Job Description

What if...   We could harness the power of Flagship’s scientific platforms and create novel treatment options that benefit more patients, sooner? 

Pioneering Medicines, an initiative of Flagship Pioneering, is building a world-class biopharmaceutical R&D capability focused on conceiving and developing life-changing treatments for patients by harnessing the power of Flagship's scientific platforms and applying those innovative approaches to serious diseases with unmet medical need. Unique to Pioneering Medicines’ approach is the opportunity to combine platforms to create truly novel and potentially transformative treatments.  

Position Summary:

We are seeking a hands-on Data Engineer to build and maintain modern data solutions that support research, data science, and informatics workflows. You’ll work closely with cloud architecture, bioinformatics, and data science teams to design and operationalize pipelines, databases, and analytics platforms in AWS.

This role is ideal for someone who thrives in a collaborative R&D environment, loves to code, and is passionate about data engineering in support of drug discovery and translational science.

Key Responsibilities:

• Build, maintain, and optimize data pipelines in AWS to support scientific and operational use cases.


• Partner with scientists, bioinformaticians, and analysts to ingest, transform, and structure data for analytics and modeling.


• Contribute to the development of scalable data lakes, marts, and warehouse solutions.


• Implement automation and CI/CD for data workflows to ensure reproducibility and scalability.


• Monitor and support production pipelines, troubleshoot issues, and drive continuous improvement.


• Collaborate with application teams to integrate data systems with scientific and operational tools.


• Ensure data security, quality, and compliance with regulatory and privacy standards.

Required Qualifications:

• 3+ years of experience in data engineering, ideally in the life sciences or healthcare domain.


• Strong experience building data pipelines using Python and SQL.


• Proficiency with AWS data services (e.g., S3, Glue, Redshift, RDS, Athena).


• Familiarity with modern data frameworks (e.g., Airflow, dbt, Spark).


• Experience working with both structured and unstructured data (CSV, JSON, Parquet, etc.).


• Working knowledge of CI/CD and Git-based development workflows.


• Comfortable collaborating with cross-functional teams in a fast-paced R&D setting.

Preferred Qualifications:

• Experience supporting bioinformatics, cheminformatics, or clinical data workflows.


• Familiarity with data visualization tools (e.g., Tableau, Spotfire) or notebook environments (e.g., Jupyter, RStudio).


• Exposure to Agile or Scrum-based development.


• AWS certification (e.g., Data Analytics or Solutions Architect Associate).

What We Look For:

• A builder’s mindset and a passion for solving complex data problems.


• Curiosity and a desire to learn scientific domains and business drivers.


• A sense of urgency and a bias toward action.


• Commitment to quality, reliability, and reproducibility in engineering work.

About Flagship Pioneering:

Flagship Pioneering is a biotechnology company that invents and builds platform companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health and sustainability exponentially accelerate scientific progress in areas ranging from cancer detection and treatment to nature-positive agriculture. What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. Many of the companies Flagship has founded 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. 

Flagship Pioneering and our ecosystem companies are  committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.

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Job Tags

Full time,

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