Statistical Bioinformatics Seminar: Dr Rongxin Fang (Stanford University)

Title: Spatial and Functional Analysis of the Mammalian Brain 

Speaker: Dr Rongxin Fang, Stanford University 

Abstract: The mammalian brain is composed of an extraordinarily diverse cell types, yet
how these cells are spatially organized in the human brain—and how this organization
differs across species or in disease—remains poorly understood.  In this talk, I will
present two innovations in spatial transcriptomics aimed at addressing this gap.  In the
first part, I will introduce genome-scale MERFISH, a transcriptome imaging method
capable of profiling over 4,000 genes in situ at single-cell resolution.  Applying this
approach to the human cerebral cortex, we identified more than 100 transcriptionally
distinct cell populations and constructed a spatially resolved, molecularly defined cell
atlas.  Comparative analysis with mouse cortex revealed conserved laminar organization,
but also species-specific differences—particularly in somatic interactions between
neurons and non-neuronal cells—highlighting unique aspects of human brain
organization.  While MERFISH has primarily been applied to thin tissue sections (~10
µm), many biological questions require volumetric analysis of thicker tissue samples.
In the second part of the talk, I will present 3D MERFISH, a method that combines
MERFISH with confocal microscopy for optical sectioning and deep learning for enhanced
image reconstruction.  We applied this technique to mouse brain tissue up to 200 µm
thick, achieving high detection sensitivity and spatial fidelity.  Together, these
genome-scale and volumetric transcriptome imaging methods expand the capabilities of
spatial genomics, enabling unprecedented insight into brain organization, species
evolution, and disease mechanisms.  

About the speaker: Dr Rongxin Fang is an Assistant Professor at Stanford University in
the Departments of Neurosurgery and Genetics (by courtesy) and a member of the Wu Tsai
Neuroscience Institute.  Rongxin received his Ph.D.  in Bioinformatics and Systems
Biology in the Department of Molecular and Cellular Medicine at UC San Diego, where he
was advised by Bing Ren (2015-2019).  Rongxin has received multiple fellowships and
awards, including the HHMI/Damon Runyon Postdoctoral Fellowship, Rising Star in Health
and Engineering - Johns Hopkins and Columbia University, Next Generation Leader - Allen
Institute, Damon Runyon-Dale F.  Frey Award for Breakthrough Scientists.  

This event will be held online.  

Zoom: https://uni-sydney.zoom.us/j/85114748391