2025
35.Yu J, Lan Y, Zhu C, et al. Structure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site.
Nature Communications, 2025, 16(1): 3969.（IF=15.7）
34.Yongrui Wang; Zhen Wang; Yanjun Li; Pengju Yan; Xiaolin Li*; Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments, Journal of Chemical Information and Modeling, 2025, 65(12): 5934–5944. (IF=5.3)
33.Guojun Li‡, Jincao Yao‡, Chanjuan Peng, Yinjie Hu, Xuhan Feng,Xiaolin Li, Chulin Sha*, and Min He*; Multimodal Nested Attention Network for Lymph Node Metastasis Prediction of Thyroid Carcinoma, Big Data Mining and Analytics, 2025. (IF=6.2)
32.Zhang, R., Zhang, X., Zhao, S., Zou, Q., Ding, Y., Guo, X.*, & Wu, H. (2025). Beyond ST‐246: Unveiling Potential Inhibitors Targeting VP37 Protein in Silico From Herb and Marine Databases. Journal of Computational Chemistry, 2025. 46(11), e70111. (IF=3.4)
31.Qian, Y.‡, Zhang, X.‡, Wang, Y., Zou, Q., Cao, C., Ding, Y., & Guo, X*. (2025). DTI-RME: a robust and multi-kernel ensemble approach for drug-target interaction prediction. AAAI BMC biology, 23(1), 225. (IF=5.4)
30.Junwei Zhang, Tianheng Wang, Zeyi Zhang, et al. QiMLP: Quantum-inspired Multilayer Perceptron with Strong Correlation Mining and Parameter Compression. In AAAI, 2025: 22452-22460. （CCF-A）
29.Junwei Zhang, Xiaolin Li. Quantum-inspired Non-homologous Representation Constraint Mechanism for Long-tail Senses of Word Sense Disambiguation. In AAAI, 2025: 25877-25885.（CCF-A）
28.Junwei Zhang, Tianheng Wang, Tao Huang, et al. An Evaluation Framework for Long-tail Senses in Large Language Models and Word Sense Disambiguation. In DASFAA, 2025: 1-16.（CCF-B）
27.Wenkang Zhang, Hengfeng Jiang, Liang Han, Jie Liu, Jie Wang, Feng He, Leilei Tian*, POSA for fast, amplified and multiplexed protein imaging, Nature Communications, 2025, 16, 2300. (IF: 15.7)
26.Jin Y‡, Sun G‡, Chen B‡, Feng S‡, Tang M‡, Wang H, Zhang Y, Wang Y, An Y, Xiao Y, Liu Z, Liu P, Tian Z, Yin H, Zhang S, Luan X. Delivering miR-23b-3p by small extracellular vesicles to promote cell senescence and aberrant lipid metabolism. BMC Biol.2025, 11;23(1):41.(IF:5.4)
25.Su G‡, Xu Y‡, Chen B‡, Ju K, Jin Y, Chen H, Zhang S, Luan X. Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition. Commun Biol. 2025, 16;8(1):619.(IF:5.1)
24.Zhen Wang‡, Yizhen Feng‡, Qingwen Tian, Ziqi Liu, Pengju Yan*, Xiaolin Li*. RNADiffFold: Generative RNA Secondary Structure Prediction using Discrete Diffusion Models. Briefings in Bioinformatics, 2025, 26(1): bbae618. (IF=7.7)
