徐建震

1. Mingrong Bei and Jianzhen Xu*(2024): SR proteins in cancer: function, regulation, and small inhibitor. Cell Mol Biol Lett. 2024 May 22;29(1):78.

2. Mingrong Bei, Shijia Hao, Kai Lin, Qiuyang Chen, Yujie Cai, Xing Zhao, Leiming Jiang, Lirui Lin, Geng Dong and Jianzhen Xu (2023) Splicing factor TRA2A contributes to esophageal cancer progression via a noncanonical role in lncRNA m6A methylation. Cancer Science. 114(8):3216-3229

3. Leiming Jiang, Shijia Hao, Lirui Lin, Xuefei Gao, Jianzhen Xu* (2023) fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data. Comput Struct Biotechnol J. ;21:2276-2285. 

4. Mengting Shao^#, Shijia Hao^#, Leiming Jiang, Yujie Cai, Xing Zhao, Qiuyang Chen, Xuefei Gao,

    and Jianzhen Xu*(2022): CRIT: identifying RNA binding protein regulator in circRNA life

    cycle via non-negative matrix factorization Molecular Therapy-Nucleic Acids 28;30:398-406

5.  Qianqian Zhao, Shuaibing Yang, Shijia Hao, Zejia Chen, Lihua Tang, Zhaoting Wu, Jiaxin Wu, Mingqian Xu, Zebiao Ma, Li Zhou*, Jianzhen Xu*, Qingsong Qin* (2024). Identification of transcriptionally-active HPV integrants through Nanopore sequencing reveals viable targets for gene therapy against cervical cancer. Journal of Medical Virology Jun;96(6):e29769

6.  Shuaibing Yang, Qianqian Zhao, Lihua Tang, Zejia Chen, Zhaoting Wu, Kaixin Li, Ruoru Lin, Yang Chen, Danlin Ou, Li Zhou*, Jianzhen Xu* and Qingsong Qin* (2022). Whole Genome Assembly of Human Papillomavirus by Nanopore Long-Read Sequencing.  Frontiers in Genetics 12:798608

沈文君

(1) Hu Y, Xie M, Li Y, Rao M, Shen W, Luo C, Qin H, Baek J, Zhou XM. Benchmarking clustering, alignment, and integration methods for spatial transcriptomics. Genome Biol. 2024 Aug 9;25(1):212.

(2) He JZ, Chen Y, Zeng FM, Huang QF, Zhang HF, Wang SH, Yu SX, Pang XX, Liu Y, Xu XE, Wu JY, Shen WJ, Li ZY, Li EM, Xu LY. Spatial analysis of stromal signatures identifies invasive front carcinoma-associated fibroblasts as suppressors of anti-tumor immune response in esophageal cancer. J Exp Clin Cancer Res. 2023 May 31;42(1):136.

(3) Song QP, Li GY, Wu S, Shen WJ, Wong H-S. Discriminator feature-based progressive GAN inversion. Knowledge-Based Systems. 2023, 261:110186.

(4) Huo XY, Zeng XP, Wu S, Shen WJ, Wong H-S. Collaborative Learning with Unreliability Adaptation for Semi-Supervised Image Classification. Pattern Recognition. 2022, 133: 109032.

(5) Wang G, Lv C, Liu C, Shen W. Neutrophil-to-lymphocyte ratio as a potential biomarker in predicting influenza susceptibility. Front Microbiol. 2022 Oct 6;13:1003380.

(6) Wen ZH, Langsam JL, Zhang L, Shen W, Zhou X. A Bayesian factorization method to recover single-cell RNA sequencing data. Cell Rep Methods. 2021 Dec 20;2(1):100133.

(7) Shen W, Wang G, Cooper GR, Jiang Y, Zhou X. The Epithelial and Stromal Immune Microenvironment in Gastric Cancer: A Comprehensive Analysis Reveals Prognostic Factors with Digital Cytometry. Cancers (Basel). 2021 Oct 27;13(21):5382.

林李锐

1）Lin L, Lin K, Wu X, Liu J, Cheng Y, Xu LY, Li EM, Dong G. Potential Inhibitors of Fascin From A Database of Marine Natural Products: A Virtual Screening and Molecular Dynamics Study. Front Chem. 2021 Oct 7;9:719949. doi: 10.3389/fchem.2021.719949. PMID: 34692638; PMCID: PMC8529705.

