Shi-jie Chen



Curators Distinguished Professor



BS Physics Zhejiang University China
PhD Physics University of California, San Diego San Diego, Calif.

Research Area

Prediction of RNA structure and functions and computational design of RNA-based therapeutic strategies.

Research Description

We develop computer models for biomolecular structure and function with focus on RNA molecules. Biological molecules are large organic molecules composed of hundreds or thousands of atoms bound together by covalent bonds into a chain-like structure. One of the best known challenges in biology is to understand how biomolecules fold properly into compact structures to perform biological functions and how they misfold to cause disease. We develop computational methods to study RNA folding, predict RNA 3D structures, and model RNA-small molecule and RNA-metal ion interactions, RNA in vivo folding kinetics, and cellular functions at the level of gene expression and regulation. Furthermore, through collaborations with experimental labs, we design RNA-based therapeutic strategies involving aptamer binding and CRISPR-Cas9 gene editing.

Notable Honors and Service

  • Fellow, American Association for the Advancement of Science, 2018
  • Curators Distinguished Professor, University of Missouri System, 2018
  • Founding Council Member: International Society of RNA Nanotechnology and Nanomedicine (ISRNN), 2017
  • Fellow, American Physical Society, 2013

Selected Publications

Sun LZ, Zhou Y, Chen SJ. (2019). Predicting Monovalent Ion Correlation Effects in Nucleic Acids. ACS Omega. 4(8):13435-13446. doi: 10.1021/acsomega.9b01689. eCollection 2019 Aug 20. [PubMed]

Chen SJ. (2019). Minimizing off-target effects in CRISPR-Cas9 genome editing. Cell Biol Toxicol. 2019 Jul 17. doi: 10.1007/s10565-019-09486-4. Epub ahead of print. [PubMed]

Xu X, Zhao C, Chen SJ. (2019). VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures. J Struct Biol. 207(3):235-240. doi: 10.1016/j.jsb.2019.06.002. [PubMed]

Chen SJ. (2019). Site-Specific Binding of Non-Site-Specific Ions. Biophys J. 116(12):2237-2239. doi: 10.1016/j.bpj.2019.04.038. [PubMed]

Zhang D, Hurst T, Duan D, Chen SJ. (2019). Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proc Natl Acad Sci U S A. 116(18):8693-8698. doi: 10.1073/pnas.1820523116. [PubMed]

Sun LZ, Chen SJ. (2019). Predicting RNA-Metal Ion Binding with Ion Dehydration Effects. Biophys J. 116(2):184-195. doi: 10.1016/j.bpj.2018.12.006. [PubMed]

Sun TT, Zhao C, Chen SJ. (2018). Predicting Cotranscriptional Folding Kinetics For Riboswitch. J Phys Chem B. 122(30):7484-7496. doi: 10.1021/acs.jpcb.8b04249. [PubMed]

Hurst T, Xu X, Zhao P, Chen SJ. (2018). Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. J Phys Chem B. 122(18):4771-4783. doi: 10.1021/acs.jpcb.8b00575. [PubMed]

Yu T, Chen SJ. (2018). Hexahydrated Mg(2+) Binding and Outer-Shell Dehydration on RNA Surface. Biophys J. 114(6):1274-1284. doi: 10.1016/j.bpj.2018.01.040. [PubMed]

Zhang D, Chen SJ. (2018). IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. J Chem Theory Comput. 14(4):2230-2239. doi: 10.1021/acs.jctc.7b01228. [PubMed]

Sun LZ, Heng X, Chen SJ. (2017). Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation. Front Mol Biosci. 4:92. doi: 10.3389/fmolb.2017.00092. eCollection 2017. Review. [PubMed]

Xu X, Chen SJ. (2018). Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. J Phys Chem B. 122(21):5327-5335. doi: 10.1021/acs.jpcb.7b10102. [PubMed]

Zhao C, Xu X, Chen SJ. (2017). Predicting RNA Structure with Vfold. Methods Mol Biol. 1654:3-15. doi: 10.1007/978-1-4939-7231-9_1. [PubMed]

Kranawetter C, Brady S, Sun L, Schroeder M, Chen SJ, Heng X. (2017). Nuclear Magnetic Resonance Study of RNA Structures at the 3′-End of the Hepatitis C Virus Genome. Biochemistry. 56(37):4972-4984. doi: 10.1021/acs.biochem.7b00573. [PubMed]

Sun LZ, Kranawetter C, Heng X, Chen SJ. (2017). Predicting Ion Effects in an RNA Conformational Equilibrium. J Phys Chem B. 121(34):8026-8036. doi: 10.1021/acs.jpcb.7b03873. [PubMed]

Sun LZ, Chen SJ. (2017). A New Method to Predict Ion Effects in RNA Folding. Methods Mol Biol. 1632:1-17. doi: 10.1007/978-1-4939-7138-1_1. [PubMed]