A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. - Su-Juan Wu; Junyi Li 004; Mushui Cao; Jing Yang; Yi-Xue Li; Yuan-Yuan Li (BMC Syst. Biol., 2016)

Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. - Quanxue Li; Junyi Li 004; Wentao Dai; Yi-Xue Li; Yuan-Yuan Li (Artif. Intell. Medicine, 2017)

rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering. - Bo Liu 023; Tao Jiang 021; Siu-Ming Yiu; Junyi Li 004; Yadong Wang 001 (Bioinform., 2017)

DeepDNA: a hybrid convolutional and recurrent neural network for compressing human mitochondrial genomes. - Rongjie Wang; Yang Bai; Yan-Shuo Chu; Zhenxing Wang; Yongtian Wang; Mingrui Sun; Junyi Li 004; Tianyi Zang; Yadong Wang 001 (BIBM, 2018)

Prediction of Human LncRNAs Based on Integrated Information Entropy Features. - Junyi Li 004; Huinian Li; Li Zhang; Qingzhe Xu; Yuan Ping; Xiaozhu Jing; Wei Jiang 023; Bo Liu 023; Yadong Wang 001 (ICIC (2), 2019)

rMETL: sensitive mobile element insertion detection with long read realignment. - Tao Jiang 021; Bo Liu 023; Junyi Li 004; Yadong Wang 001 (Bioinform., 2019)

Integrated entropy-based approach for analyzing exons and introns in DNA sequences. - Junyi Li 004; Li Zhang; Huinian Li; Yuan Ping; Qingzhe Xu; Rongjie Wang; Renjie Tan; Zhen Wang; Bo Liu 023; Yadong Wang 001 (BMC Bioinform., 2019)

GONET: A Deep Network to Annotate Proteins via Recurrent Convolution Networks. - Junyi Li 004; Lixin Wang; Xiaoshuai Zhang; Bo Liu 023; Yadong Wang 001 (BIBM, 2020)

HGAlinker: Drug-Disease Association Prediction Based on Attention Mechanism of Heterogeneous Graph. - Xiaozhu Jing; Wei Jiang 023; Zhongqing Zhang; Yadong Wang 001; Junyi Li 004 (ICIC (2), 2020)

Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network. - Junyi Li 004; Yuan Ping; Hong Li; Huinian Li; Ying Liu; Bo Liu 023; Yadong Wang 001 (Comput. Biol. Chem., 2020)

ScSSC: Semi-supervised Single Cell Clustering Based on 2D Embedding. - Naile Shi; Yulin Wu 001; Linlin Du; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (ICIC (3), 2021)

Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction. - Ming He; Chen Huang; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (BMC Bioinform., 2021)

IIMLP: integrated information-entropy-based method for LncRNA prediction. - Junyi Li 004; Huinian Li; Xiao Ye; Li Zhang; Qingzhe Xu; Yuan Ping; Xiaozhu Jing; Wei Jiang 023; Qing Liao 001; Bo Liu 023; Yadong Wang 001 (BMC Bioinform., 2021)

ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering. - Junyi Li 004; Wei Jiang 023; Henry Han; Jing Liu; Bo Liu 023; Yadong Wang 001 (Comput. Biol. Chem., 2021)

deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph. - Hongzhe Guo; Yilei Fu; Yan Gao 031; Junyi Li 004; Yadong Wang 001; Bo Liu 023 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

NSAP: A Neighborhood Subgraph Aggregation Method for Drug-Disease Association Prediction. - Qiqi Jiao; Yu Jiang 002; Yang Zhang; Yadong Wang 001; Junyi Li 004 (ICIC (2), 2022)

Prediction of the disease causal genes based on heterogeneous network and multi-feature combination method. - Lexiang Wang; Mingxiao Wu; Yulin Wu 001; Xiaofeng Zhang; Sen Li; Ming He; Fan Zhang; Yadong Wang 001; Junyi Li 004 (Comput. Biol. Chem., 2022)

OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection. - Zhongqing Zhang; Qiqi Jiao; Yang Zhang; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (Comput. Biol. Chem., 2022)

Mixed-protocol multi-party computation framework towards complex computation tasks with malicious security. - Yulin Wu 001; Xuan Wang 002; Willy Susilo; Guomin Yang; Zoe Lin Jiang; Junyi Li 004; Xueqiao Liu (Comput. Stand. Interfaces, 2022)

Deepgmd: A Graph-Neural-Network-Based Method to Detect Gene Regulator Module. - Xiao Ye; Yulin Wu 001; Jiangsheng Pi; Hong Li; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

NIEE: Modeling Edge Embeddings for Drug-Disease Association Prediction via Neighborhood Interactions. - Yu Jiang 002; Jingli Zhou; Yong Zhang; Yulin Wu 001; Xuan Wang 002; Junyi Li 004 (ICIC (3), 2023)

ScCCL: Single-Cell Data Clustering Based on Self-Supervised Contrastive Learning. - Linlin Du; Rui Han; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction. - Kaitao Wu; Lexiang Wang; Bo Liu 023; Yang Liu 039; Yadong Wang 001; Junyi Li 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Prot2GO: Predicting GO Annotations From Protein Sequences and Interactions. - Xiaoshuai Zhang; Lixin Wang; Hucheng Liu; Xiaofeng Zhang; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

SLGNN: synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network. - Yan Zhu; Yuhuan Zhou; Yang Liu 039; Xuan Wang 002; Junyi Li 004 (Bioinform., 2023)

HNetGO: protein function prediction via heterogeneous network transformer. - Xiaoshuai Zhang; Huannan Guo; Fan Zhang; Xuan Wang 002; Kaitao Wu; Shizheng Qiu; Bo Liu 023; Yadong Wang 001; Yang Hu 008; Junyi Li 004 (Briefings Bioinform., 2023)

Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information. - Peishun Jiao; Beibei Wang; Xuan Wang 002; Bo Liu 023; Yadong Wang 001; Junyi Li 004 (Bioinform., 2023)

SLGNNCT: Synthetic Lethality Prediction Based on Knowledge Graph for Different Cancers Types. - Jingru Chen; Jianyong Pan; Yan Zhu; Junyi Li 004 (ICIC (LNBI 1), 2024)

PF2PI: Protein Function Prediction Based on AlphaFold2 Information and Protein-Protein Interaction. - Ruiqi Li; Peishun Jiao; Junyi Li 004 (ICIC (LNBI 2), 2024)

MKDTI: Predicting drug-target interactions via multiple kernel fusion on graph attention network. - Yuhuan Zhou; Yulin Wu 001; Weiwei Yuan; Xuan Wang 002; Junyi Li 004 (CoRR, 2024)

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network. - Keliang Cen; Zheming Xing; Xuan Wang 002; Yadong Wang 001; Junyi Li 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

DIRMC: a database of immunotherapy-related molecular characteristics. - Yue Liu 034; Yuhuan Zhou; Xiumei Hu; Wuri Le-Ge; Haoyan Wang; Tao Jiang 021; Junyi Li 004; Yang Hu 008; Yadong Wang 001 (Database J. Biol. Databases Curation, 2024)

E-MSNGO: Explainable Multi-species Protein Function Prediction Model Based on Aggregated Networks. - Beibei Wang; Siyuan Zhou; Shiqu Chen; Junyi Li 004 (ICIC (26), 2025)

MKDTI: Predicting Drug-Target Interactions via Multiple Kernel Fusion on Graph Attention Network. - Yuhuan Zhou; Yaqiu Wang; Yulin Wu 001; Qian Chen 028; Weiwei Yuan; Xuan Wang 002; Junyi Li 004 (ICIC (25), 2025)

MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation. - Beibei Wang; Boyue Cui; Shiqu Chen; Xuan Wang 002; Yadong Wang 001; Junyi Li 004 (CoRR, 2025)