A new strategy of outlier detection for QSAR/QSPR. - Dong-Sheng Cao 001; Yi-Zeng Liang; Qing-Song Xu; Hong-Dong Li; Xian Chen (J. Comput. Chem., 2010)

Recipe for Uncovering Predictive Genes Using Support Vector Machines Based on Model Population Analysis. - Hong-Dong Li; Yi-Zeng Liang; Qing-Song Xu; Dong-Sheng Cao 001; Bin-Bin Tan; Bai-Chuan Deng; Chen-Chen Lin (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

An interpretable model for predicting side effects of analgesics for osteoarthritis. - Liangliang Liu 001; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu; Hong-Dong Li; Ying Yu; Zhihui Fei (BIBM, 2017)

BioRank: A Similarity Assessment Method for Single Cell Clustering. - Yunpei Xu; Hong-Dong Li; Yi Pan 001; Feng Luo 001; Jianxin Wang 001 (BIBM, 2018)

A Global Similarity Learning for Clustering of Single-Cell RNA-Seq Data. - Xiaoshu Zhu; Lilu Guo; Yunpei Xu; Hong-Dong Li; Xingyu Liao; Fang-Xiang Wu; Xiaoqing Peng (BIBM, 2019)

BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets. - Hong-Dong Li; Tianjian Bai; Erin Sandford; Margit Burmeister; Yuanfang Guan (Bioinform., 2019)

Joint Learning of Primary and Secondary Labels based on Multi-scale Representation for Alzheimer's Disease Diagnosis. - Hong-Dong Li; Rui Guo; Junjian Li; Jianxin Wang 001; Yi Pan 001; Jin Liu 012 (BIBM, 2020)

Identification of Disease-Associated Genes Based on Differential Intron Retention. - Zhenpeng Wu; Jiantao Zheng; Hong-Dong Li (BIBM, 2020)

A network enhancement-based method for clustering of single cell RNA-seq data. - Xiaoshu Zhu; Lilu Guo; Rongyuan Li; Yunpei Xu; Fang-Xiang Wu; Xiaoqing Peng; Hong-Dong Li (Int. J. Data Min. Bioinform., 2020)

ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. - Hong-Dong Li; Yunpei Xu; Xiaoshu Zhu; Quan Liu; Gilbert S. Omenn; Jianxin Wang 001 (J. Bioinform. Comput. Biol., 2020)

Improving the Prediction of Disease-associated Genes by Integrating Annotated Gene Sets. - Chao Deng; Cui-Xiang Lin; Hong-Dong Li (BIBM, 2021)

GraphIsoFun: a graph neural network based approach for splice isoform function prediction. - Shuo Zhang; Changhuo Yang; Hong-Dong Li; Jianxin Wang 001 (BIBM, 2021)

REBET: a method to determine the number of cell clusters based on batch effect removal. - Zhao-Yu Fang; Cui-Xiang Lin; Yun-Pei Xu; Hong-Dong Li; Qing-Song Xu (Briefings Bioinform., 2021)

Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. - Xiaoqing Peng; Hong-Dong Li; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation. - Hong-Dong Li; Changhuo Yang; Zhimin Zhang; Mengyun Yang; Fang-Xiang Wu; Gilbert S. Omenn; Jianxin Wang 001 (Bioinform., 2021)

A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering. - Yunpei Xu; Hong-Dong Li; Yi Pan 001; Feng Luo 001; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

KL-RF: Predicting disease-gene associations with model fusion. - Hai Liu; Hong-Dong Li (BIBM, 2022)

An Alzheimer's disease gene prediction method based on ensemble of genome-wide association study summary statistics. - Jia-Hao Song; Cui-Xiang Lin; Hong-Dong Li (BIBM, 2022)

An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. - Cui-Xiang Lin; Hong-Dong Li; Chao Deng; Weisheng Liu; Shannon Erhardt; Fang-Xiang Wu; Xing-Ming Zhao; Yuanfang Guan; Jun Wang 153; Daifeng Wang; Bin Hu 001; Jianxin Wang 001 (Briefings Bioinform., 2022)

A comparison of computational approaches for intron retention detection. - Jiantao Zheng; Cuixiang Lin; Zhenpeng Wu; Hong-Dong Li (Big Data Min. Anal., 2022)

