个人信息
Personal Information
联系方式
Contact Information
个人简介
Personal Profile
2010.9-2015.7，武汉大学，研究生，获理学博士学位；
2015.7-至今，武汉纺织大学，副教授；
2022.3–2023.3，深圳湾实验室，访问学者（合作导师：周耀旗研究员；
2024.1–2025.1，澳大利亚Griffith University信息与通信技术学院（ICT），从事访问研究（合作导师：Prof. Alan Liew）。
长期致力于生物大分子空间结构与功能的理论建模与智能计算。其研究特色在于：
1. 基于物理原理与能量函数开展RNA/DNA折叠动力学与空间结构预测研究；
2. 融合图神经网络与深度学习方法，发展RNA结构合理性评估与序列设计的新型算法；
3. 探索生命系统的数学与物理建模，并将相关方法应用于复杂疾病（如肿瘤）的发生发展机制解析。
迄今已在Nucleic Acids Research、PLoS Computational Biology、Biophysical Journal、The Journal of Chemical Physics、RNA、Molecules 等国际主流SCI期刊发表论文30余篇；主持国家自然科学基金面上项目、青年项目各1项，以及湖北省科技厅和教育厅科研项目多项。
上传附件
支持扩展名：.rar .zip .doc .docx .pdf .jpg .png .jpeg上传附件
支持扩展名：.rar .zip .doc .docx .pdf .jpg .png .jpeg上传附件
支持扩展名：.rar .zip .doc .docx .pdf .jpg .png .jpeg1. 国家自然科学基金面上项目，2026.1.1-2029.12.31, 48万，主持，在研
2. 国家自然科学基金青年项目，2017.1.1-2019.12.31，20万， 主持，结题
3. 国家自然科学基金面上项目， 2023.1.1-2026.12.31,42万，参与，在研
4. 湖北省自然科学基金面上项目，2018.1.1-2020.12.31， 5万，主持，结题
5. 湖北省教育厅人才项目， 2017.1.1-2018.12.31, 3万元，主持，结题
6. 校企合作项目，基于机器学习的单细胞数据挖掘，2023.1.1-2024.12.31，60万，主持，结题
(25) Wang X, Zhou Z, Yu S, Tan YL*, Shi Ya-Zhou*, Tan ZJ*. TiRNA: a coarsegrained method with temperature and ion effects for RNA structure folding and prediction. Nucleic Acids Res. 54(2):gkaf1499, 2026.
(24) Li S, Xu Q, Tan, Y.-L, Jiang J, Zhang B, and Shi, YZ*. gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure. Biomolecules, 16(2), 230, 2026.
(23) Wang X, Shi YZ*. Spatial confinement reshapes the folding of an ion-stabilized DNA with a three-way junction. Chinese Journal of Physics, 102, 472-488, 2026.
(22) Yang H, Qiao N, Zhang B, Shi Y.-Z*, and Tan Y.-L*. R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure. Biology, 15(6), 457, 2026
(21) Xunxun Wang, Ya-Zhou Shi*. 3D structure and stability prediction of DNA withmulti-way junctions in ionic solutions. PLoS Comput Biol 21(8): e1013346, 2025.
(20) Zi-Chun Mu#, Ya-Lan Tan#, Ben-Gong Zhang, Jie Liu, Ya-Zhou Shi*. Ab initiopredictions for 3D structure and stability of single- and double-stranded DNAs inion solutions. PLoS Comput Biol, 18(10):e1010501, 2022.
(19) Ya-Zhou Shi#, Hao Wu#, Sha-Sha Li, Hui-Zhen Li, Ben-Gong Zhang*, Ya-LanTan*. ABC2A: A straightforward and fast method for the accurate backmapping ofRNA coarse-grained models to all-atom structures. Molecules, 29:1244, 2024.
(18) Jinle Tang#, Ya-Zhou Shi#, Zhe Zhang, Dailin Luo, Jian Zhan*, Yaoqi Zhou*.RNA-MobiSeq: Deep mutational scanning and mobility-based selection for RNAstructure inference. bioRxiv 2024.02.21.581340, 2024 (Nature Communication, Under review).
(17) Rui Sun, Wenjie Cao, Shengxuan Li, Jian Jiang, Ya-Zhou Shi*, Bengong Zhang*.scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data andgene regulation network-based transfer entropy. PLoS Comput Biol,20(11):e1012638, 2024.
