{"id":314988,"url":"https://alion.io/job/flagship-pioneering-lead-data-engineer","title":"Lead Data Engineer","company":{"id":8393,"name":"Flagship Pioneering","domain":"flagshippioneering.com","url":"https://alion.io/company/flagshippioneering","size_band":"1001-5000","is_staffing_agency":false,"employer_type":"direct","is_intermediary":true,"listed_via":null,"ats_vendor":"Greenhouse","truth_index":{"grade":"B","score":79,"open_postings":10,"ghost_share":0,"stale_share":0.8,"repost_share":0.1,"time_to_fill_p50_days":54,"computed_at":"2026-10-27T05:46:45Z"}},"role":"Data Science","role_family":"Data Science","seniority":"lead","employment_type":"contractor","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"explicit","locations":["Cambridge, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":128000,"max":176000,"currency":"USD","period":"year","gross":null,"usd_annual":176000},"salary_estimate":null,"experience_years_min":6,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Amazon ECS","optional":false},{"name":"AWS","optional":false},{"name":"CI/CD","optional":false},{"name":"Claude Code","optional":false},{"name":"Dagster","optional":false},{"name":"dbt","optional":false},{"name":"Docker","optional":false},{"name":"Git","optional":false},{"name":"Platform Engineering","optional":false},{"name":"Python","optional":false},{"name":"Spark","optional":false},{"name":"SQL","optional":false},{"name":"Agile","optional":true},{"name":"Benchling","optional":true},{"name":"Scrum","optional":true}],"status":"live","first_seen_at":"2026-09-05T15:20:05Z","employer_posted_date":"2026-10-19","last_verified_at":"2026-10-28T00:25:38Z","board_verified":true,"closed_at":null,"days_open":52,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":52},"description":"ABOUT FLAGSHIP PIONEERING \nFlagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies. \nAbout Scientific Cloud: Scientific Cloud is Flagship Pioneering's portfolio-facing IT organization, responsible for the cloud engineering, data and informatics engineering, research systems, lab systems, and vendor management capabilities that power Flagship's emerging companies. The team operates with a portfolio-first orientation - building durable, shared infrastructure that individual ventures can rely on at every stage of company formation and growth. \nAbout Scientific Cloud:Scientific Cloud is Flagship Pioneering's portfolio-facing IT organization, responsible for the cloud engineering, data and informatics engineering, research systems, lab systems, and vendor management capabilities that power Flagship's emerging companies. The team operates with a portfolio-first orientation - building durable, shared infrastructure that individual ventures can rely on at every stage of company formation and growth. \nABOUT THE POSITION\nWe are seeking a Lead Data Engineer to lead complex initiatives aimed at modernizing and professionalizing our data infrastructure, platforms, and pipelines. You will lead the implementation of core platform systems and help to set the directions and standards of our data infrastructure and pipelines. You will work closely with other engineers and stakeholders across Infrastructure & Operations (I&O), Lab IT, Pioneering Intelligence (PI) Tech, and the internal scientific community to turn evolving scientific needs into secure, reliable and scalable data engineering solutions. \nReporting into the Associate Director, Data Architecture & Engineering, this is a technical, senior individual-contributor role that will champion engineering best practices, build complex data pipelines, lead data platform implementations, and handle the troubleshooting and optimization of data warehouse and storage solutions. \nCORE RESPONSIBILITIES \nData & Platform Engineering \nServe as the technical lead and subject matter expert on complex data engineering projects involving interdependent systems, legacy environments, and emerging cloud-first platforms. \nLead the implementation of data infrastructure, platforms, tools, and other data products. \nLead the optimization and reliability of data storage solutions (lakehouses, marts, warehouses, etc.). \nImplement complex backend and data integration pipelines to support data lakes, marts, and other platforms. \nEstablish and reinforce engineering standards for testing, documentation, release management, and monitoring across the team. \nLead implementations for platform observability, management, resilience, capacity, and performance. \nDiagnose and resolve complex failures spanning infrastructure and data pipelines; lead incident reviews and ensure corrective actions improve the wider system. \nCross-Functional Collaboration & Technical Leadership \nCollaborate across I&O, Lab IT, PI Tech, data science, and bioinformatics teams to ensure architectural alignment, reuse of components, and shared understanding of system states and dependencies. \nMentor junior engineers and establish engineering standards that drive excellence, reproducibility, and innovation across the team. \nLeverage generative AI tools and frameworks to accelerate pipeline development, data transformation, and metadata enrichment at scale. \nREQUIRED QUALIFICATIONS \n6+ years of hands-on experience in data engineering, preferably in life sciences, biotech, or healthcare environments. \nProven expertise in designing and operating cloud-native data architectures, particularly within AWS. \nAdvanced proficiency in Python and SQL for data manipulation, pipeline development, and system automation. \nExtensive experience with modern frameworks and tools such as Dagster, dbt, Spark, Iceberg, Lake Formation, Athena, Glue, etc. \nStrong experience with Git, CI/CD, CDK, containerized workloads, Docker, and ECS. \nExperience supporting both structured and unstructured data (CSV, JSON, Parquet, imaging, etc.). \nDemonstrated success in leading complex, cross-functional projects involving technical and scientific stakeholders. \nPractical experience using generative AI tools (e.g., Claude Code, GPT-based tools, etc.) to boost engineering velocity and reduce boilerplate. \nA track record of leading complex technical initiatives under ambiguity, making explicit trade-offs and remaining accountable for reliable operational outcomes. \nPREFERRED QUALIFICATIONS \nExperience supporting bioinformatics, cheminformatics, or clinical data workflows. \nFamiliarity with scientific software and ELN’s, particularly Benchling and CDD. \nExposure to Agile or Scrum-based development methodologies. \nRelevant certifications (e.g., AWS Solutions Architect Associate, Data Analytics Specialty). \nABOUT FLAGSHIP PIONEERING:\nFlagship 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. \nFlagship 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.\nAt Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.\nWe 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.\nWe 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.\nRecruitment & 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.\nPrivacy 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 . \nThe salary range for this role is $128,000 - $176,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.\nPrivacy 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. 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