(Senior) Data Engineer

About ProFound Therapeutics

ProFound Therapeutics is pioneering the discovery of the expanded human proteome to unlock a new universe of potential therapeutics. By integrating multi-omics, advanced computation, and translational biology, we aim to reveal and characterize thousands of previously uncharted proteins and systematically explore their role in health and disease.

The Role

We're seeking a (Senior) Data Engineer to join our data team. This individual will play a central role in building the data foundation that powers ProFound's drug discovery platform. You'll architect systems that integrate diverse biological data—from genomics and proteomics to imaging and perturbation experiments—enabling our scientists to make breakthrough discoveries and our ML models to identify novel therapeutic targets.

This role offers the unique challenge of working at the intersection of computational biology, machine learning, and modern data engineering, with the impact of accelerating life-saving therapeutics.

Key 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.

Required Qualifications

• 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 Qualifications

• 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).

Why ProFound

This role offers the opportunity to shape the technical and scientific foundation of a next-generation drug discovery platform. You will operate with real ownership, influence core architectural decisions, and work directly with leaders in AI, human genetics, and computational biology to expand the human proteome and uncover new therapeutic opportunities

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

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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