--- title: 'Principal Data Engineer at Flagship Pioneering, Inc.' canonical: 'https://feeny.ai/job/principal-data-engineer-flagship-pioneering-inc-cambridge-sv1sekyxhkr4' type: 'job' last_seen: '2026-10-30' --- # Principal Data Engineer at Flagship Pioneering, Inc. - **Company:** Flagship Pioneering, Inc. - **Location:** Cambridge, MA - **Posted:** 2026-10-27 - **Last confirmed live:** 2026-10-30 - **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8919733002?gh_jid=8919733002 ## Job 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](https://www.flagshippioneering.com/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. Required Qualifications - 10+ years building and operating production data infrastructure, with a track record of architecting and owning platforms end to end. - Deep AWS expertise: S3, IAM, EC2, Batch, Lambda, and Spark (EMR or equivalent). Experience as technical owner of production cloud environments, including multi-account architecture and cross-account access. - Strong Python and SQL, with a background in production-grade pipeline development. - Production experience with workflow orchestration (Nextflow, Airflow, Temporal, Step Functions, Redun, or similar) and the judgement to evaluate and select among them. - Infrastructure as code (CloudFormation/CDK), CI/CD, containers, and observability. DevOps is a core competency for this role. - Data modelling and warehouse or lakehouse design, including metadata management, lineage, and data quality practice. - Cost governance at scale, including budgets, tagging, rightsizing, and storage lifecycle across hundreds of terabytes. - Fluency with scientific data semantics (studies, samples, donors, cell lines, assays) and the ability to partner directly with scientists to translate their questions into data models. ## Preferred Qualifications - Familiarity with genetics and genomics data. - Microscopy or high-content screening data, including large binary object stores, transfer optimization, and image streaming for model training. - Databricks, OpenMetadata, or a comparable 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). - Experience leading data platform architecture as a senior or principal individual contributor, ideally in biotech, pharma R&D, or a research institute. 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. Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com. The salary range for this role is $179,000 - $236,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Vesalius Therapeutics currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Vesalius Therapeutics's good faith estimate as of the date of publication and may be modified in the future. Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com. ## About Flagship Pioneering, Inc. ## Company Overview - **One-liner**: Flagship Pioneering is a life sciences venture creation firm that conceives, creates, and capitalizes breakthrough bioplatform companies in biotechnology, health, and sustainability. - **Entity Type**: Private (Venture Creation Firm) - **Headquarters**: Cambridge, Massachusetts, United States - **Founded**: 2000 - **Founders**: Noubar Afeyan (Co-Founder & CEO) ## Core Business - **Primary industry/industries**: Biotechnology Research, Life Sciences Venture Creation, Company Incubation - **Target customers**: B2B / B2G – partners with academic institutions, pharma companies, and investors; also acts as an employer for scientists, entrepreneurs, and corporate builders - **Mission or purpose statement**: “To harness the 21st century's most powerful technological forces for good to deliver a better future for all.” ## Products & Services Flagship does not sell products directly; its offerings are the companies it creates and the innovation platform it operates. - **Innovation Platform**: A systematic, institutionalized process to identify “unreasonable” scientific questions, test them rigorously, and spin out independent companies that develop therapeutics, diagnostics, agricultural technologies, and more. - **Portfolio Companies**: Over 120 companies founded, including Moderna, Generate:Biomedicines, Inari Agriculture, Tessera Therapeutics, Lila Sciences, and others. Each is a separate enterprise with its own products (e.g., mRNA vaccines, gene-editing tools, AI-driven drug discovery). ## Market Standing - **Valuation/Market Cap**: Not publicly disclosed (privately held) - **Key Metric**: Annual revenue of approximately $800 million (2025/2026 estimate) and 620 employees (+9.7% YoY growth) - **Notable Investors/Partners**: Flagship is itself an investor and partner; key collaborations include AWS (to accelerate drug discovery), Harvard Medical School, Broad Institute, and multiple top-tier biopharma companies. Portfolio company Moderna is a publicly traded giant. - **Growth Signals**: 78 active job postings (+50% quarterly), recent formation of Terion (digital agriculture infrastructure) and Serif Biomedicines (modified DNA platform), and expanded presence in Europe and Asia. ## Competitive Advantages - **Unique Model**: Combines scientific exploration, company creation, and capital investment under one roof – “a way that is largely without precedent” - **Deep Talent Pool**: Exceptional network of scientist-entrepreneurs and company builders; top hires from MIT, Harvard, Biogen, Novartis, and Pfizer - **Track Record**: Over two decades of founding transformational companies (e.g., Moderna’s COVID‑19 vaccine), demonstrating repeatable innovation - **Process-Driven**: Systematic methodology for turning “what‑if” questions into patentable bioplatforms, reducing risk compared to ad‑hoc startup creation ## Strategic Focus - **Current priorities**: Expanding AI/machine learning integration across drug discovery and life sciences (highlighted by AWS collaboration); entering preemptive health and medicine; advancing sustainable agriculture and climate solutions; growing international operations (UK, Singapore, Canada, Switzerland, Japan) - **Direction for growth**: Launching new platform companies at a steady cadence (e.g., Terion, Serif in 2026); deepening expertise in computational protein design, modified DNA, and gene editing ## Why Work Here - **Culture**: “Brave and bold organization of creative-thinkers with insurgent mindsets” – emphasis on fearlessness, mentorship, and teamwork across science and business - **Work Environment**: Headquarters in Cambridge, MA with 5 US offices; roles span research, strategy, finance, and operations; hybrid/remote flexibility varies by role - **Notable Perks**: Opportunity to work on world-changing science (e.g., COVID‑19 vaccine, gene editing) alongside top scientists and company builders; strong compensation (salary range example: Sr. Associate ~$68K, ML Engineer ~$122K; overall comp rating 3.7/5) - **Engineering/Science Culture**: Heavy investment in R&D (15% of workforce in research), cutting-edge tools (Cryo‑EM, AI/ML), and a process that encourages bold leaps ## Sources 1. [flagshippioneering.com](https://www.flagshippioneering.com/) 2. [flagshippioneering.com/about](https://www.flagshippioneering.com/about) 3. [flagshippioneering.com/join](https://www.flagshippioneering.com/join) 4. [flagshippioneering.com/join/roles](https://www.flagshippioneering.com/join/roles) 5. 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