Guojie Zhong  
(钟 国杰)

PhD in Systems Biology, Postdoctoral Research Associate at New York Genome Center.

prof_pic.jpg

New York Genome Center

Ren Lab

101 Avenue of the Americas

New York, NY 10013

I am currently a Postdoctoral Research Associate in Dr. Bing Ren’s lab at the New York Genome Center.

I build biologically-inspired machine learning models to bridge the gap between complex diseases and effective treatments, deciphering disease mechanisms from high-throughput genomics data to identify new therapeutic targets.

My current research interests include:

  1. Building DNA sequence-to-function foundation models that predict cell-type-specific transcriptional regulatory grammar in the human brain.
  2. Neuropsychological disease mechanism discovery utilizing a combination of high-throughput screening techniques and deep learning.
  3. Generative deep learning models for synthetic regulatory element design.

Previously, I had the honor of completing my PhD under the guidance of Dr. Yufeng Shen at the Department of Systems Biology, Columbia University.

My past work has spanned several areas including:

  1. Single-cell spatial transcriptomics and cancer immunology: CSOmap, Hepatocellular Carcinoma
  2. Statistical genetics and developmental disorders: VBASS, EA/TEF
  3. Missense variant effect predictions: PreMode, RESCVE, MisFit

Prior to Columbia, I earned my B.S. in the Integrated Science Program at Peking University with training primarily in biology, statistics, and computer science. I was privileged to work in Dr. Zemin Zhang’s Lab for my undergraduate thesis on developing computational methods to infer cellular spatial organization and cellular interactions from single-cell genomics data.

In my free time, I enjoy playing fingerstyle guitar and badminton, both of which require a balance of power and control.

selected publications

  1. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context
    G. Zhong, Y. Zhao, D. Zhuang, W. K. Chung, and Y. Shen
    2025
  2. A probabilistic graphical model for estimating selection coefficients of nonsynonymous variants from human population sequence data
    Y. Zhao, T. Lan, G. Zhong, J. Hagen, H. Pan, and 2 more authors
    2025
  3. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants
    G. Zhong, Y. A. Choi, and Y. Shen
    2023
  4. MLSB 2022
    Representation of missense variants for predicting modes of action
    G. Zhong, and Y. Shen
    Machine Learning in Structural Biology, Workshop at the 36th Conference on Neural Information Processing Systems (NeurIPS), 2022
  5. Statistical models of the genetic etiology of congenital heart disease
    G. Zhong, and Y. Shen
    Curr Opin Genet Dev, 2022
  6. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas
    G. Zhong*, P. Ahimaz*, N. A. Edwards*, J. J. Hagen, C. Faure, and 13 more authors
    HGG Adv, 2022
  7. Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly
    X. Ren*, G. Zhong*, Q. Zhang, L. Zhang, Y. Sun, and 1 more author
    Cell Res, 2020
  8. Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma
    Q. Zhang, Y. He, N. Luo, S. J. Patel, Y. Han, and 20 more authors
    Cell, 2019