Academic Outputs (2025)
Academic Outputs of Centre of AI-driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University in 2025
1. Wang X, Yin X, Zhang X, Zhao H, Gu S, Wu Z, Zhang O, Qian W, Huang Y, Li Y, Jiang D, Wang M, Liu H, Yao X, Hsieh CY, Hou T: A virtual platform for automated hybrid organic-enzymatic synthesis planning. Nature Communications 2025, 16.
2. Tian Y, Lu R, Gong X, Zhao W, Li Y, Wang X, Jia X, Li Q, Yang Y, Tong HHY, Arrais JP, Yao X, Liu H: Enhancing kinase-inhibitor activity and selectivity prediction through contrastive learning. Nature Communications 2025, 16.
3.Qiao J, Jin J, Wang D, Teng S, Zhang J, Yang X, Liu Y, Wang Y, Cui L, Zou Q, Su R, Wei L: A self-conformation-aware pre-training framework for molecular property prediction with substructure interpretability. Nature Communications 2025, 16.
4. He W, Chen C, Zheng J, Li Y, Shi H, Zhou Y, Li M, Gong P, Liu K, Shao X, Yao X, Li H, Chen L, Fang L: Targeted degradation of cell surface proteins through endocytosis triggered by cell-penetrating peptide-small molecule conjugates. Nature Communications 2025, 16.
5. Zou L, Zhang T, Yang C, Liu W, Fahira A, Yang D, Zheng B, Yao X, Liu Y, Huang Z: Downregulation of SLC7A11 by Bis(4-Hydroxy-3,5-Dimethylphenyl) Sulfone Induces Ferroptosis in Hepatocellular Carcinoma Cell. Molecular Carcinogenesis 2025, 64, 580-596.
6. Zhou T, Zhang H, Yu X, Pan K, Yao X, Shen X, Lei H: Fc-Binding Cyclopeptide Induces Allostery from Fc to Fab: Revealed Through in Silico Structural Analysis to Anti-Phenobarbital Antibody. Foods 2025, 14.
7. Zhao L, Qiu X, Li H, Liu Z, Du Z, Xie J, Tong HHY, Huang M, Yao X, Zhang Q, Liu H: Discovery of Putative GyrB Inhibitors against Mycobacterium tuberculosis: A Combined Virtual Screening and Experimental Study. Current Medicinal Chemistry 2025.
8. Zhao L, Ma X, Liu B, Yao X, Liu H, Zhang Q: Investigating the unbinding mechanisms and kinetics of MmpL3 inhibitors: A computational study. Protein Science 2025, 34.
9. Zhao L, Liu H, Yao X, Ma X, Liu B, Li B, Tong HHY, Zhang Q: Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis. Journal of Chemical Information and Modeling 2025, 65, 10673-10687.
10. Zhang Q, Gong X, Liu H, Yao X: Application of computational methods in the drug discovery and development of Alzheimer's disease. Acta Pharmaceutica Sinica B 2025.
11. Zhang J, Cheng X, Chen G, Chen X, Zhao X, Chen W, Du W, He Z, Yao X, Han B, Yao D: Discovery of a Novel Selective PAK1/HDAC6/ HDAC10 Inhibitor ZMF-25 that Induces Mitochondrial Metabolic Breakdown and Autophagy-Related Cell Death in Triple-Negative Breast Cancer. Research 2025, 8.
12. Zhai S, Zhao H, Wang J, Lin S, Liu T, Gu S, Jiang D, Liu H, Kang Y, Yao X, Hou T: PepPCBench is a Comprehensive Benchmarking Framework for Protein–Peptide Complex Structure Prediction. Journal of Chemical Information and Modeling 2025, 65, 8497-8513.
13. Zhai S, Yao X: Latent diffusion on evolutionary-scale embeddings accelerates antimicrobial peptide discovery. Cell Biomaterials 2025, 1.
14. Zhai S, Liu T, Lin S, Li D, Liu H, Yao X, Hou T: Artificial intelligence in peptide-based drug design. Drug Discovery Today 2025, 30.
15. Yin X, Wang X, Wu Z, Li Q, Kang Y, Deng Y, Luo P, Liu H, Shi G, Wang Z, Yao X, Hsieh CY, Hou T: Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates. Journal of Cheminformatics 2025, 17.
16. Yang Y, Gu S, Liu B, Gong X, Lu R, Qiu J, Yao X, Liu H: DiffMC-Gen: A Dual Denoising Diffusion Model for Multi-Conditional Molecular Generation. Advanced Science 2025, 12.
17. Yang S, Wang N, Ren X, Sun M, Pian T, Lv J, Gan Z, Yao X, Jia C: Quenching method introduced oxygen defect type Zn2V2O7·2H2O for long-life aqueous zinc ion batteries. Journal of Power Sources 2025, 626.
18. Yan X, Zhu L, Li Q, Tian Y, Qiu J, Liu X, Tong HHY, Ouyang Q, Yao X, Liu H: QM/MM study reveals novel mechanism of KRAS and KRASG12R catalyzed GTP hydrolysis. International Journal of Biological Macromolecules 2025, 297.
19. Xu QH, Yin XY, Chen ZQ, Huang EK, Yao X, Li X, Liu PN: Construction of In Situ Personalized Cancer Vaccines by Bioorthogonal Catalytic Microneedles for Augmented Melanoma Immunotherapy. Small 2025, 21.
20. Xu Q, Liu P, Nie Q, Chu Y, Yao X, Fang J, Zhang J: Structural simplification of quaternary benzophenanthridine alkaloids generating a candidate for the treatment of non-small cell lung cancer. European Journal of Medicinal Chemistry 2025, 290.
21. Xu K, Wang J, Liu M, Zhou K, Lin S, Li W, Shi L, Zhou P, Liu H, Yao X: Efficient Generation of Protein and Protein–Protein Complex Dynamics via SE(3)-Parameterized Diffusion Models. Journal of Chemical Information and Modeling 2025, 65, 12366-12376.
22. Xi J, Wu Q, Wang Y, Liu Y, Yang G, Wang Y, Yao X, Zhang Z, Fang J: Disruption of cellular redox homeostasis by bigelovin triggers oxidative stress-mediated apoptosis in Fibrosarcoma. Bioorganic Chemistry 2025, 166.
23. Wang N, Zhang M, Ren X, Sun M, Pian T, Wang P, Cui YF, Yao X, Jia C, Yang HY: High-Entropy Deep Eutectic Solvent Achieves Ultra-Low Polarization Zinc Anode Chemistry. Angewandte Chemie - International Edition 2025, 64.
24. Tan S, Chen Z, Lu R, Liu H, Yao X: Rational Proteolysis Targeting Chimera Design Driven by Molecular Modeling and Machine Learning. Wiley Interdisciplinary Reviews: Computational Molecular Science 2025, 15.
25. Tan L, Wang L, Ren X, Zou Q, Yao X, Zeng X, Fu X: SQ-DiffuPep: A multimodal information-guided quantitative latent diffusion model for antimicrobial peptide discovery. Information Fusion 2025, 121.
26. Shi L, Liang P, Sun Z, Xie L, Sun R, Zhao N, Peng L, Yao X: BF3·Et2O-Promoted Annulation of 2-Propynolphenols With Thiophenols to Yield 2-Substituted 3-Sulfenylbenzofurans With Anti-Prostate Cancer Activities. Asian Journal of Organic Chemistry 2025.
