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Senior / Principal Data Infrastructure Engineer

Flagship Pioneering, Inc.Cambridge, MA USAComputational & Data Sciences
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Salary
$108K - $209K.
Job type
Full-time
Experience
Senior · 8+ yrs
Posted
8 Oct 2026
Status
Open · checked 7d ago

About this role

Based in Cambridge, MA USA, Expedition Medicines is hiring a full-time Senior / Principal Data Infrastructure Engineer. This senior individual-contributor role suits an experienced engineer ready to design and own core data systems for machine learning and proteomics research.

Role Overview

Expedition Medicines operates in Cambridge, MA USA, focusing on protein editing through small molecules and machine learning. The organization seeks a hands-on technical lead to build production-grade data architecture that makes proteomics data usable across various scientific teams. Operating independently, the chosen engineer shapes the data roadmap and transforms raw instrument output into machine learning-ready datasets.

Key Responsibilities

Architect and build the core data platform integrating experimental proteomics data with computational tools, ensuring high availability, scalability, and security while writing production code.
Own the technical vision by defining and driving the data infrastructure roadmap and identifying key technical priorities.
Automate and integrate workflows across proteomics research environments, connecting instruments, pipelines, and laboratory information management systems like Dotmatics.
Develop and operate data pipelines using workflow orchestration tools such as Flyte and design medallion-style data architectures.
Design, deploy, and maintain cloud infrastructure for biological data processing and storage utilizing infrastructure-as-code and CI/CD practices.
Establish data integrity, lineage, and traceability standards across manual and automated workflows.
Partner directly with proteomics, chemistry, biology, and machine learning teams to translate scientific objectives into technical solutions.
Set engineering standards through code reviews, design reviews, and mentoring of engineers and scientists.

Requirements

Bachelor's degree in Computer Science, Data Engineering, Computational Biology, Proteomics, or a related technical field.
Minimum of 8 years of hands-on experience in data infrastructure, data engineering, informatics, or related fields within biotech or life sciences environments.
Proven track record of independently designing, building, and operating terabyte-scale data systems.
Demonstrated ability to set technical direction and deliver complex projects with minimal oversight.
Expertise in cloud infrastructure including AWS or Azure, Kubernetes, and infrastructure management as code tools such as Terraform, CDK, or CFN.
Deep understanding of data modeling with database and data warehouse systems like Postgres, Redshift, or Snowflake, alongside lakehouse and medallion-style architectures.
Experience with data pipeline architecture and workflow orchestration tools like Flyte, Dagster, or Airflow.
Strong proficiency in Python and SQL, with comfort in R.
Hands-on experience with DevOps, software design lifecycle, and automation tools.
Strong written and verbal communication skills for technical and non-technical audiences.

Nice to Have

Experience using large language models and agentic tooling to build natural-language query interfaces for scientific teams.
Experience with mass spectrometry, next-generation sequencing data sets, and biomarker discovery workflows.
Experience with laboratory information management systems such as Dotmatics or CORE LIMS.
Familiarity with laboratory automation systems and robotic sample management platforms.

Skills and Tools

Python
SQL
R
AWS / Azure
Kubernetes
Terraform / CDK / CFN
Postgres / Redshift / Snowflake
Delta Lake / Iceberg
Flyte / Dagster / Airflow
Dotmatics / LIMS

Salary and Benefits

The salary range for this position is $108,000 to $209,000.

About the Company

Expedition Medicines is a privately held, early-stage biotechnology company pioneering protein editing. The company is backed by Flagship Pioneering, an organization that invents and builds platform companies focused on human health and sustainability. Flagship Pioneering has originated more than 100 scientific ventures since 2000.

How to Apply

Candidates should apply directly on the official company careers page.

Skills and tech stack

PythonSQLRAWSAzureKubernetesTerraformCDKCFNARMPostgresRedshiftSnowflakeDelta LakeIcebergFlyteDagsterAirflowDotmaticsCORE LIMSLLMsMachine Learning

Questions candidates ask

What is the salary range for this role?

The salary range is between $108,000 and $209,000.

Where is the position located?

The position is located in Cambridge, MA USA.

What level of experience is required?

The role requires 8+ years of hands-on experience in data infrastructure, data engineering, informatics, or related fields.

What educational background is needed?

A bachelor's degree in Computer Science, Data Engineering, Computational Biology, Proteomics, or a related technical field is required, and an advanced degree is a plus.

Is visa sponsorship available?

Visa sponsorship is not explicitly stated in the posting.

Ready to apply?

The application is on the official Flagship Pioneering, Inc. careers page.

Apply on company site