AlzCode: a platform for multiview analysis of genes related to Alzheimer's disease. - Cui-Xiang Lin; Hong-Dong Li; Chao Deng; Shannon Erhardt; Jun Wang 153; Xiaoqing Peng; Jianxin Wang 001 (Bioinform., 2022)

TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. - Cui-Xiang Lin; Hong-Dong Li; Chao Deng; Yuanfang Guan; Jianxin Wang 001 (Nucleic Acids Res., 2022)

GTFtools: a software package for analyzing various features of gene models. - Hong-Dong Li; Cui-Xiang Lin; Jiantao Zheng (Bioinform., 2022)

Training Methods of Innovative Talents in Medical Imaging Informatics Under the Background of New Engineering. - Jin Liu; Qian Bi; Ping Zhong; Hong-Dong Li; Fei Guo; Junwen Duan (ICCSE (3), 2023)

CellBRF: a feature selection method for single-cell clustering using cell balance and random forest. - Yunpei Xu; Hong-Dong Li; Cui-Xiang Lin; Ruiqing Zheng; Yaohang Li; Jinhui Xu 001; Jianxin Wang 001 (Bioinform., 2023)

A Gene Set-Integrated Approach for Predicting Disease-Associated Genes. - Hong-Dong Li; Chao Deng; Xiao-Qi Zhang; Cui-Xiang Lin (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

A Comparison of Topologically Associating Domain Callers Based on Hi-C Data. - Kun Liu 028; Hong-Dong Li; Yaohang Li; Jun Wang 153; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

IsoCell: An Approach to Enhance Single Cell Clustering by Integrating Isoform-Level Expression Through Orthogonal Projection. - Yingyi Liu; Hong-Dong Li; Yunpei Xu; Yi-Wei Liu; Xiaoqing Peng; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Computational approaches for detecting disease-associated alternative splicing events. - Jiashu Liu; Cui-Xiang Lin; Xiaoqi Zhang; Zongxuan Li; Wenkui Huang; Jin Liu; Yuanfang Guan; Hong-Dong Li (Briefings Bioinform., 2023)

DeepRetention: A Deep Learning Approach for Intron Retention Detection. - Zhenpeng Wu; Jiantao Zheng; Jiashu Liu; Cuixiang Lin; Hong-Dong Li (Big Data Min. Anal., 2023)

FEED: a feature selection method based on gene expression decomposition for single cell clustering. - Chao Zhang; Zhi-Wei Duan; Yun-Pei Xu; Jin Liu; Hong-Dong Li (Briefings Bioinform., 2023)

IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions. - Yiwei Liu; Changhuo Yang; Hong-Dong Li; Jianxin Wang 001 (Bioinform., 2023)

MVFormer: Predicting the pathogenicity of missense variants using gated transformers. - Zongxuan Li; Wenkui Huang; Hong-Dong Li (BCB, 2024)

Pre-trained Feature Fusion and Matching for Mild Cognitive Impairment Detection. - Junwen Duan; Fangyuan Wei; Hong-Dong Li; Jin Liu (INTERSPEECH, 2024)

LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes. - Cui-Xiang Lin; Hong-Dong Li; Jianxin Wang 001 (Briefings Bioinform., 2024)

Multi-Task Learning for Alzheimer's Disease Diagnosis and Mini-Mental State Examination Score Prediction. - Jin Liu 012; Xu Tian; Hanhe Lin; Hong-Dong Li; Yi Pan 001 (Big Data Min. Anal., 2024)

Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks. - Chao Deng; Hong-Dong Li; Li-Shen Zhang; Yiwei Liu; Yaohang Li; Jianxin Wang 001 (Bioinform., 2024)

Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis. - Rui Guo; Xu Tian; Hanhe Lin; Stephen J. McKenna; Hong-Dong Li; Fei Guo 001; Jin Liu 012 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Inspired by pathogenic mechanisms: A novel gradual multi-modal fusion framework for mild cognitive impairment diagnosis. - Xu Tian; Hong-Dong Li; Hanhe Lin; Chao Li 031; Yu-Ping Wang; Harrison X. Bai; Wei Lan; Jin Liu 012 (Neural Networks, 2025)