Flagship Pioneering · 18 hours ago
(Senior) Data Engineer
Boston, MA
Full-time
Onsite
New Grad, Entry, Mid, Senior Level
$74K/yr - $176K/yr
0+ years expFlagship Pioneering is a company that invents and builds platform companies to transform human health and sustainability. They are seeking a Senior Data Engineer to join ProFound Therapeutics, where the individual will build the data foundation for drug discovery by integrating diverse biological data and enabling machine learning models.
FinanceFinancial ServicesVenture Capital
Responsibilities
Contribute to design and scaling of our multi-modal data platform that integrates public and proprietary biological data (genomics, transcriptomics, proteomics, imaging, perturbation data) across data lakes, graph databases, relational and NoSQL databases, and data warehouses, enabling ML training, computational biology pipelines, and scientific exploration
Build production data pipelines and workflows that automate data ingestion and transformation, working with domain experts to optimize analysis pipelines for scientific discovery
Partner with computational and wet-lab scientists to model experimental data, manage instrument outputs and electronic lab notebook data, and ensure seamless integration into our data platform
Develop and manage cloud infrastructure on AWS following best practices and the Well-Architected framework, with focus on scalability, security, and cost optimization
Contribute to the data engineering team’s best practices including comprehensive documentation, monitoring and observability, and robust testing frameworks
Collaborate with external partners including CROs, vendors, and consultants to coordinate data transfers and support platform integrations
Qualification
Required
BS, MS, or PhD in Computer Science, Bioinformatics, or related field with 0-4 years of professional data engineering experience
Background in scientific domains (biology, chemistry, or related fields)
Python expertise including data science libraries and testing frameworks
AWS experience with storage, database, compute, and analytics services (S3, RDS, DynamoDB, Redshift, Lambda, EC2, Batch, ECS, Glue, Athena)
Proven experience designing, deploying, and maintaining production data pipelines at scale
Hands-on experience with workflow orchestration systems (AWS Step Functions, NextFlow, dbt, Dagster) and event-driven architectures
Working knowledge of CI/CD frameworks, infrastructure-as-code (CloudFormation or AWS CDK), and containerization (Docker)
Strong technical communication skills with ability to translate complex technical concepts for scientific audiences and collaborate effectively across disciplines
Demonstrated ability to thrive in dynamic environments, prioritize competing demands, and make pragmatic trade-offs in a fast-paced startup setting
Preferred
Experience with data lakes and open table formats (Iceberg preferred)
Experience with knowledge graph technologies and graph databases (Neo4j)
Familiarity with lab data management systems (LIMS, ELN, integrated data lakes)
Experience with MLOps practices and tools for model training pipelines, experiment tracking, and model deployment
AWS certification (Associate or Professional level)
Benefits
Healthcare coverage
Annual incentive program
Retirement benefits
Broad range of other benefits
Company
Flagship Pioneering
Flagship Pioneering is a venture capital firm that invests in life sciences and healthcare companies.
501-1000 employees
H1B Sponsorship
Flagship Pioneering has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (8)
2024 (4)
2023 (4)
2022 (4)
2021 (1)
Funding
Current Stage
Late StageLeadership Team
Noubar Afeyan
Founder and CEO
Chuck Carelli
Chief Financial Officer
Recent News
2026-01-16
2026-01-16
Company data provided by crunchbase