27. Pian T, Wang N, Huang Z, Ren X, Sun M, Gan Z, Yao X, Jia C: Grotthuss Topochemistry Realizes Ah-Level Fast-Chargeable Zinc-Vanadium Pouch Battery. Advanced Functional Materials 2025.
28. Pang C, Wang Y, Jiang Y, Wang R, Yao X, Zou Q, Zeng X, Su R, Wei L: Multiview Deep Learning-Based Molecule Design and Structural Optimization Accelerates Inhibitor Discover. IEEE Transactions on Neural Networks and Learning Systems 2025, 36, 14022-14036.
29. Pan K, Yao X, Li Z, Huang XA, Wen J, Lei Y, Chen J, Lei H: A rapid and sensitive paper-based immunoassay for fenfluramine detection in slimming foods. Microchemical Journal 2025, 211.
30. Pan K, Fang Y, Chen J, Wang Y, Wen J, Lei Y, Yu X, Mo Q, Wang B, Yao X, Lei H: Pharmacophore-guided production of high-affinity antibodies for rapid detection of antipyrine in food and environment. Journal of Hazardous Materials 2025, 497.
31. Liu X, Li Q, Yan X, Wang L, Qiu J, Yao X, Liu H: A Specialized and Enhanced Deep Generation Model for Active Molecular Design Targeting Kinases Guided by Affinity Prediction Models and Reinforcement Learning. Journal of Chemical Information and Modeling 2025, 65, 3294-3308.
32. Liu S, Chen M, Yao X, Liu H: Fingerprint-enhanced hierarchical molecular graph neural networks for property prediction. Journal of Pharmaceutical Analysis 2025, 15.
33. Liu Q, Ding W, Yao X, Ling S, Tian C: MPBuild: An Automated Pipeline for High-Fidelity Membrane Protein Simulation System Construction. Journal of Chemical Theory and Computation 2025, 21, 11233-11244.
34. Liu B, Zhao L, Tan Y, Yao X, Liu H, Zhang Q: Discovery and Characterization of Novel Receptor-Interacting Protein Kinase 1 Inhibitors Using Deep Learning and Virtual Screening. ACS Chemical Neuroscience 2025, 16, 1617-1630.
35. Liang TL, Pan HD, Yan PY, Mi JN, Liu XC, Bao WQ, Lian LR, Zhang CF, Chen Y, Wang JR, Xie Y, Zhou H, Yao X, Graham P, Leung ELH, Liu L, Li RZ: Serum taurine affects lung cancer progression by regulating tumor immune escape mediated by the immune microenvironment. Journal of Advanced Research 2025, 73, 427-442.
36. Liang TL, Chen Y, Zhou NJ, Shu X, Mi JN, Ma GY, Xiao Y, Yang X, Huang C, Li JX, Xie Y, Yan PY, Yao X, Liu L, Pan HD, Leung ELH, Li RZ: Taurine and proline promote lung tumour growth by co-regulating Azgp1/mTOR signalling pathway. npj Precision Oncology 2025, 9.
37. Li J, Tan Y, Lu R, Liang P, Liu H, Yao X: Artificial intelligence for RNA–ligand interaction prediction: advances and prospects. Drug Discovery Today 2025, 30.
38. Jin Y, Qi X, Yu X, Cheng X, Chen B, Wu M, Zhang J, Yin H, Lu Y, Zhou Y, Pang A, Lin Y, Jiang L, Shi Q, Geng S, Zhou Y, Yao X, Li L, Duan H, Che J, Cao J, He Q, Dong X: Discovery of a potential hematologic malignancies therapy: Selective and potent HDAC7 PROTAC degrader targeting non-enzymatic function. Acta Pharmaceutica Sinica B 2025, 15, 1659-1679.
39. Huang XF, Liang P, Yin X, Hou YC, Wang TT, Li RW, Zhang Z, Yao X, Luo P, Qing LS: Development and Validation of a Highly Sensitive Isotope-Coded Equivalent Reporter Ion Assay for the Semi-Quantification of Isocoumarins in Complex Matrices. Analytical Chemistry 2025, 97, 1711-1718.
40. He W, Chen C, Cai R, Zheng J, Yao M, Shim JS, Kwok HF, Yao X, Fang L, Chen L: Bifunctional compounds for targeted degradation of carbonic anhydrase IX through integrin-facilitated lysosome degradation. Journal of Biological Chemistry 2025, 301.
41. Guo S, Li L, Zhang Q, Liu H, Yao X, Liang L, Chen C: A bibliometric analysis and systematic review of drug repurposing against drug-resistant ESKAPE pathogens: a particular focus on Pseudomonas aeruginosa. Frontiers in Microbiology 2025, 16.
42. Gong Y, Dai Y, Wu Q, Guo L, Yao X, Yang Q: Benchmark of Data Integration in Single-Cell Proteomics. Analytical Chemistry 2025, 97, 1254-1263.
43. Gong X, Tan S, Yang Y, Yu Y, Yao X, Liu H: Development of LRRK2 inhibitors through computational strategies: a promising avenue for Parkinson's disease. Drug Discovery Today 2025, 30.
44. Gong X, Tan S, Wang L, Tian Y, Zhang Q, Tong HHY, Yao X, Liu H: Well-Tempered Metadynamics Simulations Combined with Free Energy Landscape Analysis Uncover the Conformational Transition Pathway of the DYG Motif in LRRK2. ACS Chemical Neuroscience 2025, 16, 2800-2811.
45. Gan Z, Hu L, Sun M, Wang N, Ren X, Jia C, Li Z, Yao X: Construction of Stable Zn Anode by 3D Flamed Reduced Graphene Oxide with Long Cycling Life. ACS Applied Energy Materials 2025, 8, 10289-10299.
46. Fu X, Du Z, Chen Y, Chen H, Zhuo L, Lyu A, Cao D, Yao X: DrugKANs: A Paradigm to Enhance Drug-Target Interaction Prediction With KANs. IEEE Journal of Biomedical and Health Informatics 2025.
47. Feng L, Fu X, Du Z, Guo Y, Zhuo L, Yang Y, Cao D, Yao X: MultiCTox: Empowering Accurate Cardiotoxicity Prediction through Adaptive Multimodal Learning. Journal of Chemical Information and Modeling 2025, 65, 3517-3528.
48. Cui W, Ye Y, Guo J, Yao X, Tong HHY: Comparative multi-task deep learning models for protein–nucleic acid interaction prediction: Unveiling the superior efficacy of the PNI-MAMBA architecture. International Journal of Biological Macromolecules 2025, 327.
49. Cui W, Qian J, Yao X, Hu G, Tong HHY: Predicting Drug-target Binding Affinity Based on Graph Isomorphism Network and iTransformer. Current Bioinformatics 2025, 20, 777-788.
50. Chen Z, Gu C, Tan S, Wang X, Li Y, He M, Lu R, Sun S, Hsieh CY, Yao X, Liu H, Heng PA: Interpretable PROTAC Degradation Prediction With Structure-Informed Deep Ternary Attention Framework. Advanced Science 2025.