34.Yongrui Wang; Zhen Wang; Yanjun Li; Pengju Yan; Xiaolin Li*; Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments, Journal of Chemical Information and Modeling, 2025, 65(12): 5934–5944. (IF=5.3)
33.Guojun Li‡, Jincao Yao‡, Chanjuan Peng, Yinjie Hu, Xuhan Feng,Xiaolin Li, Chulin Sha*, and Min He*; Multimodal Nested Attention Network for Lymph Node Metastasis Prediction of Thyroid Carcinoma, Big Data Mining and Analytics, 2025. (IF=6.2)
32.Zhang, R., Zhang, X., Zhao, S., Zou, Q., Ding, Y., Guo, X.*, & Wu, H. (2025). Beyond ST‐246: Unveiling Potential Inhibitors Targeting VP37 Protein in Silico From Herb and Marine Databases. Journal of Computational Chemistry, 2025. 46(11), e70111. (IF=3.4)
31.Qian, Y.‡, Zhang, X.‡, Wang, Y., Zou, Q., Cao, C., Ding, Y., & Guo, X*. (2025). DTI-RME: a robust and multi-kernel ensemble approach for drug-target interaction prediction. AAAI BMC biology, 23(1), 225. (IF=5.4)
30.Junwei Zhang, Tianheng Wang, Zeyi Zhang, et al. QiMLP: Quantum-inspired Multilayer Perceptron with Strong Correlation Mining and Parameter Compression. In AAAI, 2025: 22452-22460. （CCF-A）
29.Junwei Zhang, Xiaolin Li. Quantum-inspired Non-homologous Representation Constraint Mechanism for Long-tail Senses of Word Sense Disambiguation. In AAAI, 2025: 25877-25885.（CCF-A）
28.Junwei Zhang, Tianheng Wang, Tao Huang, et al. An Evaluation Framework for Long-tail Senses in Large Language Models and Word Sense Disambiguation. In DASFAA, 2025: 1-16.（CCF-B）
27.Wenkang Zhang, Hengfeng Jiang, Liang Han, Jie Liu, Jie Wang, Feng He, Leilei Tian*, POSA for fast, amplified and multiplexed protein imaging, Nature Communications, 2025, 16, 2300. (IF: 15.7)
26.Jin Y‡, Sun G‡, Chen B‡, Feng S‡, Tang M‡, Wang H, Zhang Y, Wang Y, An Y, Xiao Y, Liu Z, Liu P, Tian Z, Yin H, Zhang S, Luan X. Delivering miR-23b-3p by small extracellular vesicles to promote cell senescence and aberrant lipid metabolism. BMC Biol.2025, 11;23(1):41.(IF:5.4)
25.Su G‡, Xu Y‡, Chen B‡, Ju K, Jin Y, Chen H, Zhang S, Luan X. Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition. Commun Biol. 2025, 16;8(1):619.(IF:5.1)
24.Zhen Wang‡, Yizhen Feng‡, Qingwen Tian, Ziqi Liu, Pengju Yan*, Xiaolin Li*. RNADiffFold: Generative RNA Secondary Structure Prediction using Discrete Diffusion Models. Briefings in Bioinformatics, 2025, 26(1): bbae618. (IF=7.7)
2024
23.Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Tingjun Hou*, Qiang Zhang*, Huajun Chen*.
