1. S. Jin, X. He, L. Ma, Z. Zhuang, Y. Wang, M. Lin, S. Cai, L. Wei, Z. Wang, Z. Zhao, Y. Wu, L. Sun, C. Li, W. Xie, Y. Zhao, Z. Songyang, K. Peng, J. Zhao, and J. Cui, "Suppression of ACE2 SUMOylation protects against SARS-CoV-2 infection through TOLLIP-mediated selective autophagy," Nat. Commun., vol. 13, no. 1, p. 5204, 2022. (IF=17.7)
2. D. Liu, Z. Zhao, Y. She, L. Zhang, X. Chen, L. Ma, and J. Cui, "TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation," Proc. Natl. Acad. Sci. U. S. A., vol. 119, no. 7, p. e2113454119, 2022. (IF=12.8)
3. D. Liu, S. Jin, and J. Cui, "The TRIM14-USP14-BRCC3 complex epigenetically regulates inflammation through inhibiting OPTN-mediated autophagic degradation of KDM4D," Autophagy, vol. 18, no. 8, pp. 2001-2002, 2022. (IF=13.4)
4. H. Xian, W. Huang, T. Sun, S. Yang, C. Zhang, J. Wang, Y. Zhang, and J. Cui, "Unanchored ubiquitin chain sustains RIG-I-induced interferon-I activation and controls selective gene expression," Sci. Bull., vol. 66, no. 8, pp. 794-802, 2021. (IF=11.8)
5. T. Liu, L. Wang, P. Liang, X. Wang, Y. Liu, J. Cai, Y. She, D. Wang, Z. Wang, Z. Guo, S. Bates, X. Xia, and J. Huang, "USP19 suppresses inflammation and promotes M2-like macrophage polarization by manipulating NLRP3 function via autophagy," Cell Mol. Immunol., vol. 18, no. 10, pp. 2431-2442, 2021. (IF=22.1)
6. L.-Q. Wang, T. Liu, S. Yang, L. Sun, Z.-Y. Zhao, L.-Y. Li, Y.-C. She, Y.-Y. Zheng, X.-Y. Ye, Q. Bao, G.-H. Dong, C.-W. Li, and J. Cui, "Perfluoroalkyl substance pollutants activate the innate immune system through the AIM2 inflammasome," Nat. Commun., vol. 12, no. 1, p. 2915, 2021. (IF=17.7)
7. L. Zeng, Y. Bi, P. Guo, Y. Bi, F. Wang, L. Chen, and W. Zhang, "Metabolic analysis of Schizochytrium mutants with high DNA content achieved with ARTP mutagenesis combined with iodoacetic acid and dehydroepiandrosterone screening," Front. Bioeng. Biotechnol., vol. 2, no. 2, p. 5.89, 2022.
8. S. Cai, C. Zhang, Z. Zhuang, S. Zhang, L. Ma, S. Yang, T. Zhou, Z. Wang, W. Xie, S. Jin, J. Zhao, X. Guan, J. Wu, and J. Cui, "Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex," Signal Transduct. Target. Ther., vol. 8, no. 1, p. 170, 2023. (IF=38.104)
9. Y. Zheng, L. Wang, Q. Liu, H. Xian, C. Zhang, S. Cai, S. Yang, S. Jin, and J. Cui, "Modulation of virus-induced neuroinflammation by the autophagy receptor SHISA9 in mice," Nat. Microbiol., vol. 8, no. 5, pp. 958-972, 2023. (IF=30.964)
10. L. Wang, J. Cai, X. Zhao, L. Ma, P. Zeng, L. Zhou, Y. Liu, S. Yang, Z. Cai, S. Zhang, L. Zhou, J. Yang, T. Liu, S. Jin, and J. Cui, "Palmitoylation prevents sustained inflammation by limiting NLRP3 inflammasome activation through chaperone-mediated autophagy," Mol. Cell, vol. 83, no. 2, pp. 281-297.e10, 2023. (IF=16)
11. Z. Du and Y.-H. Wu, "GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions," Brief. Bioinform., May 2022.
12. J. Jiang and J. Li, "MSE-CapsPPISP: Spatial Hierarchical Protein-Protein Interaction Sites Prediction Using Squeeze-and-Excitation Capsule Networks," in Proc. IEEE Int. Conf. Bioinformatics Biomedicine (BIBM), 2022.
13. J. Wang and Y.-H. Huang, "Heterogeneous graph embedding model for predicting interactions between TF and target gene," Bioinformatics, 2022.
14. Y. Bin and J. Xia, "DPProm: a two-layer predictor for identifying promoters and their types on phage genome using deep learning," IEEE J. Biomed. Health Inform., 2022.
15. Y. Bin and J. Xia, "PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization," PLoS Comput. Biol., 2022.
16. Y. Bin and J. Xia, "PredAPP: Predicting Anti-Parasitic Peptides with Undersampling and Ensemble Approaches," Interdiscip. Sci. Comput. Life Sci., 2022.
