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Jun Li , Ph.D.

职务：助理教授

邮箱：lijun@gbu.edu.cn

主页：https://scholar.google.com/citations?user=kWD4n-AAAAAJ&hl=en

Research Areas

uRNA structure prediction                            uBiophysics

uBioinformatics                                                  uMachine learning

Education Qualifications

u2011.09-2018.12, Doctor of Philosophy in Physics, Nanjing University

u2007.09-2011.06, Bachelor of Science in Physics, Nanjing University

Academic Experience

u2018.12-2023.11, Postdoctoral Research Fellow in Physics, University of Missouri-Columbia, USA

Selected Publications

1．Li J, Chen SJ. RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling. Nucleic Acids Research. 2023; 51(7):3341-56.

2．Li J, Zhu W, Wang J, Li W, Gong S, Zhang J, Wang W. RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks. PLoS Computational Biology. 2018; 14(11):e1006514

3．Li J, Zhang J, Wang J, Li W, Wang W. Structure prediction of RNA loops with a probabilistic approach. PLoS Computational Biology. 2016; 12(8):e1005032.

4．Li J, Zhang S, Zhang D, Chen SJ. Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences. Bioinformatics. 2022; 38(16):4042-3.

5．Li J, Chen SJ. RNA 3D structure prediction using coarse-grained models. Frontiers in Molecular Biosciences. 2021; 8:720937.

6．Li J, Zhang S, Chen SJ. Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15. Proteins: Structure, Function, and Bioinformatics. 2023.

7．Li J, Walter, G. Nils, Chen SJ. smFRET-assisted RNA structure prediction. Communications in Information and Systems. 2024; Accepted, in press.

8．Li J, Chen SJ. Embracing exascale computing in nucleic acid simulations. Current Opinion in Structural Biology. 2024; 87:102847.

9．Zhang D*, Li J*, Chen SJ. IsRNA1: de novo prediction and blind screening of RNA 3D structures. Journal of Chemical Theory and Computation. 2021; 17(3):1842-57.

10．Zhang S*, Li J*, Chen SJ. Machine learning in RNA structure prediction: advances and challenges. Biophysical Journal. 2024.

11．Wang YZ*, Li J*, Zhang S, Huang B, Yao G, Zhang J. An RNA scoring function for tertiary structure prediction based on multi-layer neural networks. Molecular Biology. 2019; 53(1):118-26.

12．Zhou Y, Li J, Hurst T, Chen SJ. SHAPER: A web server for fast and accurate SHAPE reactivity prediction. Frontiers in Molecular Biosciences. 2021; 8:721955.

13．Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K. Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models. International Journal of Molecular Sciences. 2022; 23(17):9630.

14．Samuelian JS, Gremminger TJ, Song Z, Poudyal RR, Li J, Zhou Y, Staller SA, Carballo JA, Roychowdhury-Saha M, Chen SJ, Burke DH. An RNA aptamer that shifts the reduction potential of metabolic cofactors. Nature Chemical Biology. 2022; 18(11):1263-9.

15．Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Research. 2021; 49(10):5925-42.