Members

Principal Investigator

Yi Zhang, PhD

I’m an Assistant Professor at Duke University School of Medicine in the Department of Neurosurgery and Department of Biostatistics and Bioinformatics, with affiliation at Departments of Biomedical Engineering and Cell Biology. I work on machine learning/AI for biomedical data with a focus on computational genomics. I obtained BS from University of Science and Technology of China (USTC) and PhD in Bioengineering with Dr. Jun S. Song at University of Illinois at Urbana-Champaign (UIUC). I did postdoc at Department of Data Science, Dana-Farber Cancer Institute and Harvard University School of Public Health mentored by Drs. Shirley Liu, Myles Brown, and Xihong Lin. I have worked on developing integrative genomic methods to identify functional gene regulatory mechanisms behind disease-associated human genetic variants. I have also been developing ML/AI methods for large-scale single-cell and spatial multi-omics to understand cell states in complex tissue microenvironment. My ongoing work include ML/AI models of high-definition spatial transcriptomics, computational pathology, and ML models for genetics and functional genomics. For fun, I enjoy hiking, music and wildlife photography. Our research is supported by NIH and Duke Brain Tumor Center.


Email: yi.zhang [at] duke [dot] edu Address: Duke University MSRB1 199B, 203 Research Dr, Durham, NC 27705; Hock Plaza starting Fall 2026.

Postdoctoral Researchers


Weihang Zhang

I’m a Postdoctoral Associate in Zhang lab at Duke. I earned my Ph.D. in Computational Biology and Medical Sciences (CBMS) from the University of Tokyo, where I was supervised by Prof. Kenta Nakai. My previous research focused on developing graph-based computational methods for single-cell epigenetic data. I am now working on spatial multi-omics, with a particular interest in understanding tumor microenvironment organization using high-resolution spatial data using graph and contrastive learning. Outside of research, I enjoy camping, digital painting, and playing PC and mobile games. I am BTOP Postdoctoral Fellowship Awardee.

Graduate Students and Research Staff


Zhujun (Christina) Yao

I am a 3rd year PhD student in Pathology at Duke University, co-advised by Dr Zhang and Dr David Ashley. I received my bachelor’s degree in Cell and Molecular Biology at Duke Kunshan University. My research interest is to integrate computational tools and molecular biology experiments to promote disease diagnostics or therapeutic development, with recent focus on glioblstoma cellular heterogeneity. In my free time, I enjoy drawing, swimming, and listening to Taylor Swift.


Yichen Huang

I’m Yichen, a 2nd yera PhD student in Duke’s Computational Biology and Bioinformatics (CBB) program. I earned my B.S. in Biochemistry and Mathematics from Brandeis University and M.S. in Computational Biology and Quantitative Genetics from the Harvard School of Public Health. My past research experiences focused on leveraging epigenetics to better understand complex human traits. I am exploring methods to analyze transcriptomics of cell-cell interactions using high-resolution spatial genomics data, using deep learning methods. Outside of research, I enjoy playing volleyball, traveling, and PC gaming.


Zion Sheng

I am a 1st year BME PhD student and former Research Technician II supervised by Dr. Zhang. I completed my undergraduate training at CUFE and UCLA, followed by a master’s degree in ECE at Duke. Prior to my current position, I engaged in various projects at Duke Pathology, Duke ECE, and Mizzou EECS, where I co-authored several publications and presentations. My research is centered around highly efficient learning algorithms and digital biomedicine. In the lab, I am dedicated to the development of innovative and useful computational methods for integrative omics data analysis with digital pathology. Outside work, I enjoy working out, reading, and having fun with friends.


Josie Xing

I’m a Research Technician co-supervised by Dr. Yi Zhang and Dr. Jiaoti Huang, and a recent BME Master graduate at Duke University, with a bachelor’s degree in Biological Sciences from Xi’an Jiaotong-Liverpool University. My research centers on using single-cell and spatial transcriptomic data to elucidate metabolic pathways in prostate cancer therapeutics, with a growing interest in incorporating machine-learning methods into this work. Outside of academics, I enjoy working out, baking, and exploring coffee brewing.


Palak Jolly

I’m Palak Jolly, a Research Technician in Zhang lab , and former Duke undergraduate student studying Computer Science, Bioinformatics and on the pre-medical track. I’m primarily interested in applying artificial intelligence and machine learning to larger biomedical questions, supporting the development of more effective disease response through predictive modeling and precision medicine. Previously, I have delved into protein structure prediction, and computationally modeling synthetic gene circuits for oncological applications. When free, I enjoy cooking, writing poetry and singing classical Indian music.


Yifan Deng

MS student at Yale University Computational Biology and Bioinformatics Program, Research Assistantship for summer 2026.

Undergraduate Researchers


Zijia Tang

My name is Zijia (Thomas) Tang, and I am a undergraduate research intern in Yi’s lab starting June 2024, majoring in Computer Science. My research interests lie in computational biology and machine learning. Previously, I delved into single-cell perturbation, employing Variational Autoencoders (VAEs) to predict cellular responses to perturbations. I’m working on spatial genomics foundation models and using agentic pipelines, in collaboration with Dr. Tianlong Chen’s group and UNC. In my free time, I enjoy playing drums, exercising, and reading science fiction.


Bo Chi

I am a senior Duke undergraduate student majoring in Math and Computer Science with a minor in Computational Biology & Bioinformatics. My research interests include developing optimized sequence and spatial multi-omic models to better understand cancer biology, using mathematical methods including optimal transport . In my free time, I enjoy playing word games, playing Ultimate Frisbee, and watching football.


Ruben Marcus

I’m a sophomore Duke undergraduate student studying Math and Computer Science. I’m interested in using ideas from probability, stats, optimization, and machine learning to understand complex, high-dimensional biological data. I’m working on physics models to study spatial cell distribution. In my free time, I enjoy writing music, playing piano, hiking, and reading science/philosophy.


Aashish Cheruvu

I am a junior in the Pratt School of Engineering studying Biomedical Engineering and Electrical & Computer Engineering with a minor in mathematics. Broadly, my research interests are in biomedical informatics, using multimodal machine learning and generative modeling techniques to better understand biological systems and disease. As part of a MUSER project with Dr. Zhang and Dr. Wenjun Zhao, I am applying optimal transport techniques to spatial transcriptomics data. In my free time, I enjoy working out, exploring the Triangle’s food scene, singing classical Indian music, and participating in Duke’s competitive trivia league.


Alumni

Name Role First role after graduating from lab
Xinyi Yang Duke-DukeNUS summer exchange student PhD student, Duke-NUS medical school
Tong Cheng Biostatistics Master student Staff at Rutgers Cancer Institute
Yuqian Zhang Duke Applied Math undergraduate intern Undergraduate student
Yitong Zhou Duke Data Science undergraduate intern Undergraduate student
Huiyue Li Biostatistics PhD rotation student Duke Biostatistics PhD student
Xingyuan Zhang CBB PhD rotation student Duke CBB PhD student
Chuhanwen Sun Master student, Research Intern Rutgers PhD student
Yijia Alva Jiang Master student, Harvard DBMI, Shirley Liu lab PhD student, UPenn Genomics and Computational Biology, with Nancy Zhang and Andy Minn
Jack Jiajinlong Kang Master student, Harvard CBQG, Shirley Liu lab PhD student, MD Anderson Cancer Center
Yingxiao TK Shi PhD student, Harvard BBS, Shirley Liu lab PhD student, Harvard & Dana-Farber Cancer Institute