2）Lin L, Zou H, Li W, Xu LY, Li EM, Dong G. Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation. Front Chem. 2021 Dec 14;9:797036. doi: 10.3389/fchem.2021.797036. PMID: 34970534; PMCID: PMC8713139.

3）Dong G, Lin LR, Xu LY, Li EM. Reaction mechanism of lysyl oxidase-like 2 (LOXL2) studied by computational methods. J Inorg Biochem. 2020 Oct;211:111204. doi: 10.1016/j.jinorgbio.2020.111204. Epub 2020 Jul 27. PMID: 32801097.

4）Wu X, Wen B, Lin L, Shi W, Li D, Cheng Y, Xu LY, Li EM, Dong G. New insights into the function of Fascin in actin bundling: A combined theoretical and experimental study. Int J Biochem Cell Biol. 2021 Oct;139:106056. doi: 10.1016/j.biocel.2021.106056. Epub 2021 Aug 12. PMID: 34390855.

5）Zheng C, Wu X, Zeng R, Lin L, Xu L, Li E, Dong G. Computational Prediction of Hot Spots and Binding Site of Inhibitor NSC23766 on Rac1 Binding With Tiam1. Front Chem. 2021 Feb 2;8:625437. doi: 10.3389/fchem.2020.625437. PMID: 33604328; PMCID: PMC7884829.

6）Bei M, Hao S, Lin K, Chen Q, Cai Y, Zhao X, Jiang L, Lin L, Dong G, Xu J. Splicing factor TRA2A contributes to esophageal cancer progression via a noncanonical role in lncRNA m⁶ A methylation. Cancer Sci. 2023 Jun . doi:10.1111/cas.15870. PMID: 37317053. 6

7）Jiang L, Hao S, Lin L, Gao X, Xu J. fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data. Comput Struct Biotechnol J. 2023 Mar 23;21:2276-2285. doi: 10.1016/j.csbj.2023.03.035. PMID: 37035550; PMCID: PMC10073992. 6

8）Lin L, Lin K, Chen L, Wang Y, Xu LY, Li EM, Liu Q*, Zou H*, Dong G.* Covalent Inhibitor Screening for Targeting LOXL2: Studied by Virtual Screening and Experimental Validation. Recent Pat Anticancer Drug Discov. 2025 Jan 2. doi: 10.2174/0115748928356643241216132041. PMID: 39757678.

9）Jinmei Pan, Kai Chen, Lirui Lin*, Li-Yan Xu, En-Min Li*, Geng Dong*, Exploring the Allosteric Response of Fascin to Its Inhibitor, The Journal of Physical Chemistry B, 2024, https://doi.org/10.1021/acs.jpcb.4c04813

10）Jia Liu, Lirui Lin*, Li-Yan Xu, En-Min Li*, Geng Dong*, The Effects of Inhibitor Chivosazole A on Actin Interacting with Profilin: A Theoretical Study, Advanced Theory and Simulations, 2024, DOI: https://doi.org/10.1002/adts.202400533

11）Wang, Y., Lin, L.*, Xu, LY., Li EM*, Dong G.*. Reaction Mechanism of Actin ATP Hydrolysis Studied by QM/MM Calculations. Chem. Res. Chin. Univ. (2024). https://doi.org/10.1007/s40242-024-4089-2

12）Lirui Lin, LIN Kai, ZOU Hai-Ying , XU Li-Yan , LI En-Min , DONG Geng. Insight into the Stability of LOXL2: a Computational Study[J]. Chinese Journal of Biochemistry and Molecular Biology, 2024, 40(5): 685-695 https://doi.org/10.13865/j.cnki.cjbmb.2024.03.1414 

13）Yiwen Wang, Lirui Lin, Li‐Yan Xu*, En‐Min Li*, Geng Dong* , Conformation Changes Associated with the Formation and Activation of Lysine Tyrosylquinone of LOXL2 Studied by Metadynamics Simulation, Advanced Theory and Simulations, 2024, DOI: 10.1002/adts.202300859