51. Cai Z, Hu Z, Yao X, Liang P, Zhang H: Single-crystal structure, Hirshfeld surface and DFT analyses of chrysomycin A, a marine microbe-derived promising agent for anticancer and antimicrobial therapy. Journal of Molecular Structure 2025, 1322.
52. Cai L, Yue G, Chen Y, Wang L, Yao X, Zou Q, Fu X, Cao D: ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction. Briefings in Bioinformatics 2025, 26.
53. Cai L, He Y, Fu X, Zhuo L, Zou Q, Yao X: AEGNN-M:A 3D Graph-Spatial Co-Representation Model for Molecular Property Prediction. IEEE Journal of Biomedical and Health Informatics 2025, 29, 1726-1734.
54. Bao H, Meng H, Gong S, Gong Y, Tu G, Du Z, Wang Y, Wu J, Ma C, Ma Q, Yao X: Design, synthesis and activity evaluation of 4-(quinoline-2-yl)aniline derivatives as SARS-CoV‑2 main protease inhibitors. Bioorganic and Medicinal Chemistry 2025, 121.
55. Zhao C, Mou X, Zhang Q, Chen C, Zhu Y, Hong L, Liu H, Wu J, Geng J, Bao R: Pore lipid modifications modulate MscS nanopore for enhanced single-molecule sensing. Biosensors and Bioelectronics 2025, 276.
56. Shao J, Li T, Wang X, Wang Z, Liu L, Liu H, Li H, Yao X, Yu Y: Structural elucidation and optimization of an immunomodulatory acidic polysaccharide from Amomum tsao-ko: Activity evaluation and degradation-analysis-modification paradigm. Carbohydrate Polymers 2025, 369.
57. Li Q, Luo J, Fu C, Kang W, Wang L, Tong HHY, Lun Z, Zhang Q, Lai D, Liu H: Discovery of Novel CRK12 Inhibitors for the Treatment of Human African Trypanosomiasis: An Integrated Computational and Experimental Approach. Pharmaceuticals 2025, 18.
58. Gu S, Shen C, Zhang X, Sun H, Cai H, Luo H, Zhao H, Liu B, Du H, Zhao Y, Fu C, Zhai S, Deng Y, Liu H, Hou T, Kang Y: Benchmarking AI-powered docking methods from the perspective of virtual screening. Nature Machine Intelligence 2025, 7, 509-520.
59. Gou Q, Su Q, Wang J, Zhang H, Sun H, Zhang X, Jiang L, Fang M, Kang Y, Liu H, Hou T, Hsieh CY: ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction. Journal of Chemical Information and Modeling 2025.
60. Zhang X, Xu W, Xu Z, Tong HHY, Jiao X, Li K, Wang Z: Diagnosis of Irritant Dermatitis in Colorectal Cancer Postoperative Stoma Patients Using Smartphone Photographs: A Deep Learning Approach. Journal of Multidisciplinary Healthcare 2025, 18, 2215-2223.
61. Zhai X, Ji J, Wang J, Bai J, Zhao X, Zhang W, Lv R, Deng X, Li Q, Meng W, Zhang Q, Zhao J, Cui J, Yu L, Lam CK, Zhang C, Tong HHY, Wang Y, Song X, Wang K, Li J, Li K: The association between cruciferous vegetable consumption and Perfluorooctanesulfonic acid bioaccumulation: A cross-sectional analysis of the US population and cross-country randomized clinical trial validation. Environmental Chemistry and Ecotoxicology 2025, 7, 1648-1658.
62. Xu Y, Kang W, Sun W, Tong HHY, Ke W, Lyu E: Towards multi-view sputum smear quality classification. Biomedical Signal Processing and Control 2025, 102.
63. Sha Y, Pan H, Xu W, Meng W, Luo G, Du X, Zhai X, Tong HHY, Shi C, Li K: MDD-LLM: Towards accuracy large language models for major depressive disorder diagnosis. Journal of Affective Disorders 2025, 388.
64. Peng XQ, Huang J, Tong HHY, Rao WW: Psychotropic drugs and risk of pancreatitis: a systematic review and meta-analysis. Psychiatry Research 2025, 353.
65. Liu Y, Li K, Ng H, Ye Q, Tong HHY: Predicting influenza trends in the context of post-COVID immunity gaps in Macao, China. Journal of Travel Medicine 2025, 32.
66. Kang W, Tong HHY, Li S: Discovery of Potential Tyrosinase Inhibitors via Machine Learning and Molecular Docking with Experimental Validation of Activity and Skin Permeation. ACS Omega 2025, 10, 38922-38932.
67. Jiao F, Xu R, Luo Q, Li X, Tong HHY, Guo J: Elucidating allosteric signal disruption in PBP2a: impact of N146K/E150K mutations on ceftaroline resistance in methicillin-resistant Staphylococcus aureus. Journal of Computer-Aided Molecular Design 2025, 39.
68. Jiao F, Cui W, Wang P, Tong HHY, Guo J, Tao J: Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. Journal of Biomolecular Structure and Dynamics 2025, 43, 6226-6238.
69. Guo J, Lei K, Liu J, Tong HHY, Luo YL, Han W, Li S: Cmem Builder: An Automated Tool for Curved Membrane Construction in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2025, 21, 7675-7686.
70. Gao L, Liu Y, Zou J, Deng F, Liu Z, Zhang Z, Zhao X, Chen L, Tong HHY, Ji Y, Le H, Zou X, Hao J: Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data. Briefings in Bioinformatics 2025, 26.
71. Feng B, Du H, Tong HHY, Wang X, Li K: Enhancing Local Functional Structure Features to Improve Drug–Target Interaction Prediction. International Journal of Molecular Sciences 2025, 26.
72. Deng F, Zou J, Wang M, Gu Y, Wu J, Gao L, Ji Y, Tong HHY, Chen J, Chen W, Tan L, Chu Y, Zou X, Hao J: DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle. Briefings in Bioinformatics 2025, 26.
73. Cui W, Fang X, Zhang Z, Zhang R, Huang Q, Lu R, Gao T, Tong HHY, Zheng J: Efficient colorimetric assay promotes the virtual screen of granzyme B inhibitors. Microchimica Acta 2025, 192.
74. Cheng S, Tong HHY, Zhang C, Jian L, Ji J, Li T, Wang Y, Li J, Li K: Disorganization of Small-World Functional Brain Networks in First-Episode, Treatment-Naïve Adolescents With Major Depressive Disorder. Brain and Behavior 2025, 15.
75. Bao Y, Jia F, Geng Y, Song G, Xu R, Wang H, Mu Y, Tong HHY, Zhang F, Guo J: Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives. Journal of Agricultural and Food Chemistry 2025, 73, 189-201.
76. Zhu C, Cao S, Shang T, Guo J, Su A, Li C, Duan H: Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2. Briefings in Bioinformatics 2025, 26.
77. Zhou P, Zhang D, Meng Y, Huang X, Wu Y, Bai Y, Guo J, Song H, Zhang K, Yao L, Bazan GC, Feng G, Zhou C: Light-triggered molecular mechanotherapy of tumor using membrane-mimicking conjugated oligoelectrolytes. Science Advances 2025, 11.
78. Zhang J, Jiao F, Ge Y, Cheng B, Guo J: Antibiotic Susceptibility Evaluation in Bacterial Infections from Orthopedic Inpatients with Leg Trauma. Current Microbiology 2025, 82.
