Selected Publications (After 2021)
2025
- SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression
Minghong Li, Yurong Yang, Rucheng Wu, Haiyan Gong, Zan Yuan, Jixin Wang, Erping Long, Xiaotong Zhang, Yang Chen.
Advanced Science, 2025
2024
- Temporal transcriptomic dynamics in developing macaque neocortex
Longjiang Xu, Zan Yuan, Jiafeng Zhou, Yuan Zhao, Wei Liu, Shuaiyao Lu, Zhanlong He, Boqin Qiang, Pengcheng Shu, Yang Chen, Xiaozhong Peng.
eLife, 2024 - Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer
Xinyuan Tong, Ayushi S Patel, Eejung Kim, Hongjun Li, Yueqing Chen, Shuai Li, Shengwu Liu, Julien Dilly, Kevin S Kapner, Ningxia Zhang, Yun Xue, Laura Hover, Suman Mukhopadhyay, Fiona Sherman, Khrystyna Myndzar, Priyanka Sahu, Yijun Gao, Fei Li, Fuming Li, Zhaoyuan Fang, Yujuan Jin, Juntao Gao, Minglei Shi, Satrajit Sinha, Luonan Chen, Yang Chen, Thian Kheoh, Wenjing Yang, Itai Yanai, Andre L Moreira, Vamsidhar Velcheti, Benjamin G Neel, Liang Hu, James G Christensen, Peter Olson, Dong Gao, Michael Q Zhang, Andrew J Aguirre, Kwok-Kin Wong, Hongbin Ji.
Cancer Cell, 2024 - A method for chromatin domain partitioning based on hypergraph clustering
Haiyan Gong, Sichen Zhang, Xiaotong Zhang, Yang Chen.
Computational and Structural Biotechnology Journal, 2024 - IFC-GNN: Combining interactions of functional connectivity with multimodal graph neural networks for ASD brain disorder analysis
Xuan Wang, Xiaotong Zhang, Yang Chen, Xiaopeng Yang.
Alexandria Engineering Journal, 2024
2023
- MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multimodal network
Haiyan Gong, Minghong Li, Mengdie Ji, Xiaotong Zhang, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, Yang Chen.
Cell Reports Methods, 2023 - A 3-D Chromosome Structure Reconstruction Method With High Resolution Hi-C Data Using Nonlinear Dimensionality Reduction and Divide-and-Conquer Strategy
Haiyan Gong, Fuqiang Ma, Xiaotong Zhang, Yi Yang, Minghong Li, Zhengyuan Chen, Sichen Zhang, and Yang Chen.
IEEE Trans Nanobioscience, 2023 - Computational methods for identifying enhancer-promoter interactions
Haiyan Gong, Zhengyuan Chen, Yuxin Tang, Minghong Li, Sichen Zhang, Xiaotong Zhang, Yang Chen.
Quantitative Biology, 2023
2022
- MyoD is a 3D genome structure organizer for muscle cell identity
Ruiting Wang, Fengling Chen, Qian Chen, Xin Wan, Minglei Shi, Antony K. Chen, Zhao Ma, Guohong Li, Min Wang, Yachen Ying, Qinyao Liu, Hu Li, Xu Zhang, Jinbiao Ma, Jiayun Zhong, Meihong Chen, Michael Q. Zhang, Yong Zhang, Yang Chen & Dahai Zhu.
Nature Communications, 2022 - CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster
Haiyan Gong, Yi Yang, Xiaotong Zhang, Minghong Li, Sichen Zhang, Yang Chen.
Computational and Structural Biotechnology Journal, 2022 - Profiling and characterization of constitutive chromatin-enriched RNAs
Wenlong Shen, Yan Zhang, Minglei Shi, Bingyu Ye, Man Yin, Ping Li, Shu Shi, Yifei Jin, Zhang Zhang, Michael Q. Zhang, Yang Chen, Zhihu Zhao.
iScience, 2022 - Integration of single cell data by disentangled representation learning
Tiantian Guo, Yang Chen, Minglei Shi, Xiangyu Li and Michael Q. Zhang.
Nucleic Acids Research, 2022 - MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection
Zhenyi Wang, Yanjie Zhong, Zhaofeng Ye, Lang Zeng, Yang Chen, Minglei Shi, Zhiyuan Yuan, Qiming Zhou, Minping Qian and Michael Q. Zhang.
Nucleic Acids Research, 2022 - CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming
Yawei Song, Zhengyu Liang, Jie Zhang, Gongcheng Hu, Juehan Wang, Yaoyi Li, Rong Guo, Xiaotao Dong, Isaac A. Babarinde, Wangfang Ping, Ying-Liang Sheng, Huanhuan Li, Zhaoming Chen, Minghui Gao, Yang Chen, Ge Shan, Michael Q. Zhang, Andrew P. Hutchins, Xiang-Dong Fu, Hongjie Yao.
Cell Reports, 2022
2021
- SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment
Zhiyuan Yuan, Qiming Zhou, Lesi Cai, Lin Pan, Weiliang Sun, Shiwei Qumu, Si Yu, Jiaxin Feng, Hansen Zhao, Yongchang Zheng, Minglei Shi, Shao Li, Yang Chen, Xinrong Zhang and Michael Q. Zhang.
Nature Methods, 2021 - Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective
Xuezhu Wang, Yucheng Dong, Yongchang Zheng, Yang Chen.
Journal of Genetics and Genomics, 2021 - Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6hexanediol index
Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q. Zhang, Tingting Li.
Genome Biology, 2021 - Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains
Shuai Jiang, Hao Li, Hao Hong, Guifang Du, Xin Huang, Yu Sun, Junting Wang, Huan Tao, Kang Xu, Cheng Li, Yang Chen, Hebing Chen, Xiaochen Bo.
Briefings in Bioinformatics, 2021 - Proteome-scale analysis of phase-separated proteins in immunofluorescence images
Chunyu Yu, Boyan Shen, Kaiqiang You, Qi Huang, Minglei Shi, Congying Wu, Yang Chen, Chaolin Zhang and Tingting Li.
Briefings in Bioinformatics, 2021 - 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia
Lu Yang, Fengling Chen, Haichuan Zhu, Yang Chen, Bingjie Dong, Minglei Shi, Weitao Wang, Qian Jiang, Leping Zhang, Xiaojun Huang, Michael Q. Zhang, Hong Wu.
Nature Communications, 2021