models, sharing accountability with Research for real-world performance.
Build reports, dashboards, and clinician- and patient-facing products as needed.
Establish engineering standards, help hire and mentor incoming engineers, and use AI coding agents and automation responsibly, especially around PHI.