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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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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)

Xu, X; Chen, S J

A Method to Predict the Structure and Stability of RNA/RNA Complexes (Journal Article)

Methods Mol Biol, 1490 , pp. 63-72, 2016, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

(Links | BibTeX)

Xu, X; Dickey, D D; Chen, S J; Giangrande, P H

Structural computational modeling of RNA aptamers (Journal Article)

Methods, 103 , pp. 175-9, 2016, ISSN: 1095-9130 (Electronic) 1046-2023 (Linking).

(Links | BibTeX)

Xu, X; Yu, T; Chen, S J

Understanding the kinetic mechanism of RNA single base pair formation (Journal Article)

Proc Natl Acad Sci U S A, 113 (1), pp. 116-21, 2016, ISSN: 1091-6490 (Electronic) 0027-8424 (Linking).

(Links | BibTeX)


Miao, Z; Adamiak, R W; Blanchet, M F; Boniecki, M; Bujnicki, J M; Chen, S J; Cheng, C; Chojnowski, G; Chou, F C; Cordero, P; Cruz, J A; Ferre-D'Amare, A R; Das, R; Ding, F; Dokholyan, N V; Dunin-Horkawicz, S; Kladwang, W; Krokhotin, A; Lach, G; Magnus, M; Major, F; Mann, T H; Masquida, B; Matelska, D; Meyer, M; Peselis, A; Popenda, M; Purzycka, K J; Serganov, A; Stasiewicz, J; Szachniuk, M; Tandon, A; Tian, S; Wang, J; Xiao, Y; Xu, X; Zhang, J; Zhao, P; Zok, T; Westhof, E

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (Journal Article)

RNA, 21 (6), pp. 1066-84, 2015, ISSN: 1469-9001 (Electronic) 1355-8382 (Linking).

(Links | BibTeX)

Xu, X; Chen, S J

Physics-based RNA structure prediction (Journal Article)

Biophys Rep, 1 , pp. 2-13, 2015, ISSN: 2364-3439 (Print) 2364-3439 (Linking).

(Links | BibTeX)

Zhang, X; Xu, X; Yang, Z; Burcke, A J; Gates, K S; Chen, S J; Gu, L Q

Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel (Journal Article)

J Am Chem Soc, 137 (50), pp. 15742-52, 2015, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking).

(Links | BibTeX)

Zhu, Y; He, Z; Chen, S J

TBI server: a web server for predicting ion effects in RNA folding (Journal Article)

PLoS One, 10 (3), pp. e0119705, 2015, ISSN: 1932-6203 (Electronic) 1932-6203 (Linking).

(Links | BibTeX)


Cao, S; Xu, X; Chen, S J

Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing (Journal Article)

RNA, 20 (6), pp. 835-45, 2014, ISSN: 1469-9001 (Electronic) 1355-8382 (Linking).

(Links | BibTeX)

He, Z; Zhu, Y; Chen, S J

Exploring the electrostatic energy landscape for tetraloop-receptor docking (Journal Article)

Phys Chem Chem Phys, 16 (14), pp. 6367-75, 2014, ISSN: 1463-9084 (Electronic) 1463-9076 (Linking).

(Links | BibTeX)

24 entries « 1 of 3 »