Nature Communications. 2024. (IF=15.7)
22.Bowen Li‡, Zhen Wang‡, Ziqi Liu, YanXin Tao, Chulin Sha, Min He, Xiaolin Li*. DrugMetric: quantitative drug-likeness scoring based on chemical space distance. Briefings in Bioinformatics, 2024, 25(4): bbae321. (IF=7.7)
21.Zhen Wang, Ziqi Liu, Wei Zhang, Yanjun Li, Yizhen Feng, Shaokang Lv, Han Diao, Pengju Yan*, Min He*, Xiaolin Li*. AptaDiff: de novo design and optimization of aptamers based on diffusion models. Briefings in Bioinformatics, 2024, 25(6): bbae517. (IF=7.7)
20.Xin Zhang, Shulin Zhao , Xi Su , Lifeng Xu*, From docking to dynamics: Unveiling the potential non-peptide and non-covalent inhibitors of Mpro from natural products, Computers in Biology and Medicine.181 (2024): 108963. (IF=7.0)
19.Xin Zhang, Feiran Zhou, Pinglu Zhang, Quan Zou* and Ying Zhang*, TCM@ MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine. Current Bioinformatics 20.6 (2025): 557-563. (IF=2.4)
18.Haozhe Huang‡, Beihong Ji‡, Yixian Huang, Sihan Li, Yuang Chen, Zhangyi Luo, Daniel J. Bain, Shichen Li, Jingjing Sun, Da Yang, Timothy F. Burns, Junmei Wang & Song Li*. Advanced Functional Materials, 2024. (IF=19.00)
17.Junwei Zhang, Ruifang He, Fengyu Guo, et al. Quantum Interference Model for Semantic Biases of Glosses in Word Sense Disambiguation. In AAAI, 2024: 19551-19559. （CCF-A）
16.Junwei Zhang, Tianheng Wang, Chenyang Wang, et al. Emotional Polarity Attention Mechanism for Text Sentiment Analysis. In DASFAA, 2024: 3-18.（CCF-B）
15.Wu, Qiong‡; Yu, Chunjie‡; Yu, Fang‡; Guo, Yiran; Sheng, Yue; Li, Liping; Li, Yafang; Zhang, Yutao; Hu, Chao; Wang, Jue; He, Tong-chuan; Huang, Yong; Ni, Hongyu; Huo, Zhiguang; Wu, Wenshu; Wang, Gang Greg; Lyu, Jianxin; Qian, Zhijian ; Evi1 governs Kdm6b-mediated histone demethylation to regulate the Laptm4b-driven mTOR pathway in hematopoietic progenitor cells, Journal of Clinical Investigation, 2024, 134(24) (IF=13.6)
22.Bowen Li‡, Zhen Wang‡, Ziqi Liu, YanXin Tao, Chulin Sha, Min He, Xiaolin Li*. DrugMetric: quantitative drug-likeness scoring based on chemical space distance. Briefings in Bioinformatics, 2024, 25(4): bbae321. (IF=7.7)
21.Zhen Wang, Ziqi Liu, Wei Zhang, Yanjun Li, Yizhen Feng, Shaokang Lv, Han Diao, Pengju Yan*, Min He*, Xiaolin Li*. AptaDiff: de novo design and optimization of aptamers based on diffusion models. Briefings in Bioinformatics, 2024, 25(6): bbae517. (IF=7.7)
20.Xin Zhang, Shulin Zhao , Xi Su , Lifeng Xu*, From docking to dynamics: Unveiling the potential non-peptide and non-covalent inhibitors of Mpro from natural products, Computers in Biology and Medicine.181 (2024): 108963. (IF=7.0)
19.Xin Zhang, Feiran Zhou, Pinglu Zhang, Quan Zou* and Ying Zhang*, TCM@ MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine. Current Bioinformatics 20.6 (2025): 557-563. (IF=2.4)
18.Haozhe Huang‡, Beihong Ji‡, Yixian Huang, Sihan Li, Yuang Chen, Zhangyi Luo, Daniel J. Bain, Shichen Li, Jingjing Sun, Da Yang, Timothy F. Burns, Junmei Wang & Song Li*. Advanced Functional Materials, 2024. (IF=19.00)
17.Junwei Zhang, Ruifang He, Fengyu Guo, et al. Quantum Interference Model for Semantic Biases of Glosses in Word Sense Disambiguation. In AAAI, 2024: 19551-19559. （CCF-A）
16.Junwei Zhang, Tianheng Wang, Chenyang Wang, et al. Emotional Polarity Attention Mechanism for Text Sentiment Analysis. In DASFAA, 2024: 3-18.（CCF-B）
15.Wu, Qiong‡; Yu, Chunjie‡; Yu, Fang‡; Guo, Yiran; Sheng, Yue; Li, Liping; Li, Yafang; Zhang, Yutao; Hu, Chao; Wang, Jue; He, Tong-chuan; Huang, Yong; Ni, Hongyu; Huo, Zhiguang; Wu, Wenshu; Wang, Gang Greg; Lyu, Jianxin; Qian, Zhijian ; Evi1 governs Kdm6b-mediated histone demethylation to regulate the Laptm4b-driven mTOR pathway in hematopoietic progenitor cells, Journal of Clinical Investigation, 2024, 134(24) (IF=13.6)
2023
14.Zhen Wang, Zheng Feng, Yanjun Li, Bowen Li, Yongrui Wang, Chulin Sha, Min He*, Xiaolin Li*. BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation.
