Dr. Fang Joins Department of Neurosurgery

February 3, 2025 - By Kathryn Sill

The Stanford Department of Neurosurgery extends a warm welcome to Rongxin Fang, PhD, who joins the department as an Assistant Professor of Neurosurgery and Genetics (by courtesy) and a member of the Wu Tsai Neuroscience Institute.

Fang will lead his laboratory at Stanford, focusing on the intersection of genomics, bioengineering, and neuroscience to develop technologies that advance the understanding of the genetic basis of brain complexity, function and disorder. He comes to Stanford with a remarkable training background at Harvard and UC San Diego.

Fang grew up in China, completing his undergraduate studies there until he moved to San Diego. He received his PhD in Bioinformatics and Systems Biology at UC San Diego, where he was advised by Bing Ren (2015-2019). During this time there he developed genomic technologies and computational tools to map the structure and activity of the mammalian genome at a large scale with single-cell resolution. As a part of the Brain Initiative Project, together with his colleagues and collaborators, he then applied these tools to generate one of the first single-cell maps of the mouse and human brain.

Following his time in Southern California, Fang moved out to the East Coast, beginning his time at Harvard University (2019-2024) as an HHMI-Damon Runyon Postdoctoral Fellow in the laboratory of Xiaowei Zhuang. There, he developed and applied genome-scale and volumetric 3D MERFISH transcriptome imaging methods to map the molecular and cellular architecture of the human brain during evolution and aging.

Dr. Fang's faculty appointment begins on January 1, 2025.

We spoke with Dr. Fang to learn more about his career journey:
 

Why did you pursue neuroscience as a career?

I never considered myself as a classic neuroscientist, especially based on my training trajectory one wouldn’t think I am. What got me interested in neuroscience primarily was through my collaborations. During my PhD I was privileged to have collaboration opportunities with some of the best neuroscientists in the world, including the neuroscientists at Allen Institute. There, I was as a part of the Brain Initiative Project. I developed single cell epigenomic approaches to study the cellular complexity of the brain to better understand what different cell types form the brain.

While those single-cell genomic approaches myself and others developed during my PhD were powerful in identifying different cell types in the brain, they almost always require dissociation of individual cells, therefore, disrupting their spatial context. To further understand how brain cells and cell types are spatially organized and functionally interacting, I decided to join my postdoc lab at Harvard. There, I began using an orthogonal approach - optical imaging - to study the spatial organization and structure of the mammalian brain. I then used these tools to collaborate with Catherine Dulac, who I consider, one of the greatest neuroscientists of our time. In collaboration with my fellow colleagues, we applied some of the imaging tools with the aim to identify the specific neuronal population underlying the animal social behavior.

These collaborations have continued to help me moving forward in my career. I hope to continue to advance my studies of the human brain by developing cutting-edge genomic tools.
 

What other mentors or individuals influenced you in your career journey?

My postdoc advisor, Xiaowei Zhuang was incredibly influential to my career development in multiple ways. She is an immensely talented scientist, humble, and open-minded to learning new things. I deeply admired that fact that she came from a physics background during her undergrad and PhD, but then during her postdoc at Stanford, she reinvented herself by becoming a biologist and studied biological questions.

Her experience really encouraged me to also pivot in my career. During my PhD I was trained in computational biology, where majority of my work focused on developing algorithms to analyze complex genomic data sets. When working in her lab, I had the opportunity to become a benchwork scientist, running experiments and constructing microscopy. Through her unwavering support and mentorship, I was able to reinvent myself from a computational biologist to an experimentalist, substantially broadening the scope of my research.
 

How did your training at UC San Diego and Harvard play a pivotal role in preparing you to lead your lab at Stanford now?

I think the kind of science we're performing in present day has two essential components. The first is the process of producing the data - the bench work. And the second part is having the power to analyze the data and interpret the results, which could also be referred to as computational work, if I simplify the scientific process.

During my PhD at UCSD, I was trained purely as a computational biologist. During five years of PhD research, I had never touched a pipette, but I was extremely lucky to have the opportunity to collaborate with many exceptional benchwork scientists. Through these collaborations, I learned how to develop advanced computational methods, to understand the complex biological data at a very high-level, and to come up with hypotheses in a creative way. This experience prepared me for computational work.

Then, during my postdoc, I worked on the bench for the most of my time, especially during the early days. I also had the opportunity to collaborate with my colleagues to construct microscopy, which prepared me for benchwork. Plus, I had the opportunity to work with neuroscientists, which taught me all the background knowledge that I had for the neurobiology.

The combination for experimental science, computational biology, and neuroscience during the training prepared me to lead my own lab at Stanford.
 

Can you tell us more about your research? 

My lab’s research aims to advance genomics and genomic tools to decode the complexity of the brain in terms of structure, function, and disorder.

The human brain is fascinating. It contains billions of cells, each belonging to thousands of different types and they form trillions of connections that operate with millisecond precision. Yet, every brain cell contains the same genetic material – we call it genome. My lab is interested in understanding how the same set of genetic information can give rise to the enormous complexity of the brain. For instance, why different cells or cell types have different morphology, physiological properties, and cellular identity. More importantly, we are also interested in using this knowledge to pinpoint the genetic causes underlying brain diseases.

To address these questions, I employ a combination of approaches, including single-cell genomics, spatial transcriptomics, functional genomics, and machine learning. My research follows an observe-understand-manipulate framework. First, I use these techniques to observe the complexity of the brain. Then, I develop computational methods to uncover the underlying principles based on these observations. Finally, I apply this knowledge to genetically manipulate cells, allowing me to test their functional roles in the brain and investigate potential causes of brain diseases.
 

What drew you to working at Stanford?

In science, I believe the most important thing is the people. The lab team defines the science, and the team defines the lab. What stood out to me about Stanford was that it has one of the best pools of graduate students and the name alone can attract some of the most talented postdoc in the world. It is an amazing place to conduct science and build up my own team. I also look forward to the collaborations I will form here with strong neuroscientists in the field.
 

What are some hobbies you enjoy outside of work?

I really enjoy long-distance running and biking.

When I was in graduate school in Southern California, I got into running. The warmer weather allowed me to run five to six miles a day and I began training for marathons regularly. When I moved to Boston, the winter was six months or longer and it made running not as appealing, so I am excited to get back into that hobby now that I am back in California.

I also enjoy biking. After undergrad, I spent three months biking across East Asia from my hometown to Tibet. That was such a fun experience. When I moved to the states, I biked from San Diego to San Francisco during winter for two weeks.