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Flagship Pioneering, Inc.

Senior Software Engineer (Backend)

  • Office
  • 6+ years

Salary

$108,000 - 186,000/ year

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Description

The company builds AI diagnostics products that aim to find disease before it becomes visible, giving patients and care teams earlier insight so they can act before harm becomes irreversible.

The company is an early-stage team of ML researchers, serial founders and clinical experts. It is part of a venture-creation group that builds companies at the frontier of science and technology.

This role reports to the VP of Engineering. You will own major parts of the system that turns EHR data from health-system partners into results those partners can trust.

The core work is backend, data and EHR integration engineering on AWS. The product is still taking shape, so you will also use AI tools across MLOps, infrastructure and product engineering where needed, and help decide what gets built next.

Engineering and research operate as one team, sharing code and pipelines from experiments through deployment and sharing responsibility for model performance. You will not train AI/ML models, but you will work closely with data scientists on data mapping, evaluation and model packaging.

Responsibilities

  • Design, build and run secure, auditable AWS pipelines that carry partner EHR data from ingestion to model-ready tables and evaluated results, handling PHI correctly at each stage.
  • Build and extend EHR integrations, starting with athenahealth's FHIR APIs, for new EHRs, data formats and partner environments.
  • With the data scientists, create AI-assisted tools that make onboarding partners and data sources quicker and more repeatable.
  • Lead technical go-lives with partner IT and data teams, and carry issues through to resolution.
  • Cover infrastructure, DevOps and security as needed: infrastructure as code, CI/CD, monitoring, and the HIPAA and HITRUST controls partners expect.
  • Run and monitor models in production, sharing responsibility with Research for their real-world performance.
  • Build reports, dashboards and clinician and patient products used by partners, patients and care teams.
  • Set engineering standards for a team that will grow, and help hire and mentor the engineers who join.
  • Use AI coding agents and automation to extend what a small team can deliver, judging carefully when they are safe to use near PHI.
  • Within six months, new partner sites go live through configuration instead of custom engineering, and you act as a trusted technical contact for partners.
  • Within twelve months, you have shaped the architecture of the company's first products and the engineering practices a larger team will use.

Requirements

  • A BS in computer science or a related field, or equivalent practical experience, plus at least 7 years of professional experience building and running production backend systems and data pipelines.
  • Hands-on healthcare data work with 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, with strong Python and SQL.
  • Experience running AI/ML systems in production, sharing code and pipelines with data scientists or ML researchers.
  • Daily use of AI coding agents and agentic workflows, reviewing their output and staying accountable for correctness, security and privacy.
  • Experience at an early-stage startup or similar zero-to-one setting, and willingness to work outside your core specialty when needed.
  • Experience debugging hard problems across system boundaries, from a partner's EHR or data feed through to production.
  • Clear communication with engineers, data scientists, clinicians and partner IT teams.
  • Exceptional fit: EHR integration experience with athenahealth, Epic or similar systems, including SMART on FHIR or bulk FHIR exports.
  • Exceptional fit: infrastructure as code (CDK, Terraform or similar), containers and CI/CD, including AWS setups that isolate sensitive data.
  • Exceptional fit: experience building software under HITRUST, SOC 2 or FDA quality-system expectations.
  • Exceptional fit: frontend or full-stack work, for example with React and TypeScript.
  • Exceptional fit: experience on integrated teams where engineers and data scientists share code, reviews and responsibility for results.

Conditions

The company's mission comes first, ahead of personal preference.

You take initiative and ownership, with clear outcomes and room to act without approval for every step.

Evidence decides: the team changes its mind when the data says so, even if that complicates the story or delays a milestone.

Candid challenge is welcome, and once a decision is made, the team backs it.

The team invests in relationships, celebration and recovery, aiming for work that is both joyful and balanced.

The salary range is $108,000 to $186,000. Final pay depends on qualifications, skills, competencies and experience.

Candidates who meet only some of the listed qualifications are encouraged to apply, as the company works to build diverse and inclusive teams.

Benefits

  • Healthcare coverage, an annual incentive program, retirement benefits and a broad range of other benefits.
  • Benefit and pay details reflect the company's good-faith estimate at publication and may change in the future.

Where you’d work

From the office

About the company

Flagship Pioneering, Inc.

  • Industry: HealthTech

Office in United States

Also hiring in United Kingdom

1 of their 13 open roles is remote

Your chances

Worth a look before you spend an evening tailoring a CV for it.

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  • Must-haves
Details11 facts · Role, Location, Compensation, Company
Tech stack
  • React
  • TypeScript
  • Python
  • SQL
  • AWS
  • Terraform
  • CI/CD
Seniority
Senior
Industry
HealthTech
Specialty
Backend
Region
United States
Pay period
Annual
Show 5 more factsShow less

Role

Category
Development
Specialty
Backend
Seniority
Senior
Experience
7+ years
Tech stack
  • React
  • TypeScript
  • Python
  • SQL
  • AWS
  • Terraform
  • CI/CD

Location

Work model
Office
Region
United States
Office
  • United States

Compensation

Salary
$108,000 - 186,000 / year
Pay period
Annual

Company

Industry
HealthTech

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