Associate Director, Scientific Computing and AI Engineer

Denali Therapeutics; South San Francisco (CA); On-site; USD 159,000 - 207,000; Full time

Benefits offered by this job

401k

Healthcare coverage

Employee Stock Purchase Plan (ESPP)

Job summary

Denali Therapeutics in South San Francisco seeks a Scientific Computing and AI Engineer to architect and optimize GPU clusters and cloud HPC systems. This role bridges engineering with scientific impact, ensuring robust production-grade platforms for drug discovery.

Ideal candidates will have over 10 years of experience in platform engineering, specializing in HPC optimization and AI workflows. Denali offers a competitive salary range of $159,000 to $207,000 along with a comprehensive benefits package.

Qualifications

• Typically 10-12+ years of experience in platform engineering with 3 years at a senior level.
• Deep expertise in HPC cluster administration, cloud platform engineering, and generative AI.
• Experience in regulated biotech or pharmaceutical environments with exposure to GxP.

Responsibilities

• Lead architecture and optimization of GPU clusters and HPC environments.
• Design and support compute environments for intensive workloads like molecular dynamics.
• Mentor and develop engineers across the organization.

Skills

HPC cluster administration and optimization

AI/ML platform engineering

Cloud platform engineering

Python and scripting skills

Education

Bachelor’s or Master’s degree in Computer Science or Engineering

Tools

Slurm

CUDA

Infrastructure as Code tooling

CI/CD pipelines

Job description

Neurodegenerative diseases are one of the largest medical challenges of our time. Denali Therapeutics is a biotechnology company dedicated to developing breakthrough therapies for neurodegenerative diseases through our deep commitment to degeneration biology and principles of translational medicine. Denali is founded on the collaboration of leading scientists, industry experts, and investors who share the vision that scientific discovery energetically applied to translational medicine is the key to delivering effective therapies to patients.

We invite you to consider an opportunity with Denali to help achieve our goal of delivering meaningful therapeutics to patients.

As the Scientific Computing and AI Engineer, you will provide hands‑on technical leadership in designing and evolving our GPU clusters, cloud‑scale workloads, and generative AI solutions. Architecting systems that accelerate drug discovery and clinical development, you will bridge deep engineering craft with scientific impact to deliver robust, production‑grade platforms.

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
• Typically, 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 (LangChain, LangGraph, AutoGen) 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 experience with vector databases, knowledge graphs, and RAG architectures for scientific or enterprise applications

Salary Range: $159,000.00 to $207,000.00. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Denali offers a competitive total rewards package, which includes a 401k, healthcare coverage, ESPP and a broad range of other benefits. Learn more at https://www.denalitherapeutics.com/careers

Denali is committed to its core company value of unity by creating a diverse and inclusive environment. We are proud to be an equal opportunity employer and do not discriminate against any employee or applicant for employment because of race, color, sex, age, national origin, religion, sexual orientation, gender identity and/or expression, status as a veteran, basis of disability, or any other federal, state, or local protected class.