Senior / Principal Data Infrastructure Engineer

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Senior / Principal Data Infrastructure Engineer in USA

Flagship Pioneering, Inc.
Full time
Email

USA
10/09/2026
Report

Cambridge, MA

Responsibilities

Design and build a scalable, highly available data platform integrating experimental proteomics data with computational tools.
Define the data infrastructure technical vision and roadmap while independently delivering complex systems.
Automate workflows across proteomics environments, including high-throughput assays, mass spectrometry processing, instrument integration, and LIMS connectivity.
Develop and operate data pipelines and layered data architectures that transform raw instrument output into reliable, reproducible ML-ready datasets.
Design, deploy, and maintain cloud infrastructure for biological and proteomics data processing, storage, and analysis.
Establish tooling and standards for data integrity, lineage, traceability, consistency, capture, storage, and sharing.
Partner with proteomics, chemistry, biology, and machine learning teams as the technical expert on data systems.
Set engineering standards through code and design reviews, mentorship, and knowledge sharing.

Requirements

Bachelor's degree in Computer Science, Data Engineering, Computational Biology, Proteomics, or a related technical field; an advanced degree is a plus.
At least 8 years of hands-on experience in data infrastructure, data engineering, informatics, or related fields.
Experience independently designing, building, and operating terabyte-scale data systems, preferably in biotech or life sciences.
Ability to set technical direction and deliver complex projects with minimal oversight.
Expertise with cloud infrastructure, Kubernetes, and infrastructure-as-code tools including CFN, CDK, Terraform, or ARM.
Deep experience with data modeling, databases, data warehouses, lakehouse architectures, and medallion-style architectures.
Experience architecting data pipelines and workflow orchestration using tools such as Flyte, Dagster, or Airflow.
Strong proficiency in Python and SQL, with comfort using R.
Hands-on experience with DevOps, SDLC, automation, and CI/CD practices.
Strong written and verbal communication skills for explaining technical decisions to technical and non-technical colleagues.
Preferred qualifications include experience with LLMs and agentic tooling, mass spectrometry or NGS datasets, biomarker discovery, LIMS, laboratory automation, robotic platforms, and sample management systems.

Benefits

Healthcare coverage, an annual incentive program, retirement benefits, and a broad range of other benefits are offered.
The listed compensation and benefits are based on the company's good-faith estimate and may be modified in the future.

Salary: $108k - $209k/yr

Flagship Pioneering, Inc.

Flagship Pioneering invents, builds, and finances platform biotechnology companies in human health and sustainability, providing founding science, capital, and operational support to entrepreneurs and researchers. The privately held firm, founded in 2000 and headquartered in Cambridge, MA, has or...

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