Computational Biologist, CRISPR Informatics (Biohub SF)

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.

You will

• 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.

You have

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 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. 

What We Provide

• Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease
• A collegial and collaborative environment consisting of diverse expertise
• Access to collaborators, resources and facilities at our three partner universities (Stanford University, UC Berkeley, and UC San Francisco) and at partner organizations in the SF Bay Area and beyond
• Competitive compensation and benefits commensurate with the experience

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.

Benefits

We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world's leading scientists.

The CZ Biohub Network is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.

Pursuant to the California Fair Chance Act, we will consider for employment qualified applicants with arrest and conviction records.

Headhunters and recruitment agencies may not submit resumes/CVs through this website or directly to managers. The CZ Biohub Network does not accept unsolicited headhunter and agency resumes. The CZ Biohub Network will not pay fees to any third-party agency or company that does not have a signed agreement with the CZ Biohub Network.