Jobs at Allen Institute

Build, deploy, and maintain cloud and on-premises infrastructure for high-throughput data pipelines. Define Linux configuration as code (Ansible), manage Terraform-based AWS infrastructure, support CI/CD, databases, logging and metrics, troubleshoot production/staging issues, and participate in on-hours support rotations.

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.

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.

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.

Support large-scale synapse and neuronal-population proteomics by performing mouse tissue dissections, synapse isolation, proteomic sample preparation, histology, fluorescence imaging and sorting, and related molecular biology and viral vector workflows. Maintain lab records, follow SOPs and regulatory requirements, troubleshoot and optimize protocols, coordinate with cores, and present results within a collaborative team environment.

Architect, build, and operate cloud and on‑prem AI/ML training and inference platforms (including federated learning). Partner with scientists and external collaborators, benchmark and optimize ML infrastructure, ensure security/compliance and cost effectiveness, mentor engineers, and represent the Institute in vendor and cross‑institutional technical engagements.

Designs and executes high-throughput barcoded connectomics and transcriptomics experiments, analyzes large-scale datasets, maintains and improves data production/processing software, coordinates data acquisition and deposition, publishes results, and collaborates across teams and external partners to reveal brain wiring principles.

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.

Manage a portfolio of scientific partnerships by coordinating project plans, tracking milestones and risks, running cross-team meetings, communicating with stakeholders, and ensuring partnership objectives are met using program management best practices.

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.

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.

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.

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, 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.

Design and implement modern ML and Bayesian algorithms to model multimodal disease progression (omics, pathology, imaging, genetics, clinical data), harmonize cohorts, develop causal and generative models, collaborate across teams, and publish results.

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.

Lead Oracle Fusion ERP implementations, enhancements, and production support for finance modules (GL, AP, AR, FA, Cash). Translate finance requirements into scalable solutions, drive process improvement, create documentation and training, develop and maintain reports and dashboards, and collaborate with finance, technical teams, and third parties to ensure system integrity and best practices.