SELECTED PUBLICATIONS
• Huimin Zhu, Renyi Zhou, Dongsheng Cao, Jing Tang, Min Li*; A pharmacophore-guided deep learning approach for bioactive molecular generation, Nature Communications, 2023, 14(1): 6234.
• Fuhao Zhang, Min Li*, Jian Zhang, Lukasz Kurgan*; HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins, Nucleic Acids Research, 2023, 51(5): e25-e25.
• Xuhua Yan, Ruiqing Zheng*, Jinmiao Chen, Min Li*; scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization, Bioinformatics, 2023, 39(8):btad505.
• Kaili Wang, Renyi Zhou, Jing Tang, Min Li*; GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction, Bioinformatics, 2023, 39(6): btad340.
• Xuhua Yan, Ruiqing Zheng, Fangxiang Wu, Min Li*; CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity, Bioinformatics, 2023, 39(3): btad099.
• Min Li, Baoying Zhao, Rui Yin, Chengqian Lu, Fei Guo, Min Zeng*; GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation, Briefings in Bioinformatics, 2023, 24(1): bbac565.
• Yiming Li, Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Min Li*; DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning, Bioinformatics, 2023, 39(1): btac779.
• Li Tang; Matthew C. Hill; Patrick T. Ellinor; Min Li*; Bacon：A comprehensive computation al benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies, Genome Biology, 2022, 23: 30.
• Min Li*; Zhangli Lu; Yifan Wu; YaoHang Li; BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction, Bioinformatics, 2022, 38(7): 1995-2002.
• Xiangmao Meng, Wenkai Li, Ju Xiang, Hayat Dino Bedru, Wenkang Wang, Fang-Xiang Wu, Min Li*; Temporal-spatial analysis of the essentiality of hub proteins in protein-protein interaction networks, IEEE Transactions on Network Science and Engineering, 2022, 9(5): 3504-3514.
• Yifan Wu; Min Gao; Min Zeng; Jie Zhang; Min Li*; BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interaction., Bioinformatics, 2022, 38(9): 2571-2578.
• Zhenlan Liang; Min Li*; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen; FangXiang Wu; Jianxin Wang ; SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement, Genomics Proteomics Bioinformatics, 2021, 19(2): 282-291
• Ju Xiang; Jiashuai Zhang; Ruiqing Zheng; Xingyi Li; Min Li*; NIDM: Network impulsive dynamics on multiplex biological network for disease-gene prediction, Briefings in Bioinformatics, 2021, 22(5): bbab080.
• Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li*; Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species, Briefings in bioinformatics, 2021, 22(2): 963-975.
• Li Tang; Matthew C. Hill; Jun Wang; Jianxin Wang; James F. Martin*; Min Li*; Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model, Genome Research, 2020, 30(12): 1835-1845
• Min Zeng; Fuhao Zhang; FangXiang Wu; Yaohang Li; Jianxin Wang; Min Li*; Protein-protein interaction site prediction through combining local and global features with deep neural networks, Bioinformatics, 2020, 36(4): 1114-1120
• Min Li*; Xiangmao Meng; Ruiqing Zheng; Fang-Xiang Wu; Yaohang Li; Yi Pan; Jianxin Wang ; Identification of protein complexes by using a spatial and temporal active protein interaction network, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, 17(3): 817-827
• Min Li*; Li Tang; FangXiang Wu; Yi Pan; Jianxin Wang*; SCOP: a novel scaffolding algorithm based on contig classification and optimization, Bioinformatics, 2019, 35(7): 1142-1150
• Ruiqing Zheng; Min Li*; Zhenlan Liang; FangXiang Wu; Yi Pan; Jianxin Wang ; SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation, Bioinformatics, 2019, 35(19): 3642-3650
• Ruiqing Zheng; Min Li*; Xiang Chen; FangXiang Wu; Yi Pan; Jianxin Wang ; BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks, Bioinformatics, 2019, 35(11): 1893-1990
• Min Li*; Jie Yang; FangXiang Wu; Yi Pan; Jianxin Wang ; DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization, Bioinformatics, 2018, 34(9): 1597-1599
• Fuhao Zhang, Min Li*, Jian Zhang, Lukasz Kurgan*; HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins, Nucleic Acids Research, 2023, 51(5): e25-e25.
