Director, Scientific Cloud Engineering

ABOUT FLAGSHIP PIONEERING

Flagship 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.

About 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.

THE POSITION

The Director, Scientific Cloud Engineering is a senior technical organizational leader responsible for engineering the cloud and computational infrastructure that underpins scientific discovery across the Flagship portfolio. Reporting to the Senior Director of Scientific Cloud, this individual will manage and lead a growing team of engineers — including Cloud DevOps and Bioinformatics— and serve as the primary technical authority for scientific , and scientific computing platforms.

This role sits at the intersection of cloud engineering and life sciences. The Director will bring both the technical depth of an experienced cloud architect and a meaningful understanding of the computational demands of biotech research — including genomics workflows, high-performance computing, containerized pipelines, and AI/ML infrastructure. They will partner closely with Data Architecture & Engineering, Lab Systems, and Research Systems teams to ensure that what gets built is scalable, reproducible, and grounded in the realities of scientific work.

CORE RESPONSIBILITIES

Team Leadership & Engineering Management

• Lead, mentor, and grow , including external contractors and consultants; set a high technical bar and foster a culture of rigor, collaboration, and continuous improvement.
• Serve as a player-coach — providing direct technical contributions while managing team capacity, priorities, and professional development.
• Partner with the Senior Director of Scientific Cloud to define team roadmap, resource allocation, and hiring strategy as the portfolio scales.
• Establish engineering best practices, code review standards, and documentation norms across their Scientific Cloud Engineering team.

Cloud Architecture & Infrastructure

• Own and evolve the cloud architecture strategy for Scientific Cloud, designing scalable, secure, and cost-efficient infrastructure across AWS and/or Azure environments.
• Architect and deliver reusable infrastructure-as-code (IaC) solutions — including Terraform modules, CDK constructs, and containerized service templates — that portfolio companies can adopt without custom engineering.
• Partner with Infrastructure, Operations, and Architecture (IO&A) to define and enforce cloud governance guardrails: identity and access management (IAM), networking, secrets management, cost tagging, and security posture.
• Design and maintain HPC and compute environments — including Nextflow/Cromwell execution layers, Kubernetes clusters, and GPU-enabled instances — optimized for scientific workloads.
• Evaluate and adopt emerging cloud capabilities, including serverless orchestration, data lakehouse patterns, and managed ML platforms (e.g., AWS SageMaker, Azure ML).

Scientific Computing & Bioinformatics Platforms

• and data scientists to architect robust, reproducible pipeline infrastructure for genomics, proteomics, and other -omics data types.
• Oversee the design and deployment of bioinformatics platform capabilities including workflow orchestration (Nextflow, Snakemake), container registries, reference data management, and secure data ingestion from external sources (e.g., UK Biobank, dbGaP, controlled-access repositories).
• Ensure compute environments support the full spectrum of scientific compute: interactive analysis (Jupyter, RStudio), large-scale batch processing, and real-time ML inference.
• Champion FAIR data principles and reproducibility standards in scientific compute infrastructure.

Standards, Products & Portfolio Enablement

• Develop and steward portfolio-wide engineering standards for cloud infrastructure, security, and scientific compute — ensuring consistency across all Flagship portfolio companies and research teams.
• Design and publish reusable infrastructure products, reference architectures, and deployment templates that enable portfolio companies to launch and scale scientific capabilities quickly.
• Serve as the technical standards interface for internal teams and portfolio companies, reviewing proposed architectures and ensuring alignment with Flagship IT guardrails.
• Collaborate with the Pioneering Intelligence (PI) team and portfolio companies to enable and accelerate AI/ML capabilities — including model training infrastructure, feature stores, vector databases, and LLM deployment patterns.

Cross-Functional Collaboration

• Collaborate closely with the Data Architecture & Engineering team to align on data platform design, pipeline standards, and lakehouse infrastructure.
• Partner with Lab Systems and Research Systems teams to ensure cloud infrastructure meets the integration and performance requirements of ELN platforms, LIMS, scientific instruments, and research applications.
• Engage with IT Security and Compliance to maintain a strong cloud security posture, including SOC 2, GxP, and HIPAA-relevant requirements as the portfolio matures.
• Work with portfolio company CTOs and heads of data science and bioinformatics to understand scientific infrastructure needs and ensure Scientific Cloud is delivering ahead of demand.

REQUIRED QUALIFICATIONS

• 10+ years of experience in cloud engineering, infrastructure engineering, or DevOps, with at least 3 years in a technical leadership or engineering management role.
• Deep expertise in AWS (preferred) and/or Azure, including compute, storage, networking, IAM, and managed services for data and ML.
• Demonstrated experience designing and operating infrastructure for scientific or biotech workloads — genomics pipelines, HPC, -omics data processing, or equivalent.
• Strong proficiency in infrastructure-as-code (Terraform, CDK, CloudFormation) and CI/CD automation (GitHub Actions, Jenkins, or similar).
• Experience with containerization and orchestration technologies (Docker, Kubernetes, ECS/EKS).
• Familiarity with bioinformatics workflow frameworks (Nextflow, Snakemake, WDL) and scientific compute environments.
• Background in biotech, life sciences, or pharmaceutical research — through education (e.g., B.S./M.S./Ph.D. in computational biology, bioinformatics, biochemistry, or related field) or direct industry experience in a scientific computing context.
• Track record of building and shipping reusable infrastructure products and reference architectures, not just bespoke solutions.
• Strong communicator who can translate between scientific requirements and engineering specifications, and present technical strategy to non-technical stakeholders.

PREFERRED QUALIFICATIONS

• Experience operating in a multi-tenant or portfolio model — supporting multiple independent teams or companies on shared infrastructure.
• Familiarity with AI/ML infrastructure — model training pipelines, MLflow or similar experiment tracking, SageMaker, or LLM deployment on cloud.
• Experience with data lakehouse architectures (Delta Lake, Iceberg, or equivalent) and their integration with scientific data types.
• Exposure to GxP, HIPAA, or SOC 2 compliance requirements in a cloud context.
• Prior experience at a biotech incubator, multi-portfolio organization, or venture-backed life sciences company.

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.

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 $172,000 - $236,500. 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.

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.