79. Zhang C, Xu Z, Lin K, Zhu N, Zhang C, Xu W, Guo J, Su A, Li C, Duan H: CycleDesigner: Leveraging CycRFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets. Journal of Chemical Information and Modeling 2025, 65, 6155-6165.
80. Zhang C, Wang W, Zhu N, Cao Z, Wu Y, Mao Q, Zhu C, Zhang C, Guo J, Duan H: AlphaFold3 for Noncanonical Cyclic Peptide Modeling: Hierarchical Benchmarking Reveals Accuracy and Practical Guidelines. Journal of Chemical Information and Modeling 2025, 65, 9777-9789.
81. Zeng D, Jiao F, Yang Y, Dou S, Yu J, Yu X, Zhou Y, Xue J, Li X, Duan H, Zhang Y, Guo J, Yang W: Myricetin Potentiates Antibiotics Against Resistant Pseudomonas aeruginosa by Disrupting Biofilm Formation and Inhibiting Motility Through FimX-Mediated c-di-GMP Signaling Interference. Biology 2025, 14.
82. Yue Y, Cheng Y, Marquet C, Xiao C, Guo J, Li S, He S: Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions. Journal of Chemical Information and Modeling 2025, 65, 580-588.
83. Ye Y, Duan H, Mu Y, Wu L, Guo J: BridgeNet: a high-efficiency framework integrating sequence and structure for protein and enzyme function prediction. Briefings in Bioinformatics 2025, 26.
84. Xu W, Zhang C, Shang T, Mao Q, Guo J, Duan H: HighMPNN: A Graph Neural Network Approach for Structure-Constrained Cyclic Peptide Sequence Design. IEEE Journal of Biomedical and Health Informatics 2025.
85. Xu R, Bao Y, Jiao F, Li M, Zhang X, Zhang F, Guo J: Unraveling the atomic mechanisms underlying glyphosate insensitivity in EPSPS: implications of distal mutations. Journal of Biomolecular Structure and Dynamics 2025, 43, 6625-6636.
86. Wang L, Hou X, Huang M, He B, Mao L, Hu Z, Li L, Guo J, Peng L: Design, synthesis and anti-cancer activity of novel 1,2,3-triazole hybrids of erlotinib against cervical cancer via MAPK signaling pathway. Scientific Reports 2025, 15.
87. Sui J, Cui W, Zhang X, Duan H, Guo J: Human miRNA–disease Association Prediction Via Residual GraphSAGE With Nonlinear Adaptive Feature Fusion and Triplet Contrastive Learning. Journal of Molecular Biology 2025, 437.
88. Mo J, Guo J, Duan H: Multimodal Learning of Protein–Protein Interactions for Accurate Binding Affinity Prediction. ACS Omega 2025, 10, 57137-57144.
89. Meng Y, Gao J, Huang X, Liu P, Zhang C, Zhou P, Bai Y, Guo J, Zhou C, Li K, Huang F, Cao Y: Molecular Trojan Based on Membrane-Mimicking Conjugated Electrolyte for Stimuli-Responsive Drug Release. Advanced Materials 2025, 37.
90. Mao Q, Shang T, Xu W, Zhai S, Zhang C, Guo J, Su A, Li C, Duan H: NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation. Journal of Chemical Theory and Computation 2025, 21, 4979-4991.
91. Luo Q, Mu Y, Zheng L, Guo J: AutoRevDock: An open-source toolkit for scalable reverse docking. Protein Science 2025, 34.
92. Liu Q, Hou X, Wang Y, Tian M, He B, Guo J, Yang J: Rational design of indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors featuring 1,2,3-triazole derivatives with enhanced anti-inflammatory and analgesic efficacy. Frontiers in Pharmacology 2025, 16.
93. Liu Q, Hou X, Tian M, He B, Guo J, Guo Y, Yang J: Mechanistic Insights and Anti-cancer Activity of 2H-benzo[b][1,4]oxazin-3(4H)-one Linked 1,2,3-Triazoles in Human Cancer Cells. Frontiers in Pharmacology 2025, 16.
94. Li X, Tang L, Xu R, Duan H, Li B, Guo J: SpectraNet: A unified deep learning framework for infrared spectroscopy-based prediction of plastic recyclability, type classification, and microplastic identification. Journal of Hazardous Materials 2025, 500.
95. Li X, Tang L, Li ZY, Qiu D, Yang ZL, Zhang XY, Zhang XZ, Guo J, Li BQ: Geographical origin discrimination of Chenpi using machine learning and enhanced mid-level data fusion. npj Science of Food 2025, 9.
96. Li L, Luo Q, Yang S, Wang H, Mu Y, Guo J, Zhang F: Unraveling the molecular mechanism of FgGcn5 inhibition by phenazine-1-carboxamide: combined in silico and in vitro studies. Pest Management Science 2025, 81, 937-945.
97. Jiao F, Wang P, Zeng D, Bao Y, Zhang Y, Tao J, Guo J: Identification of Potential PBP2a Inhibitors Against Methicillin-Resistant Staphylococcus aureus via Drug Repurposing and Combination Therapy. Chemical Biology and Drug Design 2025, 105.
98. Hu H, Zhang C, Xu Z, Guo J, Su A, Li C, Duan H: PepMSND: integrating multi-level feature engineering and comprehensive databases to enhance in vitro/in vivo peptide blood stability prediction. Digital Discovery 2025, 4, 2478-2490.
99. He B, Mao L, Xi L, Guo J: Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2. Neuropharmacology 2025, 269.
100. He B, Mao L, Jin X, Duan H, Guo J: Unveiling the molecular mechanism of Gi protein biased activation at mGlu2–mGlu4 heterodimers through Gaussian accelerated molecular dynamics simulations. Protein Science 2025, 34.
101. Gao M, Cui W, Duan H, Guo J: DNA methylation subtypes dictate metastatic heterogeneity of osteosarcoma via distinct tumor-stromal interactions: Multi-omics profiling and decitabine validation. International Journal of Biological Macromolecules 2025, 327.
102. Fan D, Li M, Shen Z, Li Y, Guo J, Wang D, Han T, Tang BZ: Boosting the Antimicrobial Activity of Quaternary Ammonium Photosensitizers by Janus-Type AIE Luminogens: Special Collection: 2025 Emerging Investigators. Aggregate 2025, 6.
103. Cao Z, Cao S, Wang L, Wang Z, Mao Q, Guo J, Duan H: HighFold-MeD: a Rosetta distillation model to accelerate structure prediction of cyclic peptides with backbone N-methylation and d-amino acids. Journal of Cheminformatics 2025, 17.
104. Cao S, Zhu C, Mao Q, Guo J, Zhu N, Duan H: Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3. Briefings in Bioinformatics 2025, 26.
105. Zou Q, Jiang L, Wei L: Guest Editorial: Large Language Models With Applications in Bioinformatics and Biomedicine. IEEE Journal of Biomedical and Health Informatics 2025, 29, 6957-6959.
106. Zhou P, Wang J, Li C, Wang Z, Liu Y, Sun S, Lin J, Wei L, Cai X, Lai H, Liu W, Wang L, Liu Y, Zeng X: Instruction multi-constraint molecular generation using a teacher-student large language model. BMC Biology 2025, 23.
