Publications
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