Senior Software Engineer (Backend)
Flagship Pioneering, Inc.2 days ago
Base Salary
$108k - $186k/yr
Responsibilities
- Design, build, and operate secure, auditable AWS data and EHR integration pipelines from ingestion through model-ready tables and evaluated results.
- Build and extend EHR integrations, beginning with athenahealth FHIR APIs, across EHRs, data formats, and partner environments.
- Develop AI-assisted onboarding tools with data scientists to make new partner and data-source integrations repeatable.
- Lead technical go-lives with partner IT and data teams and resolve issues across system boundaries.
- Contribute to infrastructure as code, CI/CD, monitoring, security controls, production model operations, and product or full-stack engineering as business needs require.
- Establish engineering standards, use AI coding agents responsibly near PHI, and help hire and mentor engineers.
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 with EHR data, FHIR or HL7, clinical vocabularies, and systems handling PHI under HIPAA.
- Substantial production AWS experience and proficiency in Python and SQL.
- Experience running AI/ML systems in production alongside data scientists or ML researchers using shared code and pipelines.
- Daily experience with AI coding agents and agentic workflows, including accountability for correctness, security, and privacy.
- Experience in an early-stage startup or comparable zero-to-one environment and willingness to work beyond a core specialty.
- Experience debugging complex problems from partner EHR or data feeds through production, with clear communication across technical, clinical, and partner teams.
- Preferred experience includes athenahealth, Epic, SMART on FHIR, bulk FHIR exports, infrastructure as code with CDK or Terraform, containers, CI/CD, isolated sensitive-data AWS environments, HITRUST, SOC 2, FDA quality-system expectations, React, TypeScript, and integrated engineering/data-science teams.
Benefits
- Healthcare coverage, an annual incentive program, retirement benefits, and a broad range of other benefits are offered.
- The role is based in an early-stage environment with autonomy, responsibility, relationship-building, celebration, and recovery emphasized in the company’s working practices.
About Flagship Pioneering, Inc.
Flagship Pioneering invents, builds, and finances platform biotechnology companies in human health and sustainability, providing founding science, capital, and operational support to entrepreneurs and researchers. The privately held firm, founded in 2000 and headquartered in Cambridge, MA, has originated more than 100 ventures and maintains an ecosystem of 40+ companies. Notable portfolio companies include Moderna, Denali Therapeutics, Generate:Biomedicines, Indigo Agriculture, and Tessera Therapeutics.