Principal Data Engineer
Senior hands-on data platform architect at Vesalius Therapeutics (a Flagship Pioneering company) who owns and evolves the AWS data platform behind human genetics, multi-omics, and high-content imaging programs — spanning orchestration, lakehouse/warehouse design, IaC and DevOps, cost governance, and lab-to-cloud data pipelines.
- Compensation
- $179K–$236K / yr
- Location
- Cambridge, MA USA
- Work setup
- Not specified
- Seniority
- Principal
- Employment
- Not specified
- Experience
- 10+ years
- Category
- Data engineering
- Posted
Skills
Must have
- 10+ years building and operating production data infrastructure, with track record architecting and owning platforms end to end
- Deep AWS expertise: S3, IAM, EC2, Batch, Lambda, Spark (EMR or equivalent)
- Technical owner of production cloud environments, including multi-account architecture and cross-account access
- Strong Python and SQL with production-grade pipeline development background
- Production experience with workflow orchestration (Nextflow, Airflow, Temporal, Step Functions, Redun, or similar)
- Infrastructure as code (CloudFormation/CDK), CI/CD, containers, and observability
- Data modelling and warehouse or lakehouse design, including metadata management, lineage, and data quality
- Cost governance at scale: budgets, tagging, rightsizing, storage lifecycle across hundreds of terabytes
- Fluency with scientific data semantics (studies, samples, donors, cell lines, assays) and partnering with scientists
Nice to have
- Familiarity with genetics and genomics data
- Microscopy or high-content screening data, including large binary object stores, transfer optimization, and image streaming
- Databricks, OpenMetadata, or a comparable data catalog in production
- Snowflake, particularly governed access patterns over cloud object storage
- ML infrastructure: SageMaker or Databricks ML, MLflow or Weights & Biases, feature stores
- Serving data to LLM or agent clients (MCP servers, tool APIs)
- Leading data platform architecture as senior/principal IC in biotech, pharma R&D, or a research institute
Full description
What if you could join a rapidly growing company and play a critical role in bringing new medicines to patients by helping scale the programmable infrastructure behind a new human cellular biology platform?
About Vesalius
Vesalius Therapeutics is pioneering a new platform to generate breakthrough treatments for common diseases. Our platform combines large-scale human genetics, genomics, stem cell studies, high-dimensional cellular phenotyping, and artificial intelligence to uncover causal biology and identify optimal intervention points for new therapies. Vesalius was founded in 2019 by Flagship Pioneering.
Role Overview
We are seeking a Principal Data Engineer to lead the architecture and evolution of the data platform underpinning our human genetics, multi-omics, and high-content imaging programs.
This is a senior, hands-on leadership role with broad technical authority. As the architectural lead for data engineering, you will set the direction for our AWS environment and the pipelines, catalog, and access layers built on it, defining the technical roadmap and the standards others build against. The scope spans core cloud data engineering (orchestration, warehousing, infrastructure as code, cost governance) and the distinctive challenges of scientific data: connecting each microscopy image to its cell line, donor, and study of origin, and enabling scientists to answer genotype questions directly, without specialist intervention.
You will join a focused, high-impact team supporting a research organization whose data generation and analytical ambitions are expanding rapidly. Our platform is established and productive, and is now entering a deliberate modernization phase. You will lead that transition, with significant influence over the platform's next-generation architecture.
At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.
Role Responsabilities
- Serve as technical owner and architect of our AWS environment, including account structure, IAM, networking, compute, and storage.
- Lead and extend cost governance, including budgets, alerting, tagging enforcement, rightsizing, and storage lifecycle and tiering.
- Define and own developer operations for the data platform, including infrastructure as code, CI/CD, container builds, and secrets and environment management.
- Upgrade our data lake, managed orchestration, metadata and data ingestion workflows to scale with future data production and enhance the infrastructure that transfers data from the lab to the cloud.
- Partner with ML and computational biology leaders to define the interface between platform and modelling.