Publications
| 2024 |
| Haoquan Liu, Chen Zhuo, Jiaming Gao, Chengwei Zeng and Yunjie Zhao, AI-Integrated Network for RNA Complex Structure and Dynamic Prediction, Biophysics Reviews, 2024. |
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| Chengwei Zeng, Chen Zhuo, Jiaming Gao, Haoquan Liu and Yunjie Zhao, Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction, Biomolecules, 2024, 14(10), 1245. |
| Chen Zhuo, Jiaming Gao, Anbang Li, Xuefeng Liu and Yunjie Zhao, A Machine Learning Method for RNA–Small Molecule Binding Preference Prediction, Journal of Chemical Information and Modeling, 2024, 64, 19, 7386–7397. |
| Jiaming Gao, Haoquan Liu, Chen Zhuo, Chengwei Zeng, and Yunjie Zhao, Predicting Small Molecule Binding Nucleotides in RNA Structures Using RNA Surface Topography, Journal of Chemical Information and Modeling, 2024, 64, 18, 6979–6992. |
| Yiren Jian, Chongyang Gao, Chen Zeng, Yunjie Zhao, and Soroush Vosoughi, Knowledge from Large-Scale Protein Contact Prediction Models Can Be Transferred to the Data-Scarce RNA Contact Prediction Task, ICPR, 2024. |
| Haoquan Liu, Yunjie Zhao, Integrated modeling of protein and RNA, Briefings in Bioinformatics, 2024. 25(3):bbae139. |
| Wang Xu†, Houfang Zhang†, Wenhan Guo, Lijun Jiang, Yunjie Zhao* and Yunhui Peng*, Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis, Briefings in Bioinformatics, 2024. |
| Chengwei Zeng, Yiren Jian, Chen Zhuo, Anbang Li, Chen Zeng and Yunjie Zhao*, Evaluation of DNA–protein complex structures using the deep learning method, Physical Chemistry Chemical Physics, 2024. 26(1):130-143. |
| Haoquan Liu, Yiren Jian, Jinxuan Hou, Chen Zeng and Yunjie Zhao*, RNet: a network strategy to predict RNA binding preferences, Briefings in Bioinformatics, 2024. 25(1):1–13. |
| Pooja Khatkar, Gifty Mensah, Shangbo Ning, Maria Cowen, Yuriy Kim, Anastasia Williams, Fardokht A. Abulwerdi, Yunjie Zhao, Chen Zeng, Stuart F. J. Le Grice and Fatah Kashanchi*, HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules, Pharmaceuticals, 2024. 17, 33. |
| 2023 |
| Shangbo Ning, Min Sun, Xu Dong, Anbang Li, Chen Zeng, Maili Liu, Zhou Gong*, and Yunjie Zhao*, Dynamic geometry design of cyclic peptide architectures for RNA structure. Physical Chemistry Chemical Physics, 2023. 25(41):27967-27980. (Research Highlighted in RSC英国皇家化学会 ) |
| Xin-Guan Tan, Xue-Feng Liu*, Ming-Hui Pang, Yu-Qing Wang, and Yun-Jie Zhao*, Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants Chin. Phys. B, 2023. 32(8): 088702 |
| Chen Zhuo, Chengwei Zeng, Rui Yang, Haoquan Liu and Yunjie Zhao*, RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study. International Journal of Molecular Sciences, 2023. 24(6):5497.（Research Highlighted in 研之成理 ) |
| Chengwei Zeng, Yunjie Zhao*, RNA-蛋白质复合物结构预测研究进展. 中国科学: 物理学 力学 天文学, 2023. 3(53) |
| Haoquan Liu, Zhou Gong*, and Yunjie Zhao*, Methods and Applications in Proteins and RNAs. Life, 2023. 13:672. |
| Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng, and Yunjie Zhao*, Evaluating native-like structures of RNA-protein complexes through the deep learning method. Nature Communications, 2023. 14(1):1060. (Research Highlighted in 华大主页, 华大物院, and 中国生物物理学会) |
