Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - 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

Dr. Loic A. Royer, Director of Imaging AI and Senior Group Leader, and Dr. Adrian Jacobo, Group Leader at CZ Biohub San Francisco, are collaborating on an innovative project to map gene expression patterns in developing zebrafish with unprecedented spatial resolution. This collaborative initiative builds upon Dr. Royer's work on the Multimodal Atlas of Vertebrate Development (Lange et al.) and Dr. Jacobo's expertise in biophysics and imaging. Together, they aim to integrate advanced spatial transcriptomics, cutting-edge light-sheet microscopy, microfluidics, AI, and image analysis tools to reveal the molecular architecture of developing tissues in three dimensions.

We are seeking a Scientist (PhD-level) with strong expertise in molecular biology and FISH-related or HCR-related techniques to help pioneer 3D spatial transcriptomics at an unprecedented scale and resolution in zebrafish embryos and larvae. The successful candidate will develop and optimize protocols for techniques such as serial-HCR and merFISH to visualize RNA distribution across intact tissues. Supported by our world-class bioengineering and Imaging AI teams, you will be working at the intersection of biochemistry, molecular biology, and advanced imaging, and be instrumental in bridging molecular techniques with computational approaches to create comprehensive spatial gene expression maps of developing vertebrate organisms.

You will report functionally report to Loic A. Royer and be be co-supervised by Adrian Jacobo. This role will be based in San Francisco initially, with a planned transition to Redwood City in two years.

What You'll Do

• Develop, optimize, and execute spatial transcriptomics protocols (serial-HCR, merFISH, or related methods) for intact zebrafish tissues
• Design and validate RNA probes for multiplexed detection of gene panels in fixed samples
• Establish robust sample preparation workflows for preserving RNA integrity while maintaining tissue structure
• Collaborate with our Bioengineering team to automate and scale these protocols
• Collaborate with microscopy experts to adapt imaging protocols for optimized visualization of spatial transcriptomics data
• Work with computational scientists to develop analysis pipelines for processing large-scale 3D spatial gene expression datasets
• Integrate spatial transcriptomics data with existing imaging and single-cell genomics resources
• Publish high-impact papers and present your work at premier international conferences

What You'll Bring

Essential –

• Recent (< 2 year) Ph.D. in Biochemistry, Molecular Biology, or a related discipline
• 3 years of hands-on experience with FISH-related techniques (HCR-FISH, smFISH, merFISH, or related methods)
• Strong expertise in molecular biology techniques (RNA handling, probe design, nucleic acid modifications)
• Demonstrated experience in optimizing biochemical protocols for challenging samples
• Experience with fluorescence microscopy for visualizing RNA in tissues
• Understanding of RNA biology and gene expression analysis
• Ability to troubleshoot complex molecular protocols
• Excellent written and oral communication skills
• Passion for interdisciplinary collaboration and open science

Nice to have -

• Experience with zebrafish as a model system
• Familiarity with whole-mount techniques for intact tissues or organisms
• Background in developmental biology
• Experience with light-sheet microscopy
• Basic computational skills for image analysis
• Knowledge of single-cell genomics approaches

Compensation

The San Francisco, CA base pay range for this role is Scientist I = $100,000.00 - $137,500.00 and Scientist II = $112,000.00 - $154,000.00. 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.