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Core Faculty

Shi-Jie Chen, Ph.D.


Office: 302 Physics Building

Phone: (573) 882-6626


Lab URL:

Home Department: Physics

Concentration: Bioinformatics

Education: PhD, University of California- San Diego

The current experiments on structural determination for RNA molecules cannot keep up the pace with the steadily emerging RNA sequences and new functions. This underscores the request for an accurate model for RNA three-dimensional (3D) structural prediction. Although considerable progress has been made in mechanistic studies, accurate prediction for RNA tertiary folding from sequence remains an unsolved problem. The first and most important requirement for predicting of RNA structure from physical principles is an accurate free energy model. Based on rigorous physical principles, Chen’s lab is developing computational models to predict 3D tertiary structures, energy landscapes, and kinetic mechanisms for biologically significant RNA molecules and from the physical model, to analyze and predict RNA functions in gene regulation. In parallel to the theory development, the Chen lab is developing strategies to apply the computational models developed in the lab to a broad range of problems directly related to human health such as the rational design and selection of RNA-based therapeutic drugs.

Selected Publications

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Chen, S J

NMR study of RNA structures in the 3´-end of the Hepatitis C Virus genome. (Journal Article)

Biochemistry, 56 , pp. 4972-4984, 2017.


Miao, Z; Adamiak, R W; Antczak, M; Batey, R T; Becka, A J; Biesiada, M; Boniecki, M J; Bujnicki, J M; Chen, S J; Cheng, C Y; Chou, F C; Ferre-D'Amare, A R; Das, R; Dawson, W K; Ding, F; Dokholyan, N V; Dunin-Horkawicz, S; Geniesse, C; Kappel, K; Kladwang, W; Krokhotin, A; Lach, G E; Major, F; Mann, T H; Magnus, M; Pachulska-Wieczorek, K; Patel, D J; Piccirilli, J A; Popenda, M; Purzycka, K J; Ren, A; Rice, G M; Santalucia, Jr. J; Sarzynska, J; Szachniuk, M; Tandon, A; Trausch, J J; Tian, S; Wang, J; Weeks, K M; Williams, 2nd B; Xiao, Y; Xu, X; Zhang, D; Zok, T; Westhof, E

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (Journal Article)

RNA, 23 (5), pp. 655-672, 2017, ISSN: 1469-9001 (Electronic) 1355-8382 (Linking).

(Links | BibTeX)

Sun, L Z; Chen, S J

A New Method to Predict Ion Effects in RNA Folding (Journal Article)

Methods Mol Biol, 1632 , pp. 1-17, 2017, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

(Links | BibTeX)

Sun, L Z; Kranawetter, C; Heng, X; Chen, S J

Predicting Ion Effects in an RNA Conformational Equilibrium (Journal Article)

J Phys Chem B, 121 (34), pp. 8026-8036, 2017, ISSN: 1520-5207 (Electronic) 1520-5207 (Linking).

(Links | BibTeX)

Sun, L Z; Zhang, D; Chen, S J

Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules (Journal Article)

Annu Rev Biophys, 46 , pp. 227-246, 2017, ISSN: 1936-1238 (Electronic) 1936-122X (Linking).

(Links | BibTeX)

Sun, L Z; Zhang, J X; Chen, S J

MCTBI: a web server for predicting metal ion effects in RNA structures (Journal Article)

RNA, 23 (8), pp. 1155-1165, 2017, ISSN: 1469-9001 (Electronic) 1355-8382 (Linking).

(Links | BibTeX)

Xu, X; Duan, D; Chen, S J

CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment (Journal Article)

Sci Rep, 7 (1), pp. 143, 2017, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking).

(Links | BibTeX)

Zhao, C; Xu, X; Chen, S J

Predicting RNA Structure with Vfold (Journal Article)

Methods Mol Biol, 1654 , pp. 3-15, 2017, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

(Links | BibTeX)


Sun, L Z; Chen, S J

Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations (Journal Article)

J Chem Theory Comput, 12 (7), pp. 3370-81, 2016, ISSN: 1549-9626 (Electronic) 1549-9618 (Linking).

(Links | BibTeX)

Urak, K T; Shore, S; Rockey, W M; Chen, S J; McCaffrey, A P; Giangrande, P H

In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs (Journal Article)

Methods, 103 , pp. 167-74, 2016, ISSN: 1095-9130 (Electronic) 1046-2023 (Linking).

(Links | BibTeX)

35 entries « 1 of 4 »