| Dong Yu, Yong Wu, Lijian Yang, Yunjie Zhao, Ya Jia*, Effect of topology on delay-induced multiple resonances in locally driven systems. Physica A, 2023. (609):128330 |
| 2022 | Shangbo Ning, Huiwen Wang, Chen Zeng*, Yunjie Zhao*, Prediction of allosteric druggable pockets of cyclin-dependent kinases, Briefings in Bioinformatics, 2022. 23(4):bbac290. (Research Highlighted in 华大在线 and 研之成理 ) |
| Rui Yang+, Haoquan Liu+, Liu Yang, Ting Zhou, Xinyao Li, Yunjie Zhao*, RPpocket: An RNA–Protein Intuitive Database with RNA Pocket Topology Resources. International Journal of Molecular Sciences, 2022. 23(13):6903.(Research Highlighted in 研之成理 ) |
| Huiwen Wang*, Haoquan Liu, Shangbo Ning, Chengwei Zeng, Yunjie Zhao*, DLSSAffinity: protein-ligand binding affinity prediction via a deep learning model. Physical Chemistry Chemical Physics, 2022. 24(17):10124-10133. (Research Highlighted in 研之成理 ) |
| 国家发明专利：定量计算RNA口袋拓扑特征和形状分类的方法（授权公告日：2022年4月1日） | 2021 |
| Shangbo Ning, Chengwei Zeng, Chen Zeng, Yunjie Zhao*, The TAR binding dynamics and its implication in Tat degradation mechanism. Biophysical Journal, 2021, 120(23):5158-5168. (Cover paper) (Research Highlighted in 研之成理 and 华大在线) |
| Ting Zhou, Huiwen Wang, Chen Zeng, Yunjie Zhao*. RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. BMC Bioinformatics, 2021, 22(1):428. |
| Qin Liu, Zhichao Liu, Zhipeng Gao, Guanjun Chen, Changyan Liu, Zhenghuang Wan, Chanyou Chen, Chen Zeng, Yunjie Zhao*, Lei Pan*. Insights into Temperature and Hypoxia Tolerance in Cowpea Weevil via HIF-1. Pathogens 2021, 10(6):704. |
| Guowei Wang, Mengyan Ge, Lulu Lu, Ya Jia, and Yunjie Zhao*. Study on propagation efficiency and fidelity of subthreshold signal in feed-forward hybrid neural network under electromagnetic radiation. Nonlinear Dynamics, 2021, 103(3):2627–2643. |
| Linlu Song, Shangbo Ning, Jinxuan Hou*, and Yunjie Zhao*, Performance of protein-ligand docking with CDK4/6 inhibitors: a case study, Mathematical Biosciences and Engineering, 2021, 18(1): 456–470. |
| 国家发明专利：一种分析识别蛋白质特异性药物结合口袋的方法（授权公告日：2021年1月1日） |
| 2020 |
| Huiwen Wang and Yunjie Zhao*, RBinds: a user-friendly server for RNA binding site prediction. Computational and Structural Biotechnology Journal, 2020, 18: 3762–3765. |
| Huiwen Wang, Linlu Song, Ting Zhou, Chen Zeng, Ya Jia and Yunjie Zhao*, A computational study of Tat–CDK9–Cyclin binding dynamics and its implication in transcription-dependent HIV latency. Physical Chemistry Chemical Physics, 2020, 22(44):25474-25482. (Cover paper) |
| Huiwen Wang and Yunjie Zhao*, Methods and applications of RNA contact prediction. Chinese Physics B, 2020, 29 (10):108708. (invited review) |
| Zhichao Liu, Qin Liu, Chanyou Chen, Chen Zeng, Peng Ran, Yunjie Zhao*, and Lei Pan, Twisting mode of supercoil leucine-rich domain mediates peptide sensing in FLS2–flg22–BAK1 complex. Chinese Physics B, 2020, 29(10):75-84 |
| Huiwen Wang, Zeyu Guan, Jiadi Qiu, Ya Jia, Chen Zeng and Yunjie Zhao*, Novel method to identify group-specific non-catalytic pockets of human kinome for drug design. RSC Advances, 2020, 10(4):2004-2015. |
| Ting Zhou, Huiwen Wang, Linlu Song and Yunjie Zhao*, Computational study of switching mechanism in add A-riboswitch. Journal of Theoretical and Computational Chemistry, 2020, 19(3):2040001. |
