Lead Data Engineer

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 128,000 - 176,000; Full time

Job summary

Flagship Pioneering, Inc. in Cambridge, MA seeks a Lead Data Engineer to modernize and professionalize data infrastructure, pipelines, and platforms. You will lead core platform systems and collaborate with I/O, Lab IT, PI Tech, and data science teams to deliver secure, scalable data solutions.

You will mentor engineers, set engineering standards, and leverage generative AI to accelerate development while ensuring reliable operations across complex systems.

Qualifications

• 6+ years of hands-on data engineering experience, preferably in life sciences, biotech, or healthcare environments.
• Proven ability to design and operate cloud-native data architectures (AWS).
• Advanced Python and SQL skills for data manipulation and automation.
• Experience with modern frameworks and tools (Dagster, dbt, Spark, Iceberg, Lake Formation, Athena, Glue).
• Strong Git, CI/CD, CDK, containerized workflows (Docker, ECS).
• Experience handling structured and unstructured data (CSV, JSON, Parquet, imaging).
• Proven track record leading complex cross-functional projects with stakeholders.
• Experience using generative AI tools to boost velocity and reduce boilerplate.
• Ability to lead technically under ambiguity and ensure reliable operations.

Responsibilities

• Serve as technical lead on complex data engineering projects across multi-system environments.
• Lead the implementation of data infrastructure, platforms, tools, and data products.
• Improve reliability of data storage solutions (lakehouses, marts, warehouses).
• Build data pipelines to support data lakes and platforms.
• Establish engineering standards for testing, documentation, release management, and monitoring.
• Lead observability, management, resilience, and performance improvements.
• Diagnose and resolve complex failures spanning infra and data pipelines.

Skills

6+ years of hands-on data engineering

AWS cloud-native architectures

Python

SQL

Generative AI tools

Lead cross-functional projects

Tools

Dagster

dbt

Spark

Iceberg

Lake Formation

Athena

Glue

Git

CI/CD

CDK

Docker

ECS

Generative AI tooling

Job description

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies.

Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies.

ABOUT THE POSITION

We are seeking a Lead Data Engineer to lead complex initiatives aimed at modernizing and professionalizing our data infrastructure, platforms, and pipelines. You will lead the implementation of core platform systems and help to set the directions and standards of our data infrastructure and pipelines. You will work closely with other engineers and stakeholders across Infrastructure & Operations (I&O), Lab IT, Pioneering Intelligence (PI) Tech, and the internal scientific community to turn evolving scientific needs into secure, reliable and scalable data engineering solutions.

Reporting into the Associate Director, Data Architecture & Engineering, this is a technical, senior individual-contributor role that will champion engineering best practices, build complex data pipelines, lead data platform implementations, and handle the troubleshooting and optimization of data warehouse and storage solutions.

CORE RESPONSIBILITIES

Data & Platform Engineering

• Serve as the technical lead and subject matter expert on complex data engineering projects involving interdependent systems, legacy environments, and emerging cloud-first platforms.
• Lead the implementation of data infrastructure, platforms, tools, and other data products.
• Lead the optimization and reliability of data storage solutions (lakehouses, marts, warehouses, etc.).
• Implement complex backend and data integration pipelines to support data lakes, marts, and other platforms.
• Establish and reinforce engineering standards for testing, documentation, release management, and monitoring across the team.
• Lead implementations for platform observability, management, resilience, capacity, and performance.
• Diagnose and resolve complex failures spanning infrastructure and data pipelines; lead incident reviews and ensure corrective actions improve the wider system.

Cross-Functional Collaboration & Technical Leadership

• Collaborate across I&O, Lab IT, PI Tech, data science, and bioinformatics teams to ensure architectural alignment, reuse of components, and shared understanding of system states and dependencies.
• Mentor junior engineers and establish engineering standards that drive excellence, reproducibility, and innovation across the team.
• Leverage generative AI tools and frameworks to accelerate pipeline development, data transformation, and metadata enrichment at scale.

REQUIRED QUALIFICATIONS

• 6+ years of hands-on experience in data engineering, preferably in life sciences, biotech, or healthcare environments.
• Proven expertise in designing and operating cloud-native data architectures, particularly within AWS.
• Advanced proficiency in Python and SQL for data manipulation, pipeline development, and system automation.
• Extensive experience with modern frameworks and tools such as Dagster, dbt, Spark, Iceberg, Lake Formation, Athena, Glue, etc.
• Strong experience with Git, CI/CD, CDK, containerized workloads, Docker, and ECS.
• Experience supporting both structured and unstructured data (CSV, JSON, Parquet, imaging, etc.).
• Demonstrated success in leading complex, cross-functional projects involving technical and scientific stakeholders.
• Practical experience using generative AI tools (e.g., Claude Code, GPT-based tools, etc.) to boost engineering velocity and reduce boilerplate.
• A track record of leading complex technical initiatives under ambiguity, making explicit trade-offs and remaining accountable for reliable operational outcomes.

PREFERRED QUALIFICATIONS

• Experience supporting bioinformatics, cheminformatics, or clinical data workflows.
• Familiarity with scientific software and ELN’s, particularly Benchling and CDD.
• Exposure to Agile or Scrum-based development methodologies.
• Relevant certifications (e.g., AWS Solutions Architect Associate, Data Analytics Specialty).

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, 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

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.

Privacy Notice for Applicants:

When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

The salary range for this role is $128,000 - $176,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.