107. Zhou L, Chen Z, Shen Y, Xu J, Xuan P, Zhu Y, Fang Y, Cong C, Wei L, Su R, Zhou J, Jin Q: ERSR: An Ellipse-constrained pseudo-label refinement and symmetric regularization framework for semi-supervised fetal head segmentation in ultrasound images. IEEE Journal of Biomedical and Health Informatics 2025.
108. Zhao Z, Li B, Zuo H, Chen R, Deng R, Geng J, Sun C, Wei L, Lang M, Su R: TCN-RDP: Predicting Drug-Induced Liver Injury from Time-Series Toxicogenomic Data. Journal of Chemical Information and Modeling 2025, 65, 11486-11496.
109. Yu J, Gao W, Chen S, Lu R, Qiao J, Jin J, Wei L, Shi H, Zhang Z, Cui F, Jiang X, Yan Z: MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration. Briefings in Bioinformatics 2025, 26.
110. Yang C, Fu X, Luo Z, Wei L, Li J, Cui F, Zou Q, Zhang Q, Zhang Z: GCNLA: Inferring Cell-Cell Interactions From Spatial Transcriptomics With Long Short-Term Memory and Graph Convolutional Networks. IEEE Journal of Biomedical and Health Informatics 2025, 29, 8560-8571.
111. Yan C, Zhang Z, Xu J, Meng Y, Yan S, Wei L, Zou Q, Zhang Q, Cui F: CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network. International Journal of Biological Macromolecules 2025, 308.
112. Xiong S, Cai J, Shi H, Cui F, Zhang Z, Wei L: UMPPI: Unveiling Multilevel Protein-Peptide Interaction Prediction via Language Models. Journal of Chemical Information and Modeling 2025, 65, 3789-3799.
113. Xiong A, Luo Z, Xia Y, Zou Q, Wei L, Zhang Z, Wang T, Wei L, Cui F: An interpretable geometric graph neural network for enhancing the generalizability of drug–target interaction prediction. BMC Biology 2025, 23.
114. Wu K, Sun C, Geng J, Wang P, Dai Q, Wei L, Su R: Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data. Briefings in Bioinformatics 2025, 26.
115. Wen Q, Geng A, Xu J, Meng Y, Wei L, Zhang Z, Zou Q, Cui F: DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms. Journal of Chemical Information and Modeling 2025, 65, 10011-10024.
116. Wang Z, Geng A, Xu J, Meng Y, Zhang Z, Wei L, Zou Q, Cui F: A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites. International Journal of Biological Macromolecules 2025, 330.
117. Wang Y, Li N, Wang X, Cao F, Xiong S, Wei L: Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction. Journal of Chemical Information and Modeling 2025, 65, 7800-7810.
118. Wang R, Yang X, Pang C, Wei L: A Multi-Objective Comprehensive Framework for Predicting Protein-Peptide Interactions and Binding Residues. IEEE Journal of Biomedical and Health Informatics 2025, 29, 7884-7895.
119. Wang R, Nakai K, Wei L Prediction of Protein–Peptide Binding Sites Using PepBCL. In Methods in Molecular Biology; Humana Press Inc.: 2025; Vol. 2941, pp 269-278.
120. Tran DT, Pham NT, Nguyen NDH, Wei L, Manavalan B: HyPepTox-Fuse: An interpretable hybrid framework for accurate peptide toxicity prediction fusing protein language model-based embeddings with conventional descriptors. Journal of Pharmaceutical Analysis 2025, 15.
121. Tian G, Yin C, Qiao J, Wang R, Shi H, Cui F, Zhang Z, Jiang X, Wei L: EDNTOM: An Ensemble Learning and Weight Mechanism-Based Nanopore Methylation Detection Tool. ACS Omega 2025, 10, 33031-33044.
122. Su Y, Fu X, Wei L, Zhang Z, Zou Q, Cui F: PROTCROWN: A Manually Curated Resource of Protein Corona Data for Unlocking the Potential of Protein-Nanoparticle Interactions. Nano Letters 2025, 25, 1739-1744.
123. Su Q, Phan LT, Pham NT, Wei L, Manavalan B: MST-m6A: A Novel Multi-Scale Transformer-based Framework for Accurate Prediction of m6A Modification Sites Across Diverse Cellular Contexts. Journal of Molecular Biology 2025, 437.
124. Ru X, Li Z, Wei L, Liu Y, Zou Q: Drug–Drug Interaction Prediction: Paradigm Shifts, Key Bottlenecks, and Future Directions. Wiley Interdisciplinary Reviews: Computational Molecular Science 2025, 15.
125. Qiao J, Guo X, Jin J, Wang D, Li K, Gao W, Cui F, Zhang Z, Shi H, Wei L: Taco-DDI: accurate prediction of drug-drug interaction events using graph transformer-based architecture and dynamic co-attention matrices. Neural Networks 2025, 189.
126. Qiao J, Gao W, Jin J, Wang D, Guo X, Manavalan B, Wei L: Molecular pretraining models towards molecular property prediction. Science China Information Sciences 2025, 68.
127. Nguyen NDH, Pham NT, Tran DT, Wei L, Malik A, Manavalan B: xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides. Journal of Cheminformatics 2025, 17.
128. Nguyen NDH, Pham NT, Seo H, Wei L, Manavalan B: Mulaqua: An interpretable multimodal deep learning framework for identifying PMT/vPvM substances in drinking water. Journal of Hazardous Materials 2025, 500.
129. Lv J, Li K, Wang Y, Xu J, Meng Y, Cui F, Wei L, Zhang Q, Zhang Z: ACP-EPC: an interpretable deep learning framework for anticancer peptide prediction utilizing pre-trained protein language model and multi-view feature extracting strategy. Molecular Diversity 2025.
130. Lv J, Geng A, Pan Z, Wei L, Zou Q, Zhang Z, Cui F: iBitter-GRE: A Novel Stacked Bitter Peptide Predictor with ESM-2 and Multi-View Features. Journal of Molecular Biology 2025, 437.
131. Luo Z, Geng A, Wei L, Zou Q, Cui F, Zhang Z: CPL-Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length. Advanced Science 2025, 12.
132. Lu R, Qiao J, Li K, Zhao Y, Jin J, Cui F, Zhang Z, Manavalan B, Wei L: ERNIE-ac4C: A Novel Deep Learning Model for Effectively Predicting N4-acetylcytidine Sites. Journal of Molecular Biology 2025, 437.
133. Liu S, Sun C, Geng J, Wei L, Su R: Investigating the Interaction Mechanism of CAT-BT-Br and Key Residue Mutations for Castration-Resistant Prostate Cancer through Molecular Dynamics Simulation. Journal of Physical Chemistry B 2025, 129, 4969-4981.
134. Liu R, Yan S, Zhang Z, Xu J, Meng Y, Zhang Q, Wei L, Zou Q, Cui F: PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. Computational Biology and Chemistry 2025, 118.
135. Liu J, Geng A, Cui F, Xu J, Meng Y, Wei L, Zhang Q, Zou Q, Zhang Z: NeuroCL: A deep learning approach for identifying neuropeptides based on contrastive learning. Analytical Biochemistry 2025, 705.
136. Lin X, Guan J, Wang F, Xie P, Zhao Y, Zhao Z, Xiang M, Wei L, Liu X, Lee TY, Chiang YC, Wang J, Yao L: AFPDeepPred: A Deep Learning Framework for Accurate Identification of Antifreeze Proteins. Journal of Chemical Information and Modeling 2025, 65, 12256-12267.
137. Lin C, Xiong S, Cui F, Zhang Z, Shi H, Wei L: Deep Learning in Antimicrobial Peptide Prediction. Journal of Chemical Information and Modeling 2025, 65, 7373-7392.
138. Li Z, Yu J, You S, Wei L, Lin Q, Li X, Wong KC: Elucidating spatiotemporal chromatin dynamics with multi-stage differential variations from Hi-C. Knowledge-Based Systems 2025, 317.
139. Li Y, Geng A, Zhou Z, Cui F, Xu J, Meng Y, Wei L, Zou Q, Zhang Q, Zhang Z: AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. Journal of Chemical Information and Modeling 2025, 65, 5868-5886.
140. Li X, Luo Z, Lv J, Yang C, Yan S, Xu J, Meng Y, Wei L, Zhang Z, Zou Q, Cui F: m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. Journal of Chemical Information and Modeling 2025, 65, 8079-8096.
141. Li N, Qiao J, Gao F, Wang Y, Shi H, Zhang Z, Cui F, Zhang L, Wei L: GICL: A Cross-Modal Drug Property Prediction Framework Based on Knowledge Enhancement of Large Language Models. Journal of Chemical Information and Modeling 2025, 65, 5518-5527.
142. Li J, Xiong S, Shi H, Cui F, Zhang Z, Wei L: NeuroPred-AIMP: Multimodal Deep Learning for Neuropeptide Prediction via Protein Language Modeling and Temporal Convolutional Networks. Journal of Chemical Information and Modeling 2025, 65, 4740-4750.
143. Lee KW, Pham NT, Min HJ, Park HW, Lee JW, Lo HE, Kwon NY, Seo J, Shaginyan I, Cho H, Wei L, Manavalan B, Jeon YJ: DOGpred: A Novel Deep Learning Framework for Accurate Identification of Human O-linked Threonine Glycosylation Sites. Journal of Molecular Biology 2025, 437.
144. Jin Q, Wu A, Wei L, Cui H, Xuan P, Feng X, Su R: PKDF-Net: Anticancer peptide prediction via a prior-knowledge-aware dual-path feature-entangled network. Engineering Applications of Artificial Intelligence 2025, 160.
145. Jin Q, Cui H, Wang J, Sun C, He Y, Xuan P, Wang L, Cong C, Wei L, Su R: Iterative pseudo-labeling based adaptive copy-paste supervision for semi-supervised tumor segmentation. Knowledge-Based Systems 2025, 324.
146. Hu K, Wei J, Sun C, Geng J, Wei L, Dai Q, Su R: Synergizing multimodal data and fingerprint space exploration for mechanism of action prediction. Bioinformatics 2025, 41.
147. Hu K, He Y, Wei J, Sun C, Geng J, Wei L, Su R: BFGTP: A BERT-Guided Two-Stage Molecular Representation Learning Framework for Toxicity Prediction. IEEE Journal of Biomedical and Health Informatics 2025, 29, 6960-6970.
148. Hu J, Liu Y, Zeng X, Zou Q, Su R, Wei L: Multi-Modal Deep Representation Learning Accurately Identifies and Interprets Drug-Target Interactions. IEEE Journal of Biomedical and Health Informatics 2025, 29, 5350-5360.
149. Guo F, Shi R, Zhou J, Xu J, Cui H, Xuan P, Feng X, Wei L, Su R, Jin Q: HRProtoKD: A hierarchical and relational prototype based knowledge distillation framework for few-shot cancer molecular subtyping. IEEE Journal of Biomedical and Health Informatics 2025.
150. Geng A, Luo Z, Li A, Zhang Z, Zou Q, Wei L, Cui F: ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. Journal of Chemical Information and Modeling 2025, 65, 2336-2349.
151. Cui Y, Cui Y, Wang R, Zhu Z, Zeng X, Nakai K, Cui F, Zhang Z, Shi H, Chen Y, Ye X, Sakurai T, Wei L: DiffusionST: A deep generative diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains. Briefings in Bioinformatics 2025, 26.
152. Cui Y, Cui Y, Ding Y, Nakai K, Wei L, Le Y, Ye X, Sakurai T: OmniClust: A versatile clustering toolkit for single-cell and spatial transcriptomics data. Methods 2025, 238, 84-94.
153. Zhang W, Zhang C, Zhao J, Cui J, Bai J, Deng X, Ji J, Li T, Wang Y, Li K, Qu Y, Li J: Microstructure Abnormalities of Diffusion Tensor Imaging Measures in First-Episode, Treatment-Naïve Adolescents With Major Depressive Disorder: An Integrated AFQ and TBSS Study. Brain and Behavior 2025, 15.
154. Zhang H, Shi Y, Wang Y, Yang X, Li K, Im SK, Han Y: Research on Plant RNA-Binding Protein Prediction Method Based on Improved Ensemble Learning. Biology 2025, 14.
155. Zhang H, Shi Y, Wang Y, Yang X, Li K, Im SK, Han Y: Biological Sequence Representation Methods and Recent Advances: A Review. Biology 2025, 14.
156. Zhai X, Ji J, Wang J, Bai J, Zhao X, Zhang W, Lv R, Deng X, Li Q, Meng W, Zhang Q, Zhao J, Cui J, Yu L, Lam CK, Zhang C, Tong HHY, Wang Y, Song XC, Wang K, Li J, Li K: The association between cruciferous vegetable consumption and Perfluorooctanesulfonic acid bioaccumulation: A cross-sectional analysis of the US population and cross-country randomized clinical trial validation. Environmental Chemistry and Ecotoxicology 2025, 7, 1648-1658.
157. Yang Q, Wang M, Dou W, Ren Y, Zhang T, Qian L, Xu Y, Li K, Wang M, Sun Y, Liu Z, Tan T: Parameter map guided explainable segmentation framework for breast cancer using amide proton transfer weighted imaging. Medical Physics 2025, 52, 2384-2398.
158. Yang Q, Su S, Zhang T, Wang M, Dou W, Li K, Ren Y, Zheng Y, Wang M, Xu Y, Sun Y, Liu Z, Tan T: A deep learning framework for reconstructing Breast Amide Proton Transfer weighted imaging sequences from sparse frequency offsets to dense frequency offsets. Computerized Medical Imaging and Graphics 2025, 123.
159. Xing A, Cai T, Du H, Li Z, Ng H, Li J, Jiang G, Chen L, Li K: MRanalysis: a comprehensive online platform for integrated, multimethod Mendelian randomization and associated post-GWAS analyses. GigaScience 2025, 14.
160. Xie C, Li K: Two-Stage Hierarchical Pruning (THP-CNN) of Convolutional Neural Networks for Rapid Pathogenic Bacterial Detection Using High-Resolution Colony Images in Intensive Care Units. Diagnostics 2025, 15.
161. Wang J, Li Q, Xie C, Li X, Wang H, Xu W, Lv R, Zhai X, Xu P, Li K, Song XC: Predicting In-Hospital Mortality in Intensive Care Unit Patients Using Causal SurvivalNet With Serum Chloride and Other Causal Factors: Cross-Country Study. Journal of Medical Internet Research 2025, 27.