17. Y. Bin and J. Xia, "BBPpred: sequence-based prediction of blood-brain barrier peptides with feature representation learning and logistic regression," J. Chem. Inf. Model., 2021.
18. W. Tang, R. Dai, W. Yan, W. Zhang, Y. Bin, E. Xia, and J. Xia, "Identifying Multi-functional Bioactive Peptide Functions Using Multi-label Deep Learning," Brief. Bioinform., 2021.
19. X. Tang, T. Zhang, N. Cheng, H. Wang, C.-H. Zheng, and J. Xia, "usDSM: A Novel Method for Deleterious Synonymous Mutation Prediction Using Undersampling Scheme," Brief. Bioinform., 2021.
20. Y.-H. Wu, Y.-A. Huang, J.-Q. Li, Z.-H. You, P.-W. Hu, L. Hu, V. C. M. Leung, Z.-H. Du, "Knowledge graph embedding for profiling the interaction between transcription factors and their target genes," PLOS Comput. Biol., 2023.
21. J. Ji, J. Zhou, Z. Yang, Q. Lin, C. A. Coe lo Coe lo, "AutoDock Koto: A Gradient Boosting Differential Evolution for Molecular Docking," IEEE Trans. Evol. Comput., 2022.
22. J. Wu, Q. Liu, M. Li, J. Xu, C. Wang, J. Zhang, M. Xiao, Y. Bin, J. Xia, "PhaGAA: an integrated web server platform for phage genome annotation and analysis," Bioinformatics, 2023.
23. "Microbial Single-Cell Analysis: What Can We Learn From Mammalian?," Front. Cell Dev. Biol., Jan 2022.
24. "Evaluation of Euglena gracilis 815 as a New Candidate for Biodiesel Production," Front. Bioeng. Biotechnol., Mar 2022.
25. "Euglena gracilis Promotes Lactobacillus Growth and Antioxidant Accumulation as a Potential Next-Generation Prebiotic," Front. Nutr., Jun 2022.
26. "Three new species of Macrostomum (Platyhelminthes, Macrostomorpha) from China and Australia, with notes on taxonomy and phylogenetics," ZooKeys, May 2022.
27. "Advances and challenges in cataloging the human gut virome," Cell Host Microbe, Jul 2022.
28. "RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-kB hyper-activation and inflammation," Signal Transduct Target Ther., Apr 2021.
29. "Metabolomic analysis reveals the responses of docosahexaenoic-acid-producing Schizochytrium under hyposalinity conditions," Algal Res., 2023.
30. "Propanol and 1, 3-propanediol enhance fatty acid accumulation synergistically in Schizochytrium ATCC 20888," Front. Microbiol., 2022.
31. J. Chen and J. Li, "Capsulated Graph Neural Network for Ubiquitylation Sites Prediction," in Proc. IEEE Int. Conf. Bioinformatics Biomedicine (BIBM), 2022.
32. Z. Du, "Inference of gene regulatory networks based on the Light Gradient Boosting Machine," Comput. Biol. Chem., 2022.
33. Z. Du, "Predicting TF Proteins by Incorporating Evolution Information Through PSSM," IEEE/ACM Trans. Comput. Biol. Bioinform., 2022.
34. Z. Shao and L. Ma, "Multi-resolution community detection in complex networks by using a decomposition based multiobjective memetic algorithm," Memetic Comput., 2022.
35. L. Ma and Z. Shao, "Heuristics and Metaheuristics for Biological Network Alignment: A Review," Neurocomputing, 2022.
36. Z. Gao, J. Tang, J. Xia, C.-H. Zheng, P.-J. Wei, "CNNGRN: A convolutional neural network-based method for gene regulatory network inference from bulk time-series expression data," IEEE/ACM Trans. Comput. Biol. Bioinf., 2023.
37. P.-J. Wei, Z.-Z. Pang, L.-J. Jiang, D.-Y. Tan, Y.-S. Su, C.-H. Zheng, "Promoter prediction in nannochloropsis based on densely connected convolutional neural networks," Methods, 2022.
38. Z.-M. Zhang, J.-P. Zhao, P.-J.Wei, C.-H. Zheng, "iPromoter-CLA: Identifying promoters and their strength by deep capsule networks with bidirectional long short-term memory," Comput. Methods Programs Biomed., 2022.
39. Z.-W. Ma, J.-P. Zhao, J. Tian, C.-H. Zheng, "DeeProPre: A promoter predictor based on deep learning," Comput. Biol. Chem., 2022.
40. Y. Wu, T. Zhou, J. Hu, Y. Liu, S. Jin, J. Wu, X. Guan, J. Cui, "Autophagy Activation Induces p62-Dependent Autophagic Degradation of Dengue Virus Capsid Protein During Infection," Front. Microbiol., vol. 13, p. 889693, 2022.
41. Q.-W. Wu, R.-F. Cao, J.-F. Xia, J.-C. Ni, C.-H. Zheng, Y.-S. Su, "Extra trees method for predicting LncRNA-disease association based on multi-layer graph embedding aggregation," IEEE/ACM Trans. Comput. Biol. Bioinf., 2021.
