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Associate Director, Scientific Computing and AI Engineer

Job in South San Francisco, San Mateo County, California, 94083, USA
Listing for: Denali Therapeutics Inc
Full Time position
Listed on 2026-09-10
Job specializations:
  • Software Development
    AI Engineer (Applied/Software), Machine Learning/ ML Engineer, Data Engineering
Salary/Wage Range or Industry Benchmark: 159000 - 207000 USD Yearly USD 159000.00 207000.00 YEAR
Job Description & How to Apply Below

Key Accountabilities / Core Job Responsibilities

  • Scientific Computing & HPC Platform Engineering:
    Lead the architecture, build‑out, and ongoing optimization of on‑premise GPU clusters, hybrid cloud HPC environments, and supporting storage and networking infrastructure.
  • Partner with research scientists to profile workloads, size infrastructure, and iteratively improve job performance and researcher self‑service capabilities.
  • Design, operate, and support compute environments for computationally intensive workloads such as molecular dynamics (Schrödinger), CryoEM, genomics, structural biology, and AI model training.
  • Implement job scheduler configurations (Slurm/LSF), parallel file systems, and interconnect optimization to maximize throughput and utilization for scientific users.
  • Architect cloud‑burst strategies for elastic scaling of peak HPC demand and ML training workloads.
  • Applied AI Engineering & Generative AI Solutions:
    Design and engineer production AI/ML systems and generative AI solutions spanning cloud infrastructure, data pipelines, vector databases, RAG architectures, and LLM application layers.
  • Build and deploy agentic AI workflows that automate or augment scientific processes.
  • Develop and maintain AI evaluation frameworks, prompt engineering standards, and model lifecycle management practices (MLOps) that ensure reliable, auditable outputs in a GxP‑adjacent environment.
  • Prototype and pilot emerging AI capabilities (AI agents, digital twins, foundation model fine‑tuning) and transition proven solutions to production at scale.
  • Collaborate with cross‑functional stakeholders to scope AI use cases, define success criteria, and demonstrate concrete business value through working proof‑of‑concept and production deployments.
  • Implement Infrastructure as Code and CI/CD pipelines with integrated security and compliance controls.
  • Technical Leadership & Architecture Guidance:
    Serve as the senior technical partner for scientific computing and AI platform decisions; set engineering standards, reference architectures, and technology guardrails in collaboration with Enterprise Architecture.
  • Mentor and develop engineers across the IT organization and elevate team‑wide engineering practices.
  • Translate complex technical concepts for non‑technical stakeholders including senior leadership and R&D scientists.
  • Evaluate vendor and open‑source technologies; lead proof‑of‑concept assessments and build‑vs‑buy recommendations for new platform capabilities.
  • Participate in architecture review processes to ensure cross‑functional alignment and long‑term platform coherence.
Requirements
  • Bachelor’s or Master’s degree in Computer Science, Engineering, or a closely related field.
  • 10–12+ years of progressive experience in platform engineering, scientific computing, or infrastructure engineering, with at least 3 years operating at a senior/principal individual‑contributor level.
  • Deep, hands‑on expertise in two or more of the following: HPC cluster administration and optimization (Slurm/LSF, parallel file systems, GPU/CUDA environments); cloud platform engineering at production scale; AI/ML platform engineering including model deployment, MLOps pipelines, and LLM application development.
  • Generative AI and agentic system design using modern frameworks (Lang Chain, Lang Graph, Auto Gen) and foundation models.
  • Proficiency in Infrastructure as Code and CI/CD tooling.
  • Strong Python and scripting skills.
  • Experience working in or supporting regulated biotech, pharmaceutical, or life sciences environments with exposure to GxP, 21 CFR Part
    11, or equivalent data integrity frameworks.
  • Demonstrated ability to lead technical initiatives end‑to‑end—from architecture through production delivery—in a lean, resource‑constrained organization.
  • Hands‑on…
Position Requirements
10+ Years work experience
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