(16) Ben-Gong Zhang, Hua-Hai Qiu, Jian Jiang, Jie Liu, Ya-Zhou Shi*. 3D structurestability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study. JChem Phys, 151:165101, 2019.
(15) Zi-Chun Mu, Ya-Lan Tan, Jie Liu, Ben-Gong Zhang*, Ya-Zhou Shi*.Computational modeling of DNA 3D structures: From dynamics and mechanics tofolding. Molecules, 28(12):4833, 2023. (Invited review)
(14) Xunxun Wang#, Shixiong Yu#, Chenyu Zhouzou, Ya-Lan Tan*, Ya-Zhou Shi*,Zhi-Jie Tan*. TiRNA: a coarse-grained method with temperature and ion effects forRNA structure folding and prediction. 2025 (Nucleic Acids Res, Under review).
(13) Ya-Zhou Shi, Shasha Li, Ya-Lan Tan, Jian Jiang, Bengong Zhang, Shirui Pan*,Alan Wee-Chung Liew*. pgRNA: A physics-guided graph neural network forrobust RNA 3D structure evaluation. 2025 (In preparation).
(12) Ya-Zhou Shi#, Feng-Hua Wang#, Yuan-Yan Wu, Zhi-Jie Tan*. A coarse-grainedmodel with implicit salt for RNAs: predicting 3D structure, stability and salt effect.J Chem Phys, 141:105102, 2014.
(11) Ya-Zhou Shi, Lei Jin, Feng-Hua Wang, Xiao-Long Zhu, and Zhi-Jie Tan*.Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent anddivalent ion solutions. Biophys J, 109:2654-2665, 2015.
(10) Ya-Zhou Shi#, Lei Jin#, Chen-Jie Feng, Ya-Lan Tan, Zhi-Jie Tan*. Predicting 3Dstructure and stability of RNA pseudoknots in monovalent and divalent ionsolutions. PLoS Comput Biol, 14:e1006222, 2018.
(9) Ya-Zhou Shi, Yuan-Yan Wu, Feng-Hua Wang, Zhi-Jie Tan*. RNA structureprediction: Progress and perspective. Chin Phys B, 23:078701, 2014. (Invitedreview)
(8) Chen-Jie Feng, Ya-Lan Tan, Yu-Xuan Cheng, Ya-Zhou Shi*, Zhi-Jie Tan*.Salt-dependent RNA pseudoknot stability: effect of spatial confinement. Front MolBiosci, 8:666369, 2021.
(7) Lei Jin, Ya-Lan Tan, Yao Wu, Xunxun Wang, Ya-Zhou Shi*, Zhi-Jie Tan*.Structure folding of RNA kissing complexes in salt solutions: predicting 3Dstructure, stability and folding pathway. RNA, 117, 74-86, 2019.
(6) Lei Jin#, Ya-Zhou Shi#, Chen-Jie Feng, Ya-Lan Tan, Zhi-Jie Tan*. Modelingstructure, stability, and flexibility of double-stranded RNAs in salt solutions. Biophy.J, 115, 1403-1416, 2018.
(5) Zhi-Hao Guo, Li Yuan, Ya-Lan Tan, Ben-Gong Zhang and Ya-Zhou Shi*. RNAStat:An integrated tool for statistical analysis of RNA 3D structures. Front Bioinform,1:809082, 2022.
(4) Yi Yang, Qi Gu, Ben-Gong Zhang, Ya-Zhou Shi*, Zhi-Gang Shao*. A novelknowledge-based potential for RNA 3D structure evaluation. Chin Phys B, 27:038701, 2018.
(3) Ya-Zhou Shi, Xiangpeng Li, Ben-Gong Zhang*. Traveling wave solutions of twononlinear wave equations by (G’/G)-expansion method. Adv Math Phys,2018:8583418, 2018.
(2) Ya-Lan Tan, Xunxun Wang, Ya-Zhou Shi, Wenbing Zhang*, Zhi-Jie Tan*.rsRNASP: A residue-separation-based statistical potential for RNA 3D structureevaluation. Biophys J, 121:142-156, 2022.
(1) Xunxun Wang, Ya-Lan Tan, Shixiong Yu, Ya-Zhou Shi, Zhi-Jie Tan*. Predicting3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophys J, 122:1503-1516 2023.
文件上传中...
