De novo identification of replication-timing domains in the human genome by deep learning. - Feng Liu 054; Chao Ren; Hao Li 035; Pingkun Zhou; Xiaochen Bo; Wenjie Shu (Bioinform., 2016)

Exploring spatially adjacent TFBS-clustered regions with Hi-C data. - Hebing Chen; Shuai Jiang; Zhuo Zhang; Hao Li 035; Yiming Lu; Xiaochen Bo (Bioinform., 2017)

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. - Zhuo Zhang; Hao Li 035; Shuai Jiang; Ruijiang Li; Wanying Li; Hebing Chen; Xiaochen Bo (Briefings Bioinform., 2019)

Stable H3K4me3 is associated with transcription initiation during early embryo development. - Xin Huang 005; Xudong Gao; Wanying Li; Shuai Jiang; Ruijiang Li; Hao Hong; Chenghui Zhao; Pingkun Zhou; Hebing Chen; Xiaochen Bo; Hao Li 035 (Bioinform., 2019)

New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. - Hebing Chen; Zhuo Zhang; Shuai Jiang; Ruijiang Li; Wanying Li; Chenghui Zhao; Hao Hong; Xin Huang 005; Hao Li 035; Xiaochen Bo (Briefings Bioinform., 2020)

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. - Hao Hong; Shuai Jiang; Hao Li 035; Guifang Du; Yu Sun; Huan Tao; Cheng Quan; Chenghui Zhao; Ruijiang Li; Wanying Li; Xiaoyao Yin; Yangchen Huang; et al. (PLoS Comput. Biol., 2020)

Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. - Shuai Jiang; Hao Li 035; Hao Hong; Guifang Du; Xin Huang 005; Yu Sun; Junting Wang 003; Huan Tao; Kang Xu; Cheng Li; Yang Chen; Hebing Chen; et al. (Briefings Bioinform., 2021)

Graph Neural Networks for Double-Strand DNA Breaks Prediction. - Xu Wang; Huan Zhao 002; Weiwei Tu; Hao Li 035; Yu Sun; Xiaochen Bo (CoRR, 2022)

Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks. - Hao Li 035; Yu Sun; Hao Hong; Xin Huang 005; Huan Tao; Qiya Huang; Longteng Wang; Kang Xu; Jingbo Gan; Hebing Chen; Xiaochen Bo (Nat. Mach. Intell., 2022)

3D genomic organization in cancers. - Junting Wang 003; Huan Tao; Hao Li 035; Xiaochen Bo; Hebing Chen (Quant. Biol., 2023)

Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. - Bijia Chen; Chao Ren; Zhangyi Ouyang; Jingxuan Xu; Kang Xu; Yaru Li; Hejiang Guo; Xuemei Bai; Mengge Tian; Xiang Xu; Yuyang Wang; Hao Li 035; et al. (Briefings Bioinform., 2024)

SEPDB: a database of secreted proteins. - Ruiqing Wang; Chao Ren; Tian Gao; Hao Li 035; Xiaochen Bo; Dahai Zhu; Dan Zhang; Hebing Chen; Yong Zhang (Database J. Biol. Databases Curation, 2024)