Computational Biologist II, CellxState

The Team

Biohub is the first large-scale initiative bringing frontier AI models, massive compute, and frontier experimental capabilities under one roof. We're building a general-purpose system to accelerate scientific discovery, integrating frontier AI models, biological foundation models, and lab capabilities, with the ultimate goal of curing disease. Our technology powers scientists around the world, translating AI capabilities into tools that accelerate research everywhere.

Our Work

The Team brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine.

The Opportunity

• Design, develop, and maintain scalable image analysis pipelines for large-scale fluorescent microscopy datasets, with an emphasis on image quality robustness and computational efficiency.
• Integrate emerging multi-modal data types (e.g., spatial transcriptomics) into unified, AI-ready datasets that support downstream modeling and discovery.
• Advance our bio-image analysis capabilities (e.g., segmentation, tracking, image-stitching, and image registration).
• Partner closely with biologists and automation engineers to implement end-to-end quality control metrics, ensuring the fidelity of our experimental and computational pipelines.
• Architect modular and reusable processing frameworks that can flexibly support multiple experiment types within a shared infrastructure.
• Publish and disseminate impactful findings through preprints, papers, and software repositories (e.g., GitHub).

What You'll Bring

• PhD in Computational Biology, Biology, or Computer Science, or a MS with relevant job experience.
• At least 4 years of experience in Python-based image analysis or scientific computing. Experience with fluorescence microscopy, confocal, or lightsheet is a plus.
• Fluency with computational tools and infrastructure such as Python, Github, and Slurm.
• Experience with modern biological data formats such as OME-Zarr and AnnData.
• Experience designing workflows for large, complex datasets, including scalable storage formats, and reliable metadata and experiment tracking.
• A proven track record of individual innovation, together with a strong ability to work collaboratively.
• A passion for research and understanding how cells work.
• An enthusiasm for team science and open science - this position will be embedded in a large multi-disciplinary team.
• Excellent written and oral communication skills.

Compensation

The San Francisco, CA base pay range for a new hire in this role is $153,000 - $210,100. New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process.

Better Together

We’re excited to strengthen in-person connections and cultivate a collaborative, team-oriented environment. This role is a hybrid position requiring you to be onsite for at least 60% of the working month, approximately 3 days a week, with specific in-office days determined by the team’s manager. The exact schedule will be at the hiring manager's discretion and communicated during the interview process.

Benefits for the Whole You

• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice.
• Funding for select family-forming benefits.
• Relocation support for employees who need assistance moving.

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