Briefings in Bioinformatics, 2024, 25(1): bbad400. (IF=7.7)
13.J. Huang‡, Y. Xu‡, Y. Xue, Y. Huang, X. Li, X. Chen, Y. Xu, D. Zhang, P. Zhang*, J. Zhao*, J. Ji*, Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat. Biomed. Eng. 2023, 7, 797. (IF=28.1)
12.Haixia Ge‡, Beihong Ji‡, Jiahui Fang‡, Jiayang Wang, Jing Li*, Junmei Wang*. ACS Chemical Neuroscience, 2023. (IF=5.78)
11.Junwei Zhang, Ruifang He, Fengyu Guo. Quantum-inspired Representation for Long-tail Senses of Word Sense Disambiguation. In AAAI, 2023: 13949-13957.（CCF-A）
10.Youzhi Wang, Yulong Wang, Haojie Che, Yihe Jia, Huifang Wang, Linfei Zuo, Kan Yang, Tingting Li, Jinxin Wang*, Sappanone A: A natural PDE4 inhibitor with dual anti-inflammatory and antioxidant activities from the heartwood of Caesalpinia sappan L, J Ethnopharmacol. 2023 Mar 25;304:116020. (IF: 5.4)
9.Luan XD‡, Chen BX‡, Shang WJ‡, Yin WC, Jin Y, Zhang LK, Xu HE, Zhang SY. Structure basis for inhibition of SARS-CoV-2 by the feline drug GC376. Acta Pharmacol Sin. 2023, 44(1):255-257.(IF: 8.4)
8.Zhang J, Chen B, Fang X. 3D Structural Analysis of Long Noncoding RNA by Small Angle X-ray Scattering and Computational Modeling. Methods Mol Biol. 2023;2568:147-163.
7.Y. Zhou‡, X. Ma‡, D. Wu, and X. Li*, "Communication-efficient and Attack-Resistant Federated Edge Learning with Dataset Distillation," IEEE Transactions on Cloud Computing (TCC), 2023. (IF: 6.0)
13.J. Huang‡, Y. Xu‡, Y. Xue, Y. Huang, X. Li, X. Chen, Y. Xu, D. Zhang, P. Zhang*, J. Zhao*, J. Ji*, Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat. Biomed. Eng. 2023, 7, 797. (IF=28.1)
12.Haixia Ge‡, Beihong Ji‡, Jiahui Fang‡, Jiayang Wang, Jing Li*, Junmei Wang*. ACS Chemical Neuroscience, 2023. (IF=5.78)
11.Junwei Zhang, Ruifang He, Fengyu Guo. Quantum-inspired Representation for Long-tail Senses of Word Sense Disambiguation. In AAAI, 2023: 13949-13957.（CCF-A）
10.Youzhi Wang, Yulong Wang, Haojie Che, Yihe Jia, Huifang Wang, Linfei Zuo, Kan Yang, Tingting Li, Jinxin Wang*, Sappanone A: A natural PDE4 inhibitor with dual anti-inflammatory and antioxidant activities from the heartwood of Caesalpinia sappan L, J Ethnopharmacol. 2023 Mar 25;304:116020. (IF: 5.4)
9.Luan XD‡, Chen BX‡, Shang WJ‡, Yin WC, Jin Y, Zhang LK, Xu HE, Zhang SY. Structure basis for inhibition of SARS-CoV-2 by the feline drug GC376. Acta Pharmacol Sin. 2023, 44(1):255-257.(IF: 8.4)
8.Zhang J, Chen B, Fang X. 3D Structural Analysis of Long Noncoding RNA by Small Angle X-ray Scattering and Computational Modeling. Methods Mol Biol. 2023;2568:147-163.
