Extending gene ontology with gene association networks. - Jiajie Peng; Tao Wang 082; Jixuan Wang; Yadong Wang 001; Jin Chen 004 (Bioinform., 2016)

TSGOE: A web tool for tissue-specific gene ontology enrichment. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BIBM, 2018)

Identifying Representative Network Motifs for Inferring Higher-order Structure of Biological Networks. - Tao Wang 082; Jiajie Peng; Yadong Wang 001; Jin Chen 004 (BIBM, 2018)

An automated quality control pipeline for eQTL analysis with RNA-seq data. - Tao Wang 082; Junpeng Ruan; Quanwei Yin; Xianjun Dong; Yadong Wang 001 (BIBM, 2019)

TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BMC Bioinform., 2019)

Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations. - Tao Wang 082; Zhiyuan Shao; Yifu Xiao; Xuchao Zhang; Yitian Chen; Binze Shi; Siyu Chen; Yuxian Wang; Jiajie Peng; Xuequn Shang 001 (BIBM, 2021)

A pipeline for RNA-seq based eQTL analysis with automated quality control procedures. - Tao Wang 082; Yongzhuang Liu; Junpeng Ruan; Xianjun Dong; Yadong Wang 001; Jiajie Peng (BMC Bioinform., 2021)

Exploring genetic mechanisms underlying EEG endophenotypes via summary-data-based Mendelian randomization. - Jing Chen; Pengfei Zhu; Jinghui Pan; Tao Wang 082 (BIBM, 2022)

Hypergraph-based Gene Ontology Embedding for Disease Gene Prediction. - Tao Wang 082; Hengbo Xu; Ranye Zhang; Yifu Xiao; Jiajie Peng; Xuequn Shang 001 (BIBM, 2022)

Discovering eQTL Regulatory Patterns Through eQTLMotif. - Tao Wang 082; Hui Zhao; Yifu Xiao; Hanzi Yang; Xipeng Yin; Yongtian Wang; Bing Xiao 001; Xuequn Shang 001; Jiajie Peng (BIBM, 2022)

A network-based method for brain disease gene prediction by integrating brain connectome and molecular network. - Wei Wang; Ruijiang Han; Menghan Zhang; Yuxian Wang; Tao Wang 082; Yongtian Wang; Xuequn Shang 001; Jiajie Peng (Briefings Bioinform., 2022)

Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. - Tao Wang 082; Yongzhuang Liu; Quanwei Yin; Jiaquan Geng; Jin Chen 004; Xipeng Yin; Yongtian Wang; Xuequn Shang 001; Chunwei Tian; Yadong Wang 001; Jiajie Peng (Briefings Bioinform., 2022)

Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. - Tao Wang 082; Yongzhuang Liu; Quanwei Yin; Jiaquan Geng; Jin Chen 004; Xipeng Yin; Yongtian Wang; Xuequn Shang 001; Chunwei Tian; Yadong Wang 001; Jiajie Peng (Briefings Bioinform., 2022)

A review and performance evaluation of clustering frameworks for single-cell Hi-C data. - Caiwei Zhen; Yuxian Wang; Jiaquan Geng; Lu Han; Jingyi Li; Jinghao Peng; Tao Wang 082; Jianye Hao; Xuequn Shang 001; Zhongyu Wei; Peican Zhu; Jiajie Peng (Briefings Bioinform., 2022)

DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. - Tao Wang 082; Jinjin Yang; Yifu Xiao; Jingru Wang; Yuxian Wang; Xi Zeng; Yongtian Wang; Jiajie Peng (Bioinform., 2023)

Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information. - Yongtian Wang; Xinmeng Liu; Yewei Shen; Xuerui Song; Tao Wang 082; Xuequn Shang 001; Jiajie Peng (Briefings Bioinform., 2023)

scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks. - Tao Wang 082; Hui Zhao; Yungang Xu; Yongtian Wang; Xuequn Shang 001; Jiajie Peng; Bing Xiao 001 (Briefings Bioinform., 2023)

A Scenario Model-driven Task Planning Method for Unmanned Aerial Vehicle Swarm. - Yunwei Dong; Zeshan Li; Ruiheng Zhang 002; Rubing Huang; Tao Wang 082 (Internetware, 2024)

Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster. - Tao Wang 082; Han Shu; Jialu Hu; Yongtian Wang; Jin Chen 004; Jiajie Peng; Xuequn Shang 001 (Briefings Bioinform., 2024)

VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network. - Tianjiao Zhang; Xiang Zhang; Zhenao Wu; Jixiang Ren; Zhongqian Zhao; Hongfei Zhang; Guohua Wang; Tao Wang 082 (Briefings Bioinform., 2024)

postGWAS: A web server for deciphering the causality post the genome-wide association studies. - Tao Wang 082; Zhihao Yan; Yiming Zhang; Zhuofei Lou; Xiaozhu Zheng; Duoduo Mai; Yongtian Wang; Xuequn Shang 001; Bing Xiao 001; Jiajie Peng; Jin Chen 004 (Comput. Biol. Medicine, 2024)

Scbean: a python library for single-cell multi-omics data analysis. - Haohui Zhang; Yuwei Wang; Bin Lian; Yiran Wang; Xingyi Li; Tao Wang 082; Xuequn Shang 001; Hui Yang; Ahmad Aziz; Jialu Hu (Bioinform., 2024)

Inference of gene coexpression networks from single-cell transcriptome data based on variance decomposition analysis. - Bin Lian; Haohui Zhang; Tao Wang 082; Yongtian Wang; Xuequn Shang 001; N. Ahmad Aziz; Jialu Hu (Briefings Bioinform., 2025)

cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling. - Xuchao Zhang; Jing Chen; Yongtian Wang; Xiaofeng Wang; Jialu Hu; Jiajie Peng; Xuequn Shang 001; Yanpu Wang; Tao Wang 082 (Briefings Bioinform., 2025)

MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder. - Pengfei Zhu; Han Shu; Yongtian Wang; Xiaofeng Wang; Yuan Zhao; Jialu Hu; Jiajie Peng; Xuequn Shang 001; Zhen Tian; Jing Chen; Tao Wang 082 (Briefings Bioinform., 2025)