• Xuhua Yan, Ruiqing Zheng*, Jinmiao Chen, Min Li*; scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization, Bioinformatics, 2023, 39(8):btad505.
• Kaili Wang, Renyi Zhou, Jing Tang, Min Li*; GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction, Bioinformatics, 2023, 39(6): btad340.
• Xuhua Yan, Ruiqing Zheng, Fangxiang Wu, Min Li*; CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity, Bioinformatics, 2023, 39(3): btad099.
• Min Li, Baoying Zhao, Rui Yin, Chengqian Lu, Fei Guo, Min Zeng*; GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation, Briefings in Bioinformatics, 2023, 24(1): bbac565.
• Yiming Li, Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Min Li*; DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning, Bioinformatics, 2023, 39(1): btac779.
• Li Tang; Matthew C. Hill; Patrick T. Ellinor; Min Li*; Bacon：A comprehensive computation al benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies, Genome Biology, 2022, 23: 30.
• Min Li*; Zhangli Lu; Yifan Wu; YaoHang Li; BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction, Bioinformatics, 2022, 38(7): 1995-2002.
• Xiangmao Meng, Wenkai Li, Ju Xiang, Hayat Dino Bedru, Wenkang Wang, Fang-Xiang Wu, Min Li*; Temporal-spatial analysis of the essentiality of hub proteins in protein-protein interaction networks, IEEE Transactions on Network Science and Engineering, 2022, 9(5): 3504-3514.
• Yifan Wu; Min Gao; Min Zeng; Jie Zhang; Min Li*; BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interaction., Bioinformatics, 2022, 38(9): 2571-2578.
• Zhenlan Liang; Min Li*; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen; FangXiang Wu; Jianxin Wang ; SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement, Genomics Proteomics Bioinformatics, 2021, 19(2): 282-291
• Ju Xiang; Jiashuai Zhang; Ruiqing Zheng; Xingyi Li; Min Li*; NIDM: Network impulsive dynamics on multiplex biological network for disease-gene prediction, Briefings in Bioinformatics, 2021, 22(5): bbab080.
• Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li*; Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species, Briefings in bioinformatics, 2021, 22(2): 963-975.
• Li Tang; Matthew C. Hill; Jun Wang; Jianxin Wang; James F. Martin*; Min Li*; Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model, Genome Research, 2020, 30(12): 1835-1845
• Min Zeng; Fuhao Zhang; FangXiang Wu; Yaohang Li; Jianxin Wang; Min Li*; Protein-protein interaction site prediction through combining local and global features with deep neural networks, Bioinformatics, 2020, 36(4): 1114-1120
• Min Li*; Xiangmao Meng; Ruiqing Zheng; Fang-Xiang Wu; Yaohang Li; Yi Pan; Jianxin Wang ; Identification of protein complexes by using a spatial and temporal active protein interaction network, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, 17(3): 817-827
• Min Li*; Li Tang; FangXiang Wu; Yi Pan; Jianxin Wang*; SCOP: a novel scaffolding algorithm based on contig classification and optimization, Bioinformatics, 2019, 35(7): 1142-1150
• Ruiqing Zheng; Min Li*; Zhenlan Liang; FangXiang Wu; Yi Pan; Jianxin Wang ; SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation, Bioinformatics, 2019, 35(19): 3642-3650
• Ruiqing Zheng; Min Li*; Xiang Chen; FangXiang Wu; Yi Pan; Jianxin Wang ; BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks, Bioinformatics, 2019, 35(11): 1893-1990
• Min Li*; Jie Yang; FangXiang Wu; Yi Pan; Jianxin Wang ; DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization, Bioinformatics, 2018, 34(9): 1597-1599