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Yue Qiu, Hongyang Wang, Huaye Pan, Jing Guan, Lei Yan, Mingjie Fan, Hui Zhou, Xuanhao Zhou, Kaiwen Wu, Zexiao Jia, Qianqian Zhuang, Zhaoying Lei, Mengyao Li, Xue Ding, Aifu Lin, Yong Fu, Dong Zhang, Qiuju Wang, Qingfeng Yan. AIFM1 variants associated with auditory neuropathy spectrum disorder cause apoptosis due to impaired apoptosis-inducing factor dimerization. Journal of Zhejiang University-SCIENCE B 24 (2), 172-184 (2023)
Deyin Wang, Xiaohui Wen, Dong Zhang, Xinguan Tan, Jiajun Tang. Single-polymer dynamics of starch-like branched ring polymers in steady shear flow. International Journal of Biological Macromolecules 227, 173-181 (2022)
Deyin Wang, Xiaohui Wen, Dong Zhang, Jiajun Tang. Dynamical and Structural Properties of Comb Long-Chain Branched Polymer in Shear Flow. International Journal of Molecular Sciences 23 (19), 11290 (2022)
Julita Gumna, Maciej Antczak, Ryszard W Adamiak, Janusz M Bujnicki, Shi-Jie Chen, Feng Ding, Pritha Ghosh, Jun Li, Sunandan Mukherjee, Chandran Nithin, Katarzyna Pachulska-Wieczorek, Almudena Ponce-Salvatierra, Mariusz Popenda, Joanna Sarzynska, Tomasz Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Zok, Eric Westhof, Zhichao Miao, Marta Szachniuk, Agnieszka Rybarczyk. Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models. International Journal of Molecular Sciences 23 (17), 9630 (2022)
Jun Li, Sicheng Zhang, Dong Zhang, Shi-Jie Chen. Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences. Bioinformatics 38 (16), 4042-4043 (2022)
Yi Cheng, Dong Zhang, Travis Hurst, Xiaoqin Zou, Paloma H Giangrande, Shi-Jie Chen. RNA Structural Modeling for Therapeutic Applications. RNA Nanotechnology and Therapeutics, 447-461 (2022)
Ke Li, Jiaxin Wu, Fuchen Guo, Yaxin Wang, Dong Zhang#, Linxi Zhang#. Sliding dynamics of ring on a fixed rod-like block copolymer in rotaxane: Molecular dynamics simulations vs Lifson-Jackson formula. Polymer 246, 124773 (2022)
Deyin Wang, Xiaohui Wen, Dong Zhang, Aihua Chai. External-induced self-assembly of semi-flexible polymers on spherical shell. Computational Materials Science 203, 111130 (2022)
Chady H Hakim, Sandeep RP Kumar, Dennis O Pérez-López, Nalinda B Wasala, Dong Zhang, Yongping Yue, James Teixeira, Xiufang Pan, Keqing Zhang, Emily D Million, Christopher E Nelson, Samantha Metzger, Jin Han, Jacqueline A Louderman, Florian Schmidt, Feng Feng, Dirk Grimm, Bruce F Smith, Gang Yao, N Nora Yang, Charles A Gersbach, Shi-jie Chen, Roland W Herzog, Dongsheng Duan. Cas9-specific immune responses compromise local and systemic AAV CRISPR therapy in multiple dystrophic canine models. Nature communications 12 (1), 6769 (2021)
Dong Zhang, Shi-Jie Chen, Ruhong Zhou. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. The Journal of Physical Chemistry B 125 (43), 11907–11915 (2021)
Rui Ye, Wei Song, Xinwen Ou, Zonglin Gu, Dong Zhang. Membrane Insertion of MoS2 Nanosheets: Fresh vs. Aged. Frontiers in Chemistry 9, 706917 (2021)
Dong Zhang*, Jun Li*, Shi-Jie Chen. IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. Journal of chemical theory and computation 17 (3), 1842-1857 (2021)
Travis Hurst, Dong Zhang, Yuanzhe Zhou, Shi-Jie Chen. A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field. Communications in information and systems 21 (1), 65 (2021)
Chenhan Zhao*, Dong Zhang*, Yangwei Jiang, and Shi-Jie Chen. Modeling loop composition and ion concentration effects in RNA hairpin folding stability. Biophysical Journal 119 (7), 1439-1455 (2020)
Jakub Ptacek, Dong Zhang, Liming Qiu, Sven Kruspe, Lucia Motlova, Petr Kolenko, Zora Novakova, Shambhavi Shubham, Barbora Havlinova, Petra Baranova, Shi-Jie Chen, Xiaoqin Zou, Paloma Giangrande, and Cyril Barinka. Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nucleic Acids Research 48 (19), 11130-11145 (2020)
Zhichao Miao, …, Dong Zhang, …, Eric Westhof. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA 26 (8), 982-995 (2020)
Phuong D. M. Nguyen, Jie Zheng, Thomas Gremminger, Liming Qiu, Dong Zhang, Steve Tuske, Margaret J. Lange, Patrick R. Griffin, Eddy Arnold, Shi-Jie Chen, Xiaoqin Zou, Xiao Heng, and Donald H. Burke. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Research 48 (5), 2709-2722 (2020)
Dong Zhang, Travis Hurst, Dongsheng Duan, and Shi-Jie Chen. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proceedings of the National Academy of Sciences U.S.A. 116 (18), 8693-8698 (2019)
Dong Zhang and Shi-Jie Chen. IsRNA: an iterative simulated reference state approach to modeling correlated interactions in RNA folding. Journal of chemical theory and computation 14 (4), 2230-2239 (2018)
Xinyue Zhang*, Dong Zhang*, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J. Burcke, Jing Wang, Shi-Jie Chen, and Li-Qun Gu. Nanopore electric snapshots of an RNA tertiary folding pathway. Nature Communications 8 (1), 1458 (2017)
Lizhen Sun*, Dong Zhang*, and Shi-Jie Chen. Theory and modeling of RNA structure and interactions with metal ions and small molecules. Annual review of biophysics 46, 227-246 (2017)
Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, …, Dong Zhang, Tomasz Zok, and Eric Westhof. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 23 (5), 655-672 (2017)
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