Computational Biologist, CRISPR Informatics (Biohub SF)

The Team

The Chan Zuckerberg Biohub San Francisco (CZ Biohub SF) (https://www.czbiohub.org/sf/) is an independent nonprofit research institute that brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine. CZ Biohub SF itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.

Our Vision

• We pursue large scientific challenges that cannot be pursued in conventional environments
• We enable individual investigators to pursue their riskiest and most innovative ideas
• The technologies developed at CZ Biohub San Francisco facilitate research by scientists and clinicians at our home institutions and beyond

Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network and enable disruptive innovation and scholarly excellence. We are committed to cultivating an organization where all colleagues feel inspired and know their work makes an important contribution.

The Opportunity

We’re a cross-disciplinary institute on an audacious quest: to chart the dynamic architecture of cells at a scale and resolution once thought impossible. By uniting biology, engineering, and computation, we invent the breakthrough technologies this vision demands. Recent innovations from our team include an automated CRISPR experiment design engine that performs comprehensive optimizations while operating at the genome-wide scale (Peng et al. Nucleic Acids Research 2024). Leveraging such tools, we generated open-source datasets that illuminate the spatial organization of the human proteome in healthy and diseased states (Cho et al. Science 2022, Hein et al. Cell 2025).

We’re gearing up for our most ambitious push yet, as our next Computational Biologist you will architect and build the computational backbone that powers our upcoming large scale CRISPR experiments in both human cells, organoids and even whole organisms (zebrafish). These studies will span precise knock-in/out, high-content image-based CRISPR screening and programmable expression control—converting diverse perturbation datasets into systematic biological insights. Join us in San Francisco (with a planned move to Redwood City in two years) and drive the next wave of methodological innovation and scientific discovery that will redefine how dynamic cellular systems are decoded.

This role will be based in San Francisco initially, with a planned transition to Redwood City in two years.

What You'll Do

• Architect, build and maintain computation workflows for CRISPR design and edit-outcome analysis.
• Analyze genome-scale CRISPR perturbation datasets and identify emergent gene-function and pathway networks.
• Work with molecular biologists, imaging scientists, and software engineers to plan large scale CRISPR experiments and interpret results.
• Package, document and rigorously test code, computational pipelines and datasets for open-source release.
• Author publications and present research findings at conferences.

What You'll Bring

Essential –

• Ph.D. in Computational Biology, Bioinformatics, Bioengineering, Genomics or a related discipline. Candidates with a master’s degree and 3 years of relevant experience will be considered.
• 2+ years of deep, current knowledge of CRISPR genome-engineering technologies (e.g. CRISPRi/a, base/prime editing, CRISPR-based imaging) and the underlying molecular biology.
• Proven track record of developing computational pipelines for CRISPR design and edit-outcome analysis.
• Fluency in Python (or similar), experience with workflow management frameworks (e.g., Nextflow, Snakemake), and strong software engineering practices including testing, continuous integration, documentation, and version control.
• A collaborative, team-focused mindset coupled with outstanding communication skills.

Nice to have -

• Experience in analyzing CRISPR perturbations datasets at single cell resolution (e.g. perturb-seq).
• Experience in designing, optimizing and executing bioinformatics pipelines for amplicon sequencing, whole-genome sequencing and genome variant analyses.
• Experience in utilizing high-performance computing systems for large-scale data processing and analysis.
• Prior contributions to open-source projects or data resources.

Compensation

The San Francisco, CA base pay range for a new hire in this role is Computational Biologist I = $108,000.00 - $149,000.00 and Computational Biologist II = $132,000.00 - $182,000.00. 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. 

Benefits for the Whole You 

We’re thankful to have an incredible team behind our work. To honor their commitment, we offer a wide range of benefits to support the people who make all we do possible. 

• 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

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

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