162. Sha Y, Jiang M, Luo G, Meng W, Zhai X, Pan H, Li J, Yan Y, Qiao Y, Yang W, Li K: HerbMet: Enhancing metabolomics data analysis for accurate identification of Chinese herbal medicines using deep learning. Phytochemical Analysis 2025, 36, 261-272.
163. Pan H, Sha Y, Zhai X, Luo G, Xu W, Meng W, Li K: Bootstrap inference and machine learning reveal core differential plasma metabolic connectome signatures in major depressive disorder. Journal of Affective Disorders 2025, 378, 281-292.
164. Ma Y, Zhai X, Mu D, Gao Y, Li Y, Qiu L, Li K, Cheng X: Superior prognostic value of estimated small dense LDL cholesterol for cardiovascular risk assessment: evidence from international cohort studies. Lipids in Health and Disease 2025, 24.
165. Luo YC, Huang X, Wang R, Lin Y, Sun JX, Li K, Wang DY, Yan Y, Qiao Y: Advancements in understanding tumor-resident bacteria and their application in cancer therapy. Military Medical Research 2025, 12.
166. Luo G, Xu W, Sha Y, Zhao X, Pan H, Zhai X, Li Z, Meng W, Li J, Ji J, Yu L, Li K: An interpretable machine learning model predicts the interactive and cumulative risks of different environmental chemical exposures on depression. Translational Psychiatry 2025, 15.
167. Liu Y, Xu F, Lv Z, Li K, Dong X: Causal relationship between PM2.5 exposure and population-level antidepressant medication use: A Mendelian randomization study using GWAS data from multi-biobank. Environmental Research 2025, 283.
168. Liu X, Li Q, Zhang L, He Y, Tan S, Chen X, Li K: Impacts of amino acid supplementation on renal function and nutritional parameters in patients with renal insufficiency: bibliometric analysis and meta-analysis. Frontiers in Nutrition 2025, 12.
169. Lin J, Wang Q, Liu X, Zhou M, Feng Z, Ma X, Li J, Gan R, Wang X, Li K: Causal Inference Framework Reveals Mediterranean Diet Superiority and Inflammatory Mediation Pathways in Mortality Prevention: A Comparative Analysis of Nine Common Dietary Patterns. Foods 2025, 14.
170. Li Q, Song XC, Li K, Wang J: Gut-lung immunometabolic crosstalk in sepsis: from microbiota to respiratory failure. Frontiers in Medicine 2025, 12.
171. Kumar AJ, Epler K, Wang J, Samandari N, Rolfsen ML, Barnes LA, Shadel GS, Moyzis AG, Sainz AG, Li K, Jepsen K, Fuster MM, Spragg RG, Šášik R, Vallon V, Goodluck H, Ix JH, Singh P, Hepokoski ML: Kidney mitochondrial DNA contributes to systemic IL-6 release in sepsis-associated acute kidney injury. JCI Insight 2025, 10.
172. Jiang M, Sha Y, Zou Y, Xu X, Ding M, Lian X, Wang H, Wang Q, Li K, Guo DA, Yang W: Integration of deep neural network modeling and LC-MS-based pseudo-targeted metabolomics to discriminate easily confused ginseng species. Journal of Pharmaceutical Analysis 2025, 15.
173. Huang X, Zhuang Y, Wang R, Qu J, Tan Y, Li L, Pan W, Nie H, Li K, Lin Y, Yi L, Feng X, Lan H, Wang G, Zeng X, Jiang Z, Wang DY, Qiao Y, Yan Y: Colonization by Porphyromonas gingivalis in cervical squamous cell carcinomas promotes metastasis through FimA/CD151/ITGB1 signaling. Journal of Translational Medicine 2025, 23.
174. Abd Rahman MRA, Aween MM, Hassan Z, Hassan MS, Hashim R, Ismail IS, Misenan MSM, Rajamani R, Li K, Wong LS: Agricultural waste byproduct utilization: Date pit powder 1H NMR metabolite identification for goat (Capra hircus) milk pathway analysis. Food Chemistry Advances 2025, 7.
175. Zhan X, Liu T, Yu C, Huang YA, You Z, In Siu SWI: MAARDTI: a multi-perspective attention aggregation model for the prediction of drug–target interactions. Digital Discovery 2025, 4, 2994-3007.
176. Zhan X, Liu T, Bhadra P, Huang YA, You Z, In Siu SWI CALM-AcPEP: Predicting Anticancer Peptides Using Cross-Attention and Pre-Trained Language Model. In Lecture Notes in Computer Science, 2025; Huang DS, Zhang C, Zhang Q, Pan Y, Eds. Springer Science and Business Media Deutschland GmbH: 2025; Vol. 15867 LNBI; pp 221-230.
177. Lou X, Cai J, Un CW, In Siu SWI: A Comparative Evaluation of Machine Learning and Deep Graph Learning for Chemical Ecotoxicological Prediction. ACS Omega 2025, 10, 37549-37560.
178. Liu T, Zhai S, Zhan X, In Siu SWI: Data-driven revolution of enzyme catalysis from the perspective of reactions, pathways, and enzymes. Cell Reports Physical Science 2025, 6.
179. Chen H, Xu N, Kam H, Zhao C, Chen Q, Fan G, In Siu SWI, Wong CTT, Qiu JW, Cheung AKK, Teixeira A, Rádis‑Baptista G, Wong PK, Li S, Gong G, Lee SMY: A TRPV1 agonist from the transcriptome profiling of Dipsastraea rotumana inhibits neuroinflammation in vivo through the NF-κB and MAPK pathways. Pharmacological Research 2025, 218.
180. Chen H, Kam H, In Siu SWI, Ting Wong CT, Qiu JW, Kwok-Kuen Cheung A, Rádis-Baptista G, Lee S: Neuroprotective Kunitz-like peptides identified from the octopus coral Galaxea fascicularis through transcriptomic analysis. Water Biology and Security 2025, 4.
181. Cai J, Yan J, Un CW, Wang Y, Campbell-Valois FX, In Siu SWI: BERT-AmPEP60: A BERT-Based Transfer Learning Approach to Predict the Minimum Inhibitory Concentrations of Antimicrobial Peptides for Escherichia coli and Staphylococcus aureus. Journal of Chemical Information and Modeling 2025, 65, 3186-3202.
182. Zhu B, Yang F, Duan H, Gao Z: Automatic Detection of Standard Planes in Fetal Ultrasound Images based on Convolutional Neural Networks and Ensemble Learning. Current Bioinformatics 2025, 20, 443-451.
183. Zhan W, Wan F, Yang X, Duan H, Li C: Automated high-purity fast-flow synthesis of cyclic peptide-PNA conjugates for drug discovery and nanotechnology. Chemical Engineering Journal 2025, 521.
184. Yang X, Pan Y, Ren C, Hu C, Wan F, Duan H, Li C: Transition-metal-free C(sp3)-C(sp2) couplings with secondary alcohols and boronic acids via neighboring group activation. Organic Chemistry Frontiers 2025, 12, 1786-1791.
185. Su A, Luo Y, Zhang C, Duan H: Linker-GPT: design of Antibody-drug conjugates linkers with molecular generators and reinforcement learning. Scientific Reports 2025, 15.
186. Lin K, Zhang C, Bai R, Duan H: Cyclic Peptide Therapeutic Agents Discovery: Computational and Artificial Intelligence-Driven Strategies. Journal of Medicinal Chemistry 2025.
187. Lin H, Zhu C, Shang T, Zhu N, Lin K, Zhang C, Shao X, Wang X, Duan H: HighPlay: Cyclic Peptide Sequence Design Based on Reinforcement Learning and Protein Structure Prediction. Journal of Medicinal Chemistry 2025.
188. He C, Zhang Y, Cheng Y, Su W, Duan H, Xie Y, Zhang G, Su A: Optimization of continuous flow synthesis of fluoropolyimide monomer via advanced real-time process analytics. Chemical Engineering Science 2025, 318.
189. He C, Luo G, Su W, Duan H, Xie Y, Zhang G, Su A: Ruthenium Complexes for Asymmetric Hydrogenation and Selective Dehalogenation Revealed via Bayesian Optimization. Industrial and Engineering Chemistry Research 2025, 64, 11233-11242.
190. He C, Luo G, Duan H, Xie Y, Zhang G, Su A, Su W: Optimizing Phosphine Ligands for Ruthenium Catalysts in Asymmetric Hydrogenation of β-Keto Esters: The Role of Water in Activity and Selectivity. Molecular Catalysis 2025, 574.
191. Gong Z, Zhang C, Song D, Xia W, Shen B, Su W, Duan H, Su A: ChemReactSeek: an artificial intelligence-guided chemical reaction protocol design using retrieval-augmented large language models. Chemical Communications 2025, 61, 13137-13140.
192. Ye MQ, Liu J, Wang D, Pan Z, Zhou F, Ye XB, Luo H, Lu NP, Chen Y, Wang R, Long YW: Simultaneously achieving large ferroelectric polarization and high TC in sol-gel deposited PbTiO3-based perovskite thin films. Physical Chemistry Chemical Physics 2025.
193. Wang H, Cheng H, Zhang M, Zou Y, Wen R, Li K, Wang D, Ding M, Chen Q, Wang QL, Gao XM, Yang W: Application of the Ginsenoside Multidimensional Information Library (GinMIL) Enables Accurate Characterization of Ginsenosides from Diverse Ginseng Products and Accelerates the Discovery of New Saponin Compounds. Journal of Agricultural and Food Chemistry 2025, 73, 10003-10016.
194. Shaikh M, Zhou F, Buvaneswaran S, Gowsalya R, Sahoo T, Wang D, Ghosh S: Emergence of insulating ferro- and ferrimagnetism with enhanced optical properties in double-double perovskite oxides. Physical Review B 2025, 112.
195. Pan Z, Zhou F, Ye MQ, Wang D, Liu Q, Nishikubo T, Ye XB, Wang X, Liu J, Lu NP, Kawaguchi S, Azuma M, Long YW: Realizing negative thermal expansion over an extended temperature range in PbTiO3-based perovskites. Journal of Advanced Ceramics 2025, 14.
196. Pan Z, Ye MQ, Suo Y, Zhou F, Wang D, Liu J, Ye XB, Zhang J, Pi MC, Li WH, Chen C, Lu NP, Kawaguchi S, Shen Y, Long YW: Achieving negative thermal expansion over an extended temperature range in rare-earth-modified PbTiO3-based perovskites. Rare Metals 2025, 44, 6494-6502.
197. Chen X, Zhou F, Suo Y, Shao C, Cheng X, Wang D, Sanyal B: Discovery of an ultrastable antiferromagnetic two-dimensional CrF3 phase with anisotropic quasi-one-dimensional mechanical, electronic, and thermal properties. Physical Review B 2025, 111.
198. Zheng H, Li S, Han W: A Hybrid UA–CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates. Molecules 2025, 30.
199. Zeng LN, Huang J, Guan B, Tang R, Li Y, Lu J, Li J, Peng T, Rao W: Sex differences and anti-epidemic work in psychological symptoms of healthcare workers in intensive care units during the COVID-19 pandemic: a nationwide cross-sectional study. BMJ Open 2025, 15.
200. Wang W, Wang N, Wu Y, Ye Z, Zhao L, Chen X, Ouyang D: An Integrated AI-PBPK Platform for Predicting Drug In Vivo Fate and Tissue Distribution in Human and Inter-Species Extrapolation. Clinical Pharmacology and Therapeutics 2025, 118, 865-875.
201. Rao W, D'Arcy C, Su Y: The Mediating and Moderating Role of Sleep Disturbance Between Chronic Pain and Psychological Distress: Evidence from Canadian Community Health Survey. Psychiatry (New York) 2025.
202. Peng XQ, Huang J, Tong HHY, Rao W: Psychotropic drugs and risk of pancreatitis: a systematic review and meta-analysis. Psychiatry Research 2025, 353.
203. Lu J, Huang J, Gao W, Wang Z, Yang N, Luo Y, Guo J, Pang WIP, Lok GKI, Rao W: Interventions for suicidal and self-injurious related behaviors in adolescents with psychiatric disorders: a systematic review and meta-analysis. Translational Psychiatry 2025, 15.
204. Liu M, Lu HY, Tong SF, Liang D, Sun H, Xing T, Shi X, Yu H, Tong RKY: Estimation of Fugl–Meyer Assessment Upper-Extremity Sub-Scores Using a Mixup-Augmented LSTM Autoencoder and Wearable Sensor Data. Sensors 2025, 25.
205. Liu J, Tong HHY, Zheng H, Lei MIF, Li S: Integrated Machine Learning and Structure-Based Virtual Screening Identifies Natural Product Targeting 50S Ribosome Inhibitory Activity Against Cutibacterium acnes. Molecules 2025, 30.
206. Liu B, Zeng M, Kang W, Li S, Wang X, Yu H, Wu H: Integrating serum pharmacochemistry, network pharmacology, and metabolomics to elucidate the detoxification and effect-adjusting mechanism of Chebulae Fructus-processing on Mongolian medicine Euphorbia pekinensis. Journal of Ethnopharmacology 2025, 345.
207. Liu B, Zeng M, Kang W, Li S, Wang X, Yu H, Wu H: Corrigendum to “Integrating serum pharmacochemistry, network pharmacology, and metabolomics to elucidate the detoxification and effect-adjusting mechanism of Chebulae Fructus-processing on Mongolian medicine Euphorbia pekinensis”[J. Ethnopharmacol. 345 (2025) 119582] (Journal of Ethnopharmacology (2025) 345, (S0378874125002661), (10.1016/j.jep.2025.119582)). Journal of Ethnopharmacology 2025, 346.
208. Liang D, Tong SF, Lu HY, Liu M, Wang Z, Xing T, Yu H, Tong RKY: Pediatric Lower Limb Rehabilitation Training System with Soft Exosuit and Quantitative Partial Body Weight Support. Machines 2025, 13.
209. Huang J, Peng XQ, Liu RH, Wang SB, Rao W: The twelve-month prevalence of mental disorders among Teochew adults in the Teoswa region of China: An epidemiological study. Asian Journal of Psychiatry 2025, 110.
210. Deng S, Wu Y, Ye Z, Ouyang D: In silico prediction of metabolic stability for ester-containing molecules: Machine learning and quantum mechanical methods. Chemometrics and Intelligent Laboratory Systems 2025, 257.