| 2019 |
| 《生物分子大数据分析》，“十三五”国家重点出版物出版规划项目，赵蕴杰 著，科学出版社，2019. |
| Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia and Yunjie Zhao*. HKPocket: human kinase pocket database for drug design. BMC Bioinformatics, 2019, 20(1):617. |
| Mengyan Ge, Ya Jia, Ying Xu, Lulu Lu, Huiwen Wang, and Yunjie Zhao. Wave propagation and synchronization induced by chemical autapse in chain Hindmarsh–Rose neural network. Applied Mathematics and Computation, 2019. 352:136-145 |
| Shen, Jian, Zhang, Xiaomin, Li, Qiliang, Wang, Xinyu, Zhao, Yunjie, and Jia, Ya. Intrinsic fluctuation and susceptibility in somatic cell reprogramming process. Chinese Physics B, 2019, 28(4):40503-040503. |
| Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao, Chen Zeng, DIRECT: RNA Contact Predictions by Integrating Structural Patterns. BMC Bioinformatics, 2019, 20(1):497. |
| Zhaokang Zhang, Yannan Zhou, Haitao Fan, Kirunda John Billy, Yunjie Zhao, Xuan Zhan, Lijian Yang, and Ya Jia, Effects of Lycium barbarum Polysaccharides on Health and Aging of C. elegans Depend on daf-12/daf-16. Oxidative Medicine and Cellular Longevity, 2019, 18:1-14 |
| Zhichao Liu, Erika P. Portero, Yiren Jian, Yunjie Zhao, Rosemary M. Onjiko, Chen Zeng, and Peter Nemes, Trace, Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry: A Case Study from Single-Cell Metabolomics. Analytical Chemistry, 2019, 91(9):5768-5776 |
| Ying Xu, Ya Jia, Huiwen Wang, Ying Liu, Ping Wang, Yunjie Zhao, Spiking activities in chain neural network driven by channel noise with field coupling. Nonlinear Dynamics, 2019, 95(4):3237-3247. |
| Yunjie Zhao, Hao Chen, Chenghang Du, et al., Design of Tat-activated Cdk9 Inhibitor. International Journal of Peptide Research and Therapeutics, 2019, 25(15):807-817. |
| 2018 |
| Yunjie Zhao, Jun Wang, Chen Zeng, Yi Xiao, Evaluation of RNA secondary structure prediction for both base-pairing and topology. Biophys Rep, 2018, 4(3):123–132. |
| Kaili Wang, Yiren Jian, Huiwen Wang, Chen Zeng and Yunjie Zhao*, RBind: computational network method to predict RNA binding sites. Bioinformatics, 2018, 34(18):3131-3136. |
| Mengyan Ge, Ying Xu, Lulu Lu, Yunjie Zhao, Lijian Yang, Xuan Zhan, Kaifu Gao, Anbang Li, Ya Jia1*, The effect of external periodic signals and electromagnetic radiation on autaptic regulation of neuronal firing. IET Systems Biology, 2018, 12(4):9 |
| 2017 |
| Huiwen Wang, Kaili Wang, Zeyu Guan, Yiren Jian, Ya Jia, Fatah Kashanchi, Chen Zeng*, and Yunjie Zhao*, Computational study of non-catalytic T-loop pocket on CDK proteins for drug development. Chinese Physics B, 2017, 26(12):32-40. |
| Jian Wang, Kangkun Mao, Yunjie Zhao, et al. Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis. Nucleic Acids Research, 2017, 45(11):6299–6309. |
| Yunjie Zhao, Yiren Jian, Zhichao Liu, et al. Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins. Scientific Reports, 2017. 7:2876. |
| Qin Liu, Yanhua Yu, Weida Chen, Chanyou Chen, Yunjie Zhao*, Chen Zeng*, The Lectin Hemagglutination Study and Inhibitor Design, Chem J Chinese U, 2017, 7(1):2876. |
| Kaifu Gao and Yunjie Zhao, A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State Model. J. Phys. Chem. B. 2017, 121(14):2952-2960. |
| 2016 |
| Shaojun Xing, Fengyin Li, Zhouhao Zeng, Yunjie Zhao, Shuyang Yu, et al. Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity. Nature Immunology, 2016, 17(6):695-703. |
| 2015 |
| Yunjie Zhao, Chen Zeng*, Michael Massiah*, Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain. PLoS One, 2015, 10(4): e0124377. |
| Yunjie Zhao, Zhichao Liu, Qin Liu, Gao Chen, Chanyou Chen, Chen Zeng, Plant lectin protein structural classification and drug design. World Journal of Complex Medicine, 2015, 1(1):68-73. |
| Jian Wang+, Yunjie Zhao+(co-first author), Chunyan Zhu, Yi Xiao*, 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Research, 2015, 43(10):e63. |
| Jun Wang, Yunjie Zhao, Jian Wang, and Yi Xiao, Computational study of stability of an H-H-type pseudoknot motif, Phys. Rev. E, 2015, 92(6):062705. |
| 2014 |
| Hao Chen+, Yunjie Zhao+(co-first author), Haotian Li, Dongyan Zhang, Yanzhao Huang, Qi Shen, Rachel Van Duyne, Fatah Kashanchi, Chen Zeng, Shiyong Liu*, Break CDK2/Cyclin E1 Interface Allosterically with Small Peptides. PLoS One, 2014, 9(10):e109154. |
| Zhou Gong, Yunjie Zhao, Changjun Chen, Yong Duan, Yi Xiao*, Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations. PLoS One, 2014, 9(3): e92247. |
| 2013 |
| Yunjie Zhao, Chen Zeng, Nadya I Tarasova, Sergey Chasovskikh, Anatoly Dritschilo, Olga A Timofeeva*, A new role for STAT3 as a regulator of chromatin topology. Transcription, 2013, 4:227-231. |
| Yi Zhao, Jian Wang, XiaoWei Chen, HaiTao Luo, YunJie Zhao, Yi Xiao*, RenSheng Chen*, Large-scale study of long non-coding RNA functions based on structure and expression features. Sci China Life Sci, 2013, 56(10):953–959. |
| Chenhang Du, Hao Chen, Yunjie Zhao, Chen Zeng*, How Far and How Fast Can One Move on Neutral Network? J Theor Comput Chem, 2013, 12(8):279. |
| 2012 |
| Yunjie Zhao, Yangyu Huang, Zhou Gong, Yanjie Wang, Jianfen Man, Yi Xiao*, Automated and fast building of three-dimensional RNA structures. Scientific reports, 2012, 2:734. |
| Zhou Gong, Yunjie Zhao, Changjun Chen, Yi Xiao*, Computational study of unfolding and regulation mechanism of preQ1 riboswitches. PLoS One, 2012, 7(9):e45239. |
| Yangyu Huang, Xiufeng Yang, Haotian Li, Xiaofeng Ji, Hongli Cheng, Yunjie Zhao, Dachuan Guo, Lin Li, Shiyong Liu, Protein-RNA Interaction Interface Prediction and Design. Acta Physico Chimica Sinica, 2012, 28(10):2390-2400. |
| 2011 |
| Yunjie Zhao, Zhou Gong, Yi Xiao*, Improvements of the hierarchical approach for predicting RNA tertiary structure. J Biomol Struct Dyn, 2011, 28(5):815-26. |
| Zhou Gong, Yunjie Zhao, Changjun Chen, Yi Xiao*, Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation. J Biomol Struct Dyn, 2011, 29(2):403-16. |
| 2010 |
| Zhou Gong, Yunjie Zhao, Yi Xiao*, RNA stability under different combinations of amber force fields and solvation models. J Biomol Struct Dyn, 2010, 28(3):431-41. |
| 2009 |
| Yunjie Zhao, Zhou Gong, Yi Xiao*, Predicting RNA tertiary structures based on the secondary structure. Acta Biophysica Sinica, 2009, S1:96. |
| Zhou Gong, Yunjie Zhao, Yi Xiao*, RNA molecular dynamics simulation with different force fields and solvation models. Acta Biophysica Sinica, 2009, S1:329-30. |