Identification of core-attachment complexes based on maximal frequent patterns in protein-protein interaction networks. - Liang Yu 002; Lin Gao 006; Chuiliang Kong (BIBM Workshops, 2010)

A hybrid clustering algorithm for identifying modules in Protein - Protein Interaction networks. - Liang Yu 002; Lin Gao 006; Peng-Gang Sun (Int. J. Data Min. Bioinform., 2010)

Quantitative function for community structure detection. - Liang Yu 002; Lin Gao 006; Danyang Wang; Shaofeng Fu (Int. J. Data Min. Model. Manag., 2010)

A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification. - Liang Yu 002; Lin Gao 006; Kui Li; Yi Zhao; David K. Y. Chiu (Comput. Biol. Chem., 2011)

The extraction of drug-disease correlations based on module distance in incomplete human interactome. - Liang Yu 002; Bingbo Wang; Xiaoke Ma 001; Lin Gao 006 (BMC Syst. Biol., 2016)

Drug repositioning based on triangularly balanced structure for tissue-specific diseases in incomplete interactome. - Liang Yu 002; Jin Zhao; Lin Gao 006 (Artif. Intell. Medicine, 2017)

Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes. - Xiaoke Ma 001; Liang Yu 002; Peizhuo Wang; Xiaofei Yang (Comput. Biol. Chem., 2017)

Predicting potential treatments for complex diseases based on miRNA and tissue specificity. - Liang Yu 002; Jin Zhao; Lin Gao 006 (CoRR, 2017)

Prediction of Novel Drugs for Hepatocellular Carcinoma Based on Multi-Source Random Walk. - Liang Yu 002; Ruidan Su; Bingbo Wang; Long Zhang; Yapeng Zou; Jing Zhang; Lin Gao 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Human Pathway-Based Disease Network. - Liang Yu 002; Lin Gao 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Node Embedding Framework for Integration of Similarity-based Drug Combination Prediction. - Liang Yu 002; Mingfei Xia; Lin Gao 006 (CoRR, 2020)

C3: connect separate connected components to form a succinct disease module. - Bingbo Wang; Jie Hu; Yajun Wang; Chenxing Zhang; Yuanjun Zhou; Liang Yu 002; Xingli Guo; Lin Gao 006; Yunru Chen (BMC Bioinform., 2020)

A heterogeneous network embedding framework for predicting similarity-based drug-target interactions. - Qi An; Liang Yu 002 (Briefings Bioinform., 2021)

EPSOL: sequence-based protein solubility prediction using multidimensional embedding. - Xiang Wu; Liang Yu 002 (Bioinform., 2021)

Prediction of drug-target interactions based on multi-layer network representation learning. - Yifan Shang; Lin Gao 006; Quan Zou 001; Liang Yu 002 (Neurocomputing, 2021)

Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways. - Liang Yu 002; Meng Wang; Yang Yang; Fengdan Xu; Xu Zhang; Fei Xie; Lin Gao 006; Xiangzhi Li (PLoS Comput. Biol., 2021)

NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences. - Chunyan Ao; Quan Zou 001; Liang Yu 002 (Briefings Bioinform., 2022)

Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving. - Yifan Shang; Xiucai Ye; Yasunori Futamura; Liang Yu 002; Tetsuya Sakurai (Briefings Bioinform., 2022)

A network embedding framework based on integrating multiplex network for drug combination prediction. - Liang Yu 002; Mingfei Xia; Qi An (Briefings Bioinform., 2022)

MiRNA-disease association prediction based on meta-paths. - Liang Yu 002; Yujia Zheng; Lin Gao 006 (Briefings Bioinform., 2022)

Research progress of miRNA-disease association prediction and comparison of related algorithms. - Liang Yu 002; Yujia Zheng; Bingyi Ju; Chunyan Ao; Lin Gao 006 (Briefings Bioinform., 2022)

Multidrug representation learning based on pretraining model and molecular graph for drug interaction and combination prediction. - Shujie Ren; Liang Yu 002; Lin Gao 006 (Bioinform., 2022)

Cancer classification based on multiple dimensions: SNV patterns. - Bo Li; Liang Yu 002; Lin Gao 006 (Comput. Biol. Medicine, 2022)

WMSA: a novel method for multiple sequence alignment of DNA sequences. - Yanming Wei; Quan Zou 001; Furong Tang; Liang Yu 002 (Bioinform., 2022)

Application of Multi-Dimensional SNV Features in Supervised Learning. - Liang Yu 002; Lin Gao 006; Bo Li; Hongxia Hao; Lu Chen (BIBM, 2023)

Gene Expression Profile Prediction under Drug Action Based on Generative Adversarial Networks. - Liang Yu 002; Huan Zhu; Da Dong; Lin Gao 006 (BIBM, 2023)

Computational Approaches for Predicting Drug-Disease Associations: A Comprehensive Review. - Chunyan Ao; Zhichao Xiao; Lixin Guan; Liang Yu 002 (CoRR, 2023)

Potent antibiotic design via guided search from antibacterial activity evaluations. - Lu Chen; Liang Yu 002; Lin Gao 006 (Bioinform., 2023)

Identification of a novel gene signature for the prognosis of sepsis. - Kai Yang; Lin Gao 006; Hongxia Hao; Liang Yu 002 (Comput. Biol. Medicine, 2023)

Predicting new drug indications based on double variational autoencoders. - Zhaoyang Huang; Shengjian Chen; Liang Yu 002 (Comput. Biol. Medicine, 2023)

GOLF-Net: Global and local association fusion network for COVID-19 lung infection segmentation. - Xinyu Xu; Lin Gao 006; Liang Yu 002 (Comput. Biol. Medicine, 2023)

MVLncStack: A novel method for lncRNA subcellular localization prediction based on multi-view features. - Ziqi Liu; Tao Bai; Dongdong Jiang; Bin Liu; Liang Yu 002 (BIBM, 2024)

FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Briefings Bioinform., 2024)

MulStack: An ensemble learning prediction model of multilabel mRNA subcellular localization. - Ziqi Liu; Tao Bai; Bin Liu; Liang Yu 002 (Comput. Biol. Medicine, 2024)

Prediction of cancer drug combinations based on multidrug learning and cancer expression information injection. - Shujie Ren; Lu Chen; Hongxia Hao; Liang Yu 002 (Future Gener. Comput. Syst., 2024)

FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using t-blocks based on FOur Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Zenodo, 2024)

FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Zenodo, 2024)

Identifying G-Protein Coupled Receptors Using Mixed-Feature Extraction Methods and Machine Learning Methods. - Chunyan Ao; Lin Gao 006; Liang Yu 002 (IEEE Access, 2025)

deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment. - Yanming Wei; Zhaoyang Huang; Pinglu Zhang; Yizheng Wang; Liang Yu 002; Quan Zou 001 (Zenodo, 2025)

Computational approaches for predicting drug-disease associations: a comprehensive review. - Zhaoyang Huang; Zhichao Xiao; Chunyan Ao; Lixin Guan; Liang Yu 002 (Frontiers Comput. Sci., 2025)