Shi-Jie Chen Research Group

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Publications since 2000

Hurst, T, Xu, XJ, Zhao, PN, Chen, SJ. (2018) Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. J. Phys. Chem. B. DOI: 10.1021/acs.jpcb.8b00575

Zhang, D and Chen, SJ. (2018) IsRNA: An iterative simulated reference state approach to modeling correlated interactions in RNA folding. J. Chem. Theory Comput., 2018, 14 (4), pp 2230–2239. DOI: 10.1021/acs.jctc.7b01228

Yu, T, Chen, SJ. (2018) Hexahydrated Mg2+ Ion Binding and Outer-Shell Dehydration on RNA Surface. Biophys J. 114: 1274-1284. doi: 10.1016/j.bpj.2018.01.040.

Xu, X, Chen, SJ. (2017) Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. The Journal of Physical Chemistry-B. J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.7b10102

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 [Article]

Xinyue Zhang+, Dong Zhang+, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew Burcke, Jing Wang, Shi-Jie Chen*, and Li-Qun Gu* (2017) Nanopore electric snapshots of an RNA tertiary folding pathway. Nature Communications. 8: 1458. doi:10.1038/s41467-017-01588-z.

Kranawetter, C., Brady, S., Sun, LZ., Schroeder, M., Chen, SJ.*, Heng, X.* (2017) NMR study of RNA structures in the 3´-end of the Hepatitis C Virus genome. Biochemistry. 56: 4972-4984.

Sun, LZ, Kranawetter, C., Heng, X.*, Chen, SJ.* (2017) Predicting Ion Effects in RNA Conformational Equilibrium. The Journal of Physical Chemistry-B. 121: 8026–8036.

Sun, LZ, Zhang, JX, Chen, SJ. (2017) MCTBI: a web server for predicting metal ion effects in RNA structures. RNA. 23: 1155-1165. doi: 10.1261/rna.060947.117. [Faculty of 1000 Recommended]

Xu, X, Duan, DS, Chen, SJ. (2017) CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment. Sci Rep. 7(1):143. doi: 10.1038/s41598-017-00180-1.

Sun, LZ+, Zhang, D+, Chen, SJ. (2017) Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules. Annu Rev Biophys. 46:227-246. doi: 10.1146/annurev-biophys-070816-033920.

Sun, LZ and 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.

Zhao, CH, Xu, XJ, Chen SJ. (2017) Predicting RNA structure with Vfold. Methods in Molecular Biology, 1654: 3-15.

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferre-D'Amare AR, Das R, Dawson WK, Feng D, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S5, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 23(5):655-672. doi: 10.1261/rna.060368.116.

Xu, X and Chen, SJ. (2016) VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. PLoS One. 11(9):e0163454. doi: 10.1371/journal.pone.0163454.

Yu T, Zhu Y, He Z, Chen SJ. (2016) Predicting Molecular Crowding Effects in Ion-RNA Interactions. J Phys Chem B. 120(34):8837-44. doi: 10.1021/acs.jpcb.6b05625. PMID: 27490487.

Sun, LZ and Chen, SJ. (2016) Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations. J Chem Theory Comput. 12(7):3370-81. doi: 10.1021/acs.jctc.6b00028.

Xu, XJ., Dickey, DD., Chen, SJ., Giangrande, P. (2016) Structural Computational Modeling of RNA Aptamers. Methods. 103:175-9. doi: 10.1016/j.ymeth.2016.03.004.

Urak KT, Shore S, Rockey WM, Chen SJ, McCaffrey AP, Giangrande PH. (2016) In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs. Methods. S1046-2023(16)30037-8. doi: 10.1016/j.ymeth.2016.03.003

Xu, XJ., Chen, SJ. (2016) A method to predict the structure and stability of RNA/RNA complexes. Methods Mol Biol. 1490:63-72. doi: 10.1007/978-1-4939-6433-8_5.

Xu, XJ., Yu, T., Chen, SJ. (2016) Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A. 113(1):116-21. doi: 10.1073/pnas.1517511113. [PDF] [Faculty of 1000 Recommended]

Zhang, XY., Xu, XJ., Yang, ZY., Burcke, AJ., Gates, KS., Chen, SJ.*, Gu, LQ.* (2015) Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel. J. Am. Chem. Soc. 2015, 137, 15742−15752. DOI: 10.1021/jacs.5b07910. [PDF] *Corresponding authors.

Xu, XJ., Chen, SJ. (2015) Physics-based RNA structure prediction. Biophysics Reports. DOI: 10.1007/s41048-015-0001-4. [PDF]

Zhichao Miao, Ryszard W. Adamiak, Marc-Frederick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi-Jie Chen, Clarence Cheng, Grzegorz Chojnowski, Fang-Chieh Chou, Pablo Cordero, Jose Almeida Cruz, Adrian R. Ferre-D'Amare, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Stanislaw Dunin-Horkawicz, Wipapat Kladwang, Andrey Krokhotin, Grzegorz Lach, Marcin Magnus, François Major, Thomas H. Mann, Benoit Masquida, Dorota Matelska, Melanie Meyer, Alla Peselis, Mariusz Popenda, Katarzyna J. Purzycka, Alexander Serganov, Juliusz Stasiewicz, Marta Szachniuk, Arpit Tandon, Siqi Tian, Jian Wang, Yi Xiao, Xiaojun Xu, Jinwei Zhang, Peinan Zhