Publications

  • 31. Joseph Andrew Whitley, Sungjin Kim, Lei Lou, Chenming Ye, Omar Awad Alsaidan, Essilvo Sulejmani, Jingwen Cai, Ellison Gerona Desrochers, Zanna Beharry, Catherine Bowes Rickman, Mikael Klingeborn, Yutao Liu, Zhong‐Ru Xie, Houjian Cai*, Encapsulating Cas9 into extracellular vesicles by protein myristoylation, Journal of extracellular vesicles, 11, 4, e12196. (2022) DOI: 10.1002/jev2.12196

    30. Anna Zan, Zhong-Ru Xie, Yi-Chen Hsu, Yu-Hao Chen, Tsung-Hsien Lin, Yong-Shan Chang, Kuan Y. Chang*, DeepFlu: a deep learning approach for forecasting symptomatic influenza A infection based on pre-exposure gene expression. Computer Methods and Programs in Biomedicine, 213, 106495. (2022) DOI: 10.1016/j.cmpb.2021.106495

    29. Yifei Wu, David Crich, Scott D Pegan, Lei Lou, Madelyn C Hansen, Carson Booth, Ellison Desrochers, Lauren Nicole Mullininx, Edward B Starling, Kuan Y Chang*, Zhong-Ru Xie*, Polyphenols as Potential Inhibitors of SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp). Molecules 26 (24), 7438 (2021) DOI: 110.3390/molecules26247438

    28. Jian Wang, Yuxi Teng, Ruihua Zhang, Yifei Wu, Lei Lou, Yusong Zou, Michelle Li, Zhong-Ru Xie, Yajun Yan*, Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor. Nature communications 12 (1), 1-10 (2021). DOI: 10.1038/s41467-021-27290-9

    27. Yifei Wu, Scott D Pegan, David Crich, Ellison Desrochers, Edward B Starling, Madelyn C Hansen, Carson Booth, Lauren Nicole Mullininx, Lei Lou, Kuan Y Chang*, Zhong-Ru Xie*, Polyphenols as alternative treatments of COVID-19. Computational and Structural Biotechnology Journal, 19, 5371. (2021) DOI: 10.3390/biom10091223

    26. Samuel Godfrey Hendrix, Kuan Y Chang, Zeezoo Ryu, Zhong-Ru Xie*, DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method. International journal of molecular sciences 22 (11), 5510 (2021) DOI: 10.3390/ijms22115510

    25. Xin Li, Lajos Gera, Shumin Zhang, Yanhua Chen, Lei Lou, Lauren Marie Wilson, Zhong-Ru Xie, Giuseppe Sautto, Degang Liu, Alira Danaher, Kenza Mamouni, Yang Yang, Yuhong Du, Haian Fu, Omer Kucuk, Adeboye O Osunkoya, Jia Zhou, Daqing Wu, Pharmacological inhibition of noncanonical EED-EZH2 signaling overcomes chemoresistance in prostate cancer. Theranostics 11 (14), 6873 (2021). DOI: 10.7150/thno.49235

    24. Yifei Wu, Kuan Y Chang, Lei Lou, Lorette G Edwards, Bly K Doma, Zhong-Ru Xie*, In silico identification of drug candidates against COVID-19. Informatics in Medicine Unlocked, 100461 (2020) DOI: 10.1016/j.imu.2020.100461

    23. Yifei Wu, Tze-Chen Hsieh, Joseph M. Wu, Xiaoxiao Wang, Joshua S. Christopher, Amanda H. Pham, Justin David-Li Swaby, Lei Lou, Zhong-Ru Xie*, Elucidating the Inhibitory Effect of Resveratrol and Its Structural Analogs on Selected Nucleotide-Related Enzymes. Biomolecules, 10, 1223. (2020) DOI: 10.1016/j.csbj.2021.09.022

    22. Sheng C. Lo, Zhong-Ru Xie, Kuan Y. Chang*, Structural and Functional Enrichment Analyses of Antimicrobial Peptides. International journal of molecular sciences 21 (22), 8783 (2020) DOI: 10.3390/ijms21228783

    21. Yifei Wu, Lei Lou, Zhong-Ru Xie*, A pilot study of all-computational drug design protocol -- from structure prediction to interaction analysis. Frontiers in Chemistry 8, 81 (2020) DOI: 10.3389/fchem.2020.00081

    20. Amanda H Pham, Mark Andrew Phillips, Zhong-Ru Xie*, Resveratrol and Advancing Virtual Drug Discovery. Resveratrol: State of the Art Science and Health Applications. (2018) DOI: 10.1142/9789813270916_0011

    19. Mark Andrew Phillips, Marisa A. Stewart, Darby L. Woodling, Zhong-Ru Xie*, Has Molecular Docking Ever Brought Us a Medicine? Molecular Docking. (2018)

    18. Bo Wang, Zhong-Ru Xie, Jiawen Chen, and Yinghao Wu*, Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells, Structure, 26 (10),1414-1424.e3. (2018)

    17. Zhong-Ru Xie, Jiawen Chen, and Yinghao Wu*, Predicting Protein�Protein Association Rates using Coarse-grained Simulation and Machine Learning, Scientific Reports, 7, 46622. (2017)

    16. Jiawen Chen, Zhong-Ru Xie, and Yinghao Wu*, Understand protein functions by comparing the similarity of local structural environments, Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1865 (2), 142-152 (2017)

    15. Jiawen Chen, Jillian Newhall, Zhong-Ru Xie, Deborah Leckband, and Yinghao Wu*, A Computational Model for Kinetic Studies of Cadherin Binding and Clustering, Biophysical journal 111 (7), 1507-1518 (2016)

    Publications Prior to UGA

    14. Zhong-Ru Xie, Jiawen Chen, and Yinghao Wu*, A Multi-Scale Model for the Assembling Kinetics of Protein Complexes, The Journal of Physical Chemistry B, 120(4):621-32 (2016)

    13. Jiawen Chen, Zhong-Ru Xie, and Yinghao Wu*, Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method., Journal of Computational Biology, 12 (1), 205-218 (2016)

    12. Jiawen Chen, Zhong-Ru Xie, and Yinghao Wu*, Elucidating the General Principles of Cell Adhesion with a Coarse-Grained Simulation Model, Molecular BioSystems, 12, 205-218 (2016)

    11. Jiawen Chen1, Zhong-Ru Xie1, and Yinghao Wu*, Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method, Biomechanics and Modeling in Mechanobiology, 15(2) 317-329. (2016)

    10. Zhong-Ru Xie1, Jiawen Chen1, Yilin Zhao and Yinghao Wu*, Decomposing the space of protein quaternary structures with an interface fragment pair library, BMC Bioinformatics, 16 (1): 14 (2015)

    9. Zhong-Ru Xie and Ming-Jing Hwang*, Methods for predicting protein ligand binding sites, Molecular modelling of Proteins, 2nd edition, 383-398 (2015)

    8. Zhong-Ru Xie1, Jiawen Chen1, and Yinghao Wu*, Linking 3D and 2D binding kinetics of membrane proteins by multi-scale simulations, Protein Science, 23 (12): 1789-1799 (2014)

    7. Jiawen Chen1, Zhong-Ru Xie1, and Yinghao Wu*, A multiscale model for simulating binding kinetics of proteins with flexible linkers, Proteins: Structure, Function and Bioinformatics, 82(10):2512-22 (2014)

    6. Zhong-Ru Xie, Jiawen Chen, and Yinghao Wu*, A Coarse-grained model for the simulations of biomolecular interactions in cellular environments, The Journal of Chemical Physics, 140(5): 054112 (2014)

    5. Jiawen Chen, Zhong-Ru Xie, and Yinghao Wu*, Computational modeling of the interplay between cadherin-mediated cell adhesion and Wnt signaling pathway, PLOS ONE, 9(6):e100702 (2014)

    4. Zhong-Ru Xie, Chuan-Kun Liu, Fang-Chih Hsiao, Adam Yao and Ming-Jing Hwang*, LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites, Nucleic Acids Research, 41:W292-6 (2013)

    3. Zhong-Ru Xie and Ming-Jing Hwang*, Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles, Bioinformatics, 28(12): 1579-85 (2012)

    2. Zhong-Ru Xie and Ming-Jing Hwang*, An interaction-motif-based scoring function for protein-ligand docking, BMC Bioinformatics, 11: 298 (2010)

    1. Zhong-Ru Xie1, Hsih-Te Yang1, Wei-Chung Liu, and Ming-Jing Hwang*, The role of microRNA in the delayed negative feedback regulation of gene expression, Biochemical and Biophysical Research Communications, 358(3):722-726 (2007)

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