Jobs at Allen Institute

Lead and support development, maintenance, and dissemination of open educational resources and professional development for college and high-school audiences. Manage the Education Resources library, coordinate peer review and external submissions, analyze usage metrics, represent the Institute at conferences, and collaborate with scientific partners to design curriculum and training materials. Provide programmatic support, facilitate workshops, and contribute to outreach and educator networks.

Invent and evaluate novel AI/ML methods for large-scale biological data. Design experiments, benchmarks, and reusable modeling frameworks; collaborate with scientists and engineers; publish and share methods to advance scientific discovery.

Lead and deliver college-level educator professional development and resources across the Allen Institute. Build and sustain educator networks, plan and facilitate workshops/webinars, evaluate program outcomes, represent the Institute at conferences, and collaborate with scientific and external partners to develop curriculum and training materials.

Analyze multi-omics neuroimmunology data (spatial transcriptomics, scRNA-seq, proteomics, flow cytometry, imaging) to discover biological insights. Collaborate with cross-functional teams, lead projects with minimal supervision, write reports/papers/patents, present to stakeholders, and contribute to a cohesive, efficient research team.

Analyze multi-omics neuroimmunology data (spatial transcriptomics, scRNA-seq, proteomics, flow cytometry, imaging); implement and streamline omics analysis pipelines; collaborate with cross-functional teams; provide bioinformatics support to research projects and lead projects with minimal supervision.

Lead and scale CellScapes scientific programs by coordinating cross-functional operations, removing bottlenecks, driving prioritization and execution, and building internal and external partnerships. Oversee program management workflows, cultivate community and partnerships across academia and industry, support strategic planning, and foster a collaborative, mission-driven culture that enables interdisciplinary science, scalability, and external visibility.

Design and perform scalable synapse-type specific proteomics experiments, develop workflows for synapse isolation and proteomic analysis, analyze and integrate large-scale proteomic and multimodal data, coordinate with internal teams and core facilities, manage data acquisition/storage, and publish and present findings while executing collaborative projects.

Manage and maintain a Windows-based enterprise environment and cloud integrations for ~925 staff. Design, deploy, upgrade, and lifecycle-manage IT infrastructure, endpoints, patching, backup, and cybersecurity agents. Administer Google Workspace and GCP with familiarity in Microsoft 365/Azure, enable SSO/MFA via Azure AD, and support endpoint and Mac administration.

Perform mammalian cell culture and viral packaging, extract nucleic acids from cells and brain tissue, prepare NGS libraries, perform PCR and advanced molecular cloning, and follow SOPs and biosafety requirements to enable genome engineering and protein localization studies in mouse brain.

Provide high-level administrative and executive support to the Executive Director and leadership team: manage complex calendars, schedule meetings and travel, prepare presentations and materials, compose and proofread correspondence, handle purchasing and expense reconciliation, maintain filing and shared spaces, coordinate cross-department activities, and drive special projects while maintaining confidentiality and professionalism.

Provide high-level administrative and operational support to senior leadership: manage calendars, meetings, travel, events, onboarding, vendor contracting, procurement, expense reporting, and document systems. Draft and proofread communications, prepare reports and presentations, maintain spreadsheets and team website, and lead office management and culture-building activities to support employee experience.

Design, deploy, and monitor secure, cost-effective cloud and on-prem infrastructure; build CI/CD pipelines, observability dashboards, secrets and auth layers, and end-to-end testing for large-scale data processing systems.

Design and run high-throughput barcoded connectomics and transcriptomics experiments, analyze large-scale datasets, maintain data pipelines and software, coordinate cross-team data acquisition, publish findings, and execute collaborative projects.

Design, train, and deploy large-scale AI/ML models for multimodal biological data; build research-grade ML infrastructure and data pipelines; collaborate with scientists and engineers; establish best practices and community standards; publish and open-source methods and code.

Design and execute experiments combining single-cell and spatial transcriptomics, circuit tracing, and behavioral assays in mice. Analyze large-scale single-cell genomics/epigenomics data using Python/R, collaborate across teams, present and publish results, and develop enhancer AAVs to probe cell-type specific functions in hypothalamic and amygdala circuits.

Lead Institute-wide data governance, stewardship, and metadata frameworks for multimodal scientific datasets. Establish standards, drive adoption of cataloging and lifecycle management, ensure compliance with NIST/HIPAA, advise on storage/infrastructure tradeoffs, and lead cross-functional initiatives to improve data discoverability, reuse, and long-term sustainability.

Design, develop, and apply molecular and proteomic technologies (e.g., spatial and droplet-based NGS) to study immune mechanisms. Perform and analyze in vitro and ex vivo immunology experiments using cell lines, primary cells, tissues, and genetic models. Develop cellular engineering and screening approaches, collaborate with teams to execute projects on timeline, and synthesize data from molecular, cellular, and proteomic platforms.

Lead and optimize Shared Resources scientific operations: develop processes, coordinate production and capacity, manage staff, interface with finance and legal, implement metrics and compliance, support training, recruitment, collaborations, and documentation to ensure scalable, high-quality data generation.

Lead and coordinate Shared Resources scientific programs, implementing processes for internal and external collaborations. Oversee project planning, budgeting, compliance (contracts, sub-awards, agency reporting), metrics, and communications across scientific and operational teams to ensure programmatic goals are met.

Lead analysis of large-scale, multi-region neural recordings and behavioral data. Build reproducible pipelines, apply statistical and quantitative models, collaborate with experimentalists, present and publish results, and engage in theory development and journal club.