Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. - Chen, Bijia; Ren, Chao; Ouyang, Zhangyi; Xu, Jingxuan; Xu, Kang; Li, Yaru; Guo, Hejiang; Bai, Xuemei; Tian, Mengge; Xu, Xiang; Wang, Yuyang; Li, Hao; et al. (Briefings Bioinform., 2024)

SEPDB: a database of secreted proteins. - Wang, Ruiqing; Ren, Chao; Gao, Tian; Li, Hao; Bo, Xiaochen; Zhu, Dahai; Zhang, Dan; Chen, Hebing; Zhang, Yong (Database J. Biol. Databases Curation, 2024)

Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation. - Wang, Yuyang; Sun, Yu; Liu, Zeyu; Chen, Bijia; Chen, Hebing; Ren, Chao; Lin, Xuanwei; Hu, Pengzhen; Jia, Peiheng; Xu, Xiang; Xu, Kang; Liu, Ximeng; et al. (Quant. Biol., 2024)

3D genomic organization in cancers. - Wang, Junting; Tao, Huan; Li, Hao; Bo, Xiaochen; Chen, Hebing (Quant. Biol., 2023)

Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks. - Li, Hao; Sun, Yu; Hong, Hao; Huang, Xin; Tao, Huan; Huang, Qiya; Wang, Longteng; Xu, Kang; Gan, Jingbo; Chen, Hebing; Bo, Xiaochen (Nat. Mach. Intell., 2022)

Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. - Jiang, Shuai; Li, Hao; Hong, Hao; Du, Guifang; Huang, Xin; Sun, Yu; Wang, Junting; Tao, Huan; Xu, Kang; Li, Cheng; Chen, Yang; Chen, Hebing; et al. (Briefings Bioinform., 2021)

New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. - Chen, Hebing; Zhang, Zhuo; Jiang, Shuai; Li, Ruijiang; Li, Wanying; Zhao, Chenghui; Hong, Hao; Huang, Xin; Li, Hao; Bo, Xiaochen (Briefings Bioinform., 2020)

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. - Hong, Hao; Jiang, Shuai; Li, Hao; Du, Guifang; Sun, Yu; Tao, Huan; Quan, Cheng; Zhao, Chenghui; Li, Ruijiang; Li, Wanying; Yin, Xiaoyao; Huang, Yangchen; et al. (PLoS Comput. Biol., 2020)

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. - Zhang, Zhuo; Li, Hao; Jiang, Shuai; Li, Ruijiang; Li, Wanying; Chen, Hebing; Bo, Xiaochen (Briefings Bioinform., 2019)

Stable H3K4me3 is associated with transcription initiation during early embryo development. - Huang, Xin; Gao, Xudong; Li, Wanying; Jiang, Shuai; Li, Ruijiang; Hong, Hao; Zhao, Chenghui; Zhou, Pingkun; Chen, Hebing; Bo, Xiaochen; Li, Hao (Bioinform., 2019)

Exploring spatially adjacent TFBS-clustered regions with Hi-C data. - Chen, Hebing; Jiang, Shuai; Zhang, Zhuo; Li, Hao; Lu, Yiming; Bo, Xiaochen (Bioinform., 2017)

3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. - Lu, Yiming; Quan, Cheng; Chen, Hebing; Bo, Xiaochen; Zhang, Chenggang (Nucleic Acids Res., 2017)