Senior Software Engineer (Backend)

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

Who we are

FL113 is a fast-moving AI diagnostics company with a bold ambition: to define the future of pre-emptive and proactive care. We are building products that help uncover disease before it becomes visible, equip patients and care teams with earlier insight, and enable meaningful intervention before disease advances and causes irreversible harm. Our team brings together ML researchers, serial entrepreneurs, and clinical experts, united by a common commitment to make proactive care a reality.

Who we are

FL113 is a fast-moving AI diagnostics company with a bold ambition: to define the future of pre-emptive and proactive care. We are building products that help uncover disease before it becomes visible, equip patients and care teams with earlier insight, and enable meaningful intervention before disease advances and causes irreversible harm. Our team brings together ML researchers, serial entrepreneurs, and clinical experts, united by a common commitment to make proactive care a reality.

FL113 is part of the Flagship Pioneering ecosystem, a premier venture-creation platform recognized twice on FORTUNE’s “Change the World” list and twice on Fast Company’s list of the World’s Most Innovative Companies. Flagship creates companies at the frontier of science and technology, bringing together founders, operators, and investors to take bold leaps on consequential problems and turn breakthrough ideas into enduring businesses. Join an exceptional team and help shape the future of AI and healthcare.

About the role

As Senior Software Engineer, Backend & Data, you will report to the VP of Engineering and own major parts of the system that turns EHR data from our health-system partners into results our partners can trust. The core of the role is backend, data, and EHR integration engineering on AWS. Our product is still taking shape, so you will also use AI tools to take on MLOps, infrastructure, and product engineering as the company needs, and help decide what we build next.

Engineering and Research work as one team, with shared code and pipelines from experimentation through deployment and shared accountability for how our models perform. You will not be expected to train AI/ML models, but you will work side by side with our data scientists on data mapping, evaluation, and model packaging.

Key Responsibilities

Build the Data and EHR Integration Platform

• Design, build, and operate secure, auditable pipelines on AWS that take partner EHR data from ingestion to model-ready tables and evaluated results, with PHI handled correctly at every step.
• Build and extend EHR integrations, starting with athenahealth’s FHIR APIs, across new EHRs, data formats, and partner environments.
• Build AI-assisted tooling, together with our data scientists, that makes onboarding new partners and data sources faster and more repeatable.
• Lead technical go-lives with partner IT and data teams, and see issues through to resolution.

Flex Where the Company Needs You

• Infrastructure, DevOps, and security: infrastructure as code, CI/CD, monitoring, and the HIPAA and HITRUST controls our partners expect.
• ML and model operations: package, run, and monitor models in production, sharing accountability with Research for real-world performance.
• Product and full-stack: build the reports, dashboards, and clinician- and patient-facing products that our partners, patients, and care teams use.

Build the Engineering Foundation

• Set the engineering standards a growing team will inherit, and help hire and mentor the engineers who join next.
• Use AI coding agents and automation to multiply what a small team can do, with sound judgment about their use near PHI.

What success looks like

• In six months: New partner sites onboard through configuration rather than custom engineering, and you are a trusted technical counterpart for our partners.
• In twelve months: You have shaped the architecture of FL113’s first products and the engineering practices a larger team will use.

How we work

• Purpose over preference. The company’s mission comes first.
• Take initiative. Take responsibility. Clear outcomes and room to act, without needing approval for every step.
• Put evidence first. We let evidence change our minds, even when it complicates our story or delays a milestone.
• Speak honestly, move together. We choose candid challenge over smooth agreement, then support the decision.
• Work with joy and balance. We invest in relationships, celebration, and recovery.

What We Look For

• BS in Computer Science or a related field, or equivalent practical experience, and 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, and proficiency in Python and SQL.
• Experience running AI/ML systems in production, working in shared code and pipelines with data scientists or ML researchers.
• Daily use of AI coding agents and agentic workflows, while reviewing outputs and staying accountable for correctness, security, and privacy.
• Experience in an early-stage startup or a comparable zero-to-one environment, and an eagerness to work outside your core specialty as the company needs.
• 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.

What will make you an exceptional fit

• You have built EHR integrations with athenahealth, Epic, or similar systems, including SMART on FHIR or bulk FHIR exports.
• You have worked with infrastructure as code (CDK, Terraform, or similar), containers, and CI/CD, including AWS setups that keep sensitive data in its own isolated environment.
• You have built software under HITRUST, SOC 2, or FDA quality-system expectations.
• You have frontend or full-stack experience (for example, React and TypeScript).
• You have worked on integrated teams where engineers and data scientists share code, reviews, and responsibility for results.

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer

All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $108,000 - $186,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL113 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL113's good faith estimate as of the date of publication and may be modified in the future.