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.

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