Publications.

Nature

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

Ahyeon Hwang, Mario Skarica, Siwei Xu, …, Ziheng Duan, …, Matthew J. Girgenti

CIKM 2025

MUSE: A Multi-slice Joint Analysis Method for Spatial Transcriptomics Experiments

Ziheng Duan, Xi Li, Zhiqing Xiao, Rex Ying, Jing Zhang

CIKM 2024

iMIRACLE: An Iterative Multi-View Graph Neural Network to Model Intercellular Gene Regulation From Spatial Transcriptomic Data

Ziheng Duan, Siwei Xu, Cheyu Lee, Dylan Riffle, Jing Zhang

Bioinformatics

Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation

Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang

Science

Single-cell multi-cohort dissection of the schizophrenia transcriptome

W. Brad Ruzicka, Shahin Mohammadi, John F. Fullard, …, PsychENCODE Consortium, …, Manolis Kellis

Contribution through the PsychENCODE Consortium

Science

Single-cell genomics and regulatory networks for 388 human brains

Prashant S. Emani, Jason J. Liu, Declan Clarke, …, PsychENCODE Consortium, …, Ziheng Duan, …, Mark Gerstein

Science

Massively parallel characterization of regulatory elements in the developing human cortex

Chengyu Deng, Sean Whalen, Marilyn Steyert, …, PsychENCODE Consortium, …, Katherine S. Pollard

Contribution through the PsychENCODE Consortium

Science

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

Cindy Wen, Michael Margolis, Rujia Dai, …, PsychENCODE Consortium, …, Michael J. Gandal

Contribution through the PsychENCODE Consortium

Science

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex

Louise A. Huuki-Myers, Abby Spangler, Nicholas J. Eagles, …, PsychENCODE Consortium, …, Kristen R. Maynard

Contribution through the PsychENCODE Consortium

Science Advances

Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements

Henry E. Pratt, Gregory Andrews, Nicole Shedd, …, PsychENCODE Consortium, …, Zhiping Weng

Contribution through the PsychENCODE Consortium

Science Translational Medicine

Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders

Yan Xia, Cuihua Xia, Yi Jiang, …, PsychENCODE Consortium, …, Chao Chen

Contribution through the PsychENCODE Consortium

Science Advances

Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data

Rujia Dai, Tianyao Chu, Ming Zhang, …, Chunyu Liu

Contribution through the PsychENCODE Consortium

BMC Neuroscience

Characterizing dysregulations via cell-cell communications in Alzheimer’s brains using single-cell transcriptomes

Che Yu Lee, Dylan Riffle, Yifeng Xiong, …, Ziheng Duan, Jing Zhang

Briefings in Bioinformatics

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding

Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, …, Jing Zhang

APSIPA Transactions on Signal and Information Processing

ExAD-GNN: Explainable Graph Neural Network for Alzheimer’s Disease State Prediction from Single-cell Data

Ziheng Duan, Cheyu Lee, Jing Zhang

PLOS Computational Biology

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease

Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang

Bioinformatics Advances

Turtling: a time-aware neural topic model on NIH grant data

Ruiyi Zhang, Ziheng Duan, CheYu Lee, Dylan Riffle, Martin Renqiang Min, Jing Zhang

Tsinghua Science and Technology

Multivariate Time Series Forecasting with Transfer Entropy Graph

Ziheng Duan, Haoyan Xu, Yida Huang, Jie Feng, Yueyang Wang

PLOS Computational Biology

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data

Che Yu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang

Neural Networks

Multivariate time-series classification with hierarchical variational graph pooling

Ziheng Duan, Haoyan Xu, Yueyang Wang, Yida Huang, Anni Ren, Zhongbin Xu, Yizhou Sun, Wei Wang

Applied Intelligence

Connecting latent relationships over heterogeneous attributed network for recommendation

Ziheng Duan, Yueyang Wang, Weihao Ye, Qilin Fan, Xiuhua Li

Pattern Recognition Letters

MTHetGNN: A heterogeneous graph embedding framework for multivariate time series forecasting

Yueyang Wang, Ziheng Duan, Yida Huang, Haoyan Xu, Jie Feng, Anni Ren

Neurocomputing

Graph partitioning and graph neural network based hierarchical graph matching for graph similarity computation

Haoyan Xu, Ziheng Duan, Yueyang Wang, Jie Feng, Runjian Chen, Qianru Zhang, Zhongbin Xu

Powder Technology

Image-based prediction of granular flow behaviors in a wedge-shaped hopper by combing DEM and deep learning methods

Zhehan Liao, Yizhang Yang, Chengfeng Sun, Ruiqi Wu, Ziheng Duan, Yueyang Wang, Xipeng Li, Jian Xu

arXiv

Classifying herbal medicine origins by temporal and spectral data mining of electronic nose

Li Liu, Xianghao Zhan, Ziheng Duan, Yi Wu, Rumeng Wu, Xiaoqing Guan, Zhan Wang, You Wang, Guang Li

arXiv

Deep Learning Based Detection and Localization of Intracranial Aneurysms in Computed Tomography Angiography

Dufan Wu, Daniel Montes, Ziheng Duan, Yangsibo Huang, Javier M. Romero, Ramon Gilberto Gonzalez, Quanzheng Li

arXiv

Parallel Extraction of Long-term Trends and Short-term Fluctuation Framework for Multivariate Time Series Forecasting

Yifu Zhou, Ziheng Duan, Haoyan Xu, Jie Feng, Anni Ren, Yueyang Wang, Xiaoqian Wang

arXiv

CoSimGNN: Towards Large-scale Graph Similarity Computation

Haoyan Xu, Runjian Chen, Yueyang Wang, Ziheng Duan, Jie Feng

Frontiers of Mechanical Engineering

Untethered quadrupedal hopping and bounding on a trampoline

Boxing Wang, Chunlin Zhou, Ziheng Duan, Qichao Zhu, Jun Wu, Rong Xiong

AAAI 2019

Heterogeneous Attributed Network Embedding with Graph Convolutional Networks

Yueyang Wang, Ziheng Duan, Binbing Liao, Fei Wu, Yueting Zhuang