7.Y. Zhou‡, X. Ma‡, D. Wu, and X. Li*, "Communication-efficient and Attack-Resistant Federated Edge Learning with Dataset Distillation," IEEE Transactions on Cloud Computing (TCC), 2023. (IF: 6.0)
2022
6.Junwei Zhang, Ruifang He, Fengyu Guo, et al. Disentangled Representation for Long-tail Senses of Word Sense Disambiguation. In
CIKM, 2022: 2569-2579.（CCF-B）
5.Junwei Zhang, Ruifang He, Fengyu Guo. Bi-matching Mechanism to Combat Long-tail Senses of Word Sense Disambiguation. In ECML-PKDD, 2022: 621-637.（CCF-B）
4.Yihe Jia, Ke Wang, Huifang Wang, Botao Zhang, Kan Yang, Zhilan Zhang, Haijuan Dong, Jinxin Wang*,Discovery of selective covalent cathepsin K inhibitors containing novel 4-cyanopyrimidine warhead based on quantum chemical calculations and binding mode analysis, Bioorg Med Chem , 2022, 74: 117053. (IF: 3.6)
3.Y. Li#, D. Zhou, G. Zheng, D. Wu, X. Li, Y. Yuan, "DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Non-binders in Structure-based Drug Discovery," Journal of Chemical Information and Modeling, 2022. (IF=5.3)
2.Mohammad Ali Rezaei, Yanjun Li, Dapeng Oliver Wu, Xiaolin Li, Chenglong Li, "Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction," IEEE Transactions on Computational Biology and Bioinformatics, Vol. 19 (1), pp. 407-417, 2022. (IF=3.9)
1.X. Yuan#, L. Ding, L. Zhang, X. Li, and D. Wu, "ES Attack: Model Stealing against Deep Neural Networks without Data Hurdles," IEEE Transactions on Emerging Topics in Computational Intelligence, Vol. 6 (5), 2022. (2025 IEEE CIS TETCI Outstanding Paper Award) (IF: 8.4)
5.Junwei Zhang, Ruifang He, Fengyu Guo. Bi-matching Mechanism to Combat Long-tail Senses of Word Sense Disambiguation. In ECML-PKDD, 2022: 621-637.（CCF-B）
4.Yihe Jia, Ke Wang, Huifang Wang, Botao Zhang, Kan Yang, Zhilan Zhang, Haijuan Dong, Jinxin Wang*,Discovery of selective covalent cathepsin K inhibitors containing novel 4-cyanopyrimidine warhead based on quantum chemical calculations and binding mode analysis, Bioorg Med Chem , 2022, 74: 117053. (IF: 3.6)
3.Y. Li#, D. Zhou, G. Zheng, D. Wu, X. Li, Y. Yuan, "DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Non-binders in Structure-based Drug Discovery," Journal of Chemical Information and Modeling, 2022. (IF=5.3)
2.Mohammad Ali Rezaei, Yanjun Li, Dapeng Oliver Wu, Xiaolin Li, Chenglong Li, "Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction," IEEE Transactions on Computational Biology and Bioinformatics, Vol. 19 (1), pp. 407-417, 2022. (IF=3.9)
1.X. Yuan#, L. Ding, L. Zhang, X. Li, and D. Wu, "ES Attack: Model Stealing against Deep Neural Networks without Data Hurdles," IEEE Transactions on Emerging Topics in Computational Intelligence, Vol. 6 (5), 2022. (2025 IEEE CIS TETCI Outstanding Paper Award) (IF: 8.4)