--- title: 'Senior / Principal Data Infrastructure Engineer at Flagship Pioneering, Inc.' canonical: 'https://feeny.ai/job/senior-principal-data-infrastructure-engineer-flagship-pioneering-inc-cambridge-0cve2nw8geq3' type: 'job' last_seen: '2026-10-16' --- # Senior / Principal Data Infrastructure Engineer at Flagship Pioneering, Inc. - **Company:** Flagship Pioneering, Inc. - **Location:** Cambridge, MA - **Posted:** 2026-10-08 - **Last confirmed live:** 2026-10-16 - **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8869701002?gh_jid=8869701002 ## Job description What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability? About Expedition: Expedition Medicines is a privately held, early-stage biotechnology company pioneering the emerging field of Protein Editing. At Expedition Medicines we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities. Our platform integrates novel small molecule chemistry and chemoproteomic discovery technologies with Machine Learning (ML) to enable generative design. Expedition Medicines is backed by Flagship Pioneering, bringing their courage, vision, and resources to guide Expedition Medicines from platform validation to patient impact. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us! Position Summary: We are seeking a highly skilled, hands-on Senior / Principal Data Infrastructure Engineer to design, build, and own the data systems that make our proteomics data discoverable, trustworthy, and usable across the organization. Expedition Medicines develops machine learning tools trained on proteomics data generated by our experimental platform, and this role is critical to the robust, scalable collection, management, and analysis of that data at scale. This is a senior individual-contributor role for an engineer who writes the code, ships the systems, and sets the technical direction. You will work independently, with a clear point of view on where our data infrastructure needs to go, and you will turn that vision into working, production-grade systems that ML scientists, medicinal chemists, and biology teams rely on every day. Responsibilities: - Architect and build: Design and implement the core data platform that integrates experimental proteomics data with computational tools, with high availability, scalability, and security. Write production code. - Own the technical vision: Define and drive the technical roadmap for data infrastructure, identifying the highest-leverage problems. - Automate and integrate: Build automated workflows across proteomics research environments, including high-throughput assays and mass spectrometry data processing. Integrate instruments, pipelines, and LIMS (e.g., Dotmatics) for seamless, traceable data capture. - Data pipelines: Develop and operate robust data pipelines using workflow orchestration tools (e.g., Flyte), and design layered (e.g., medallion-style) data architectures turning raw instrument output into ML-ready datasets reliably and reproducibly. - Cloud infrastructure: Design, deploy, and maintain cloud-based infrastructure for biological and proteomics data processing, storage, and analysis, using infrastructure-as-code and CI/CD to enable continuous improvement of data systems. - Data integrity and quality: Establish and implement rigorous standards for data integrity, lineage, traceability, and consistency. Build the tooling that enforces best practices for data capture, storage, and sharing across manual and automated workflows. - Partner with scientists: Work directly with our proteomics, chemistry, biology and machine learning teams to translate scientific objectives into data infrastructure solutions. Be the go-to technical expert on data systems. - Engineering practices: Set engineering standards through code review, design review, and example. Mentor engineers and scientists informally and share knowledge. Qualifications: - Bachelor's degree in Computer Science, Data Engineering, Computational Biology, Proteomics, or a related technical field; advanced degree is a plus. - 8+ years of hands-on experience in data infrastructure, data engineering, informatics, or related fields, preferably in proteomics, bioinformatics, or other biotech environments. - Proven track record of independently designing, building, and operating terabyte-scale data systems in a biotech or life sciences environment. - Demonstrated ability to set technical direction and deliver complex projects with minimal oversight. - Expertise in cloud infrastructure (e.g., AWS, Azure), Kubernetes, and infrastructure management as code tools (CFN, CDK, Terraform, ARM). - Deep understanding and experience of data modeling with database and data warehouse systems (e.g., Postgres, Redshift, Snowflake). Strong familiarity with lakehouse and medallion-style architectures (e.g., Delta Lake, Iceberg). - Experience with data pipeline architecture and workflow orchestration (e.g., Flyte, Dagster, Airflow), including APIs, schedulers, and software integration. - Strong proficiency in Python, SQL; comfortable with R. - Hands-on experience with DevOps, software design lifecycle (SDLC), and automation tools (e.g., Terraform) and CI/CD practices. - Strong written and verbal communication skills, with the ability to explain technical decisions to both technical and non-technical colleagues. Preferred: - Experience using LLMs and agentic tooling (e.g., Claude, Model Context Protocol servers) to build interactive, natural-language query interfaces that give scientific teams direct access to data is highly preferred. - Experience with mass spectrometry and/or NGS data sets and biomarker discovery workflows. - Experience with LIMS and data management systems (e.g., Dotmatics, CORE LIMS). - Familiarity with laboratory automation systems, including integration with robotic and sample management platforms. About Flagship: Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.flagshippioneering.com%2F&data=05%7C01%7Cemccurdy%40flagshippioneering.com%7C723eebecb4fd441a8d4808dbc3706637%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C638318659764104453%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZLQGwoiIX4KB%2FcilEz8n9NdaOq6EQCJ3GpW8RIYr1Zw%3D&reserved=0). Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background. 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 $165,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Expedition Medicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Expedition Medicines'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. [linkedin.com/company/flagship-pioneering](https://www.linkedin.com/company/flagship-pioneering) ## Other roles at Flagship Pioneering, Inc. - [Origination Associate](https://feeny.ai/job/origination-associate-flagship-pioneering-inc-cambridge-rezba4m39nft) — Cambridge, MA - [Research Associate II, Protein Sciences](https://feeny.ai/job/research-associate-ii-protein-sciences-flagship-pioneering-inc-cambridge-zeexx76bhczw) — Cambridge, MA - [Scientific Manager – High Throughput Laboratory](https://feeny.ai/job/scientific-manager-high-throughput-laboratory-flagship-pioneering-inc-cambridge-fy1vfg2prvq6) — Cambridge, MA - [Scientist I, In Vitro Pharmacology](https://feeny.ai/job/scientist-i-in-vitro-pharmacology-flagship-pioneering-inc-watertown-ma-0mkf7pjwbjfy) — Watertown MA, United States - [Senior Scientist, Bioanalytical Sciences](https://feeny.ai/job/senior-scientist-bioanalytical-sciences-flagship-pioneering-inc-cambridge-y3z3svs22m0e) — Cambridge, MA - [Research Associate I/II, Cloning/IVT (Contract)](https://feeny.ai/job/research-associate-i-ii-cloning-ivt-contract-flagship-pioneering-inc-cambridge-fqy8868vmwsb) — Cambridge, MA - [Research Associate, Protein Production](https://feeny.ai/job/research-associate-protein-production-flagship-pioneering-inc-cambridge-73xj2rtm9ea7) — Cambridge, MA - [Senior Associate, Origination - Agriculture and Sustainability](https://feeny.ai/job/senior-associate-origination-agriculture-and-sustainability-flagship-pioneering-ba5zat81r1rt) — Cambridge, MA - [Product Concept Innovation Associate](https://feeny.ai/job/product-concept-innovation-associate-flagship-pioneering-inc-cambridge-a54bzmrcn4zt) — Cambridge, MA - [Senior Machine Learning Scientist](https://feeny.ai/job/senior-machine-learning-scientist-flagship-pioneering-inc-cambridge-5dbcemqxg7pf) — Cambridge, MA