Publications

Ziheng Duan, Siwei Xu, Cheyu Lee, Dylan Riffle, Jing Zhang (2024). iMIRACLE: an Iterative Multi-View Graph Neural Network to Model Intercellular Gene Regulation from Spatial Transcriptomic Data. CIKM-2024.

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Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang (2024). Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Bioinformatics.

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W Brad Ruzicka, Shahin Mohammadi, John F Fullard, Jose Davila-Velderrain, Sivan Subburaju, Daniel Reed Tso, Makayla Hourihan, Shan Jiang, Hao-Chih Lee, Jaroslav Bendl, PsychENCODE Consortium, Georgios Voloudakis, Vahram Haroutunian, Gabriel E Hoffman, Panos Roussos, Manolis Kellis (2024). Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science.

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Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Pengyu Ni, Xiao Zhou, PsychENCODE Consortium, Trygve E Bakken, Jaroslav Bendl, Lucy Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panos Roussos, Nenad Sestan, Zhiping Weng, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel Geschwind, Mark Gerstein (2024). Single-cell genomics and regulatory networks for 388 human brains. Science.

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Chengyu Deng, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F Przytycki, Fumitaka Inoue, Daniela A Pereira, Davide Capauto, Scott Norton, Flora M Vaccarino, PsychENCODE Consortium, Alex A Pollen, Tomasz J Nowakowski, Nadav Ahituv, Katherine S Pollard (2024). Massively parallel characterization of regulatory elements in the developing human cortex. Science.

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Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F. Przytycki, Daniel D. Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L. Walker, Christos Chatzinakos, Declan Clarke, Henry Pratt, PsychENCODE Consortium, Mette A. Peters, Mark Gerstein, Nikolaos P. Daskalakis, Zhiping Weng, Andrew E. Jaffe, Joel E. Kleinman, Thomas M. Hyde, Daniel R. Weinberger, Nicholas J. Bray, Nenad Sestan, Daniel H. Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L. Stein, Michael I. Love, Katherine S. Pollard, Chunyu Liu, Michael J. Gandal (2024). Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science.

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Prashant S Emani, Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Boyi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew N Tran, Arta Seyedian, PsychENCODE Consortium, Thomas M Hyde, Joel E Kleinman, Alexis Battle, Stephanie C Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard (2024). A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science.

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Henry E Pratt, Gregory Andrews, Nicole Shedd, Nishigandha Phalke, Tongxin Li, Anusri Pampari, Matthew Jensen, Cindy Wen, PsychENCODE Consortium, Michael J Gandal, Daniel H Geschwind, Mark Gerstein, Jill Moore, Anshul Kundaje, Andrés Colubri, Zhiping Weng (2024). Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science Advances.

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Yan Xia, Cuihua Xia, Yi Jiang, Yu Chen, Jiaqi Zhou, Rujia Dai, Cong Han, Zhongzheng Mao, PsychENCODE Consortium, Chunyu Liu, Chao Chen (2024). Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders. Science Translational Medicine.

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Rujia Dai, Tianyao Chu, Ming Zhang, Xuan Wang, Alexandre Jourdon, Feinan Wu, Jessica Mariani, Flora M Vaccarino, Donghoon Lee, John F Fullard, Gabriel E Hoffman, Panos Roussos, Yue Wang, Xusheng Wang, Dalila Pinto, Sidney H Wang, Chunling Zhang, PsychENCODE consortium, Chao Chen, Chunyu Liu (2024). Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data. Science Advances.

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Che Yu Lee, Dylan Riffle, Yifeng Xiong, Nadia Momtaz, Yutong Lei, Joseph M Pariser, Diptanshu Sikdar, Ahyeon Hwang, Ziheng Duan, Jing Zhang (2024). Characterizing dysregulations via cell-cell communications in Alzheimer’s brains using single-cell transcriptomes. BMC Neuroscience.

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Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Che Yu Lee, Feng Yue, Mark Gerstein, Yu Luan, Matthew Girgenti, Jing Zhang (2024). scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings in Bioinformatics.

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Ziheng Duan, CheYu Lee, Jing Zhang (2023). ExAD-GNN: explainable graph neural network for Alzheimer’s disease state prediction from single-cell data. APSIPA Transactions on Signal and Information Processing.

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Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang (2023). iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. Plos Computational Biology.

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Ruiyi Zhang, Ziheng Duan, CheYu Lee, Dylan Riffle, Martin Renqiang Min, Jing Zhang (2023). Turtling: A Time-aware Neural Topic Model on NIH Grant Data. Bioinformatics Advances.

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Che Yu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang (2022). Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. Plos Computational Biology.

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Ziheng Duan, Haoyan Xu, Yueyang Wang, Yida Huang, Anni Ren, Yizhou Sun, Wei Wang (2022). Multivariate Time Series Classification with Hierarchical Variational Graph Pooling. Neural Networks.

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Ziheng Duan, Haoyan Xu, Yida Huang, Jie Feng, Yueyang Wang (2022). Multivariate Time Series Forecasting with Transfer Entropy Graph. Tsinghua Science and Technology.

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Ziheng Duan, Yueyang Wang, Weihao Ye, Qilin Fan, Xiuhua Li (2022). Connecting Latent ReLationships over Heterogeneous Attributed Network for Recommendation. Applied Intelligence.

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Yueyang Wang, Ziheng Duan, Yida Huang, Haoyan Xu, Jie Feng, Anni Ren (2021). MTHetGNN: a heterogeneous graph embedding framework for multivariate time series forecasting. Pattern Recognition Letter.

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Haoyan Xu, Ziheng Duan, Yueyan Wang, Jie Feng, Runjian Chen, Qianru Zhang, Zhongbin Xu (2021). Graph Partitioning and Graph Neural Network based Hierarchical Graph Matching for Graph Similarity Computation. Neurocomputing.

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Zhehan Liao, Yizhang Yang, Chengfeng Sun, Ruiqi Wu, Ziheng Duan, Yueyang Wang, Xipeng Li, Jian Xu (2021). Image-based prediction of granular flow behaviors in a wedge-shaped hopper by combing DEM and deep learning methods. Powder Technology.

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Dufan Wu, Daniel Montes, Ziheng Duan, Yangsibo Huang, Javier M. Romero, Ramon Gilberto Gonzalez, Quanzheng Li (2021). Deep Learning Based Detection and Localization of Cerebal Aneurysms in Computed Tomography Angiography.

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Li Liu, Xianghao Zhan, Ziheng Duan, Yi Wu, Rumeng Wu, Xiaoqing Guan, Zhan Wang, You Wang, Guang Li (2021). Classifying herbal medicine origins by temporal and spectral data mining of electronic nose.

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Yifu Zhou, Ziheng Duan, Haoyan Xu, Jie Feng, Anni Ren, Yueyang Wang, Xiaoqian Wang (2020). Parallel Extraction of Long-term Trends and Short-term Fluctuation Framework for Multivariate Time Series Forecasting.

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Haoyan Xu, Runjian Chen, Yunsheng Bai, Ziheng Duan, Jie Feng, Ke Luo, Yizhou Sun, Wei Wang (2020). CoSimGNN: Towards Large-scale Graph Similarity Computation.

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Boxing Wang, Chunlin Zhou, Ziheng Duan, Qichao Zhu, Jun Wu, Rong Xiong (2019). Untethered quadrupedal hopping and bounding on a trampoline. Frontiers of Mechanical Engineering.

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Yueyang Wang, Ziheng Duan, Binbing Liao, Fei Wu, Yueting Zhuang (2019). Heterogeneous Attributed Network Embedding with Graph Convolutional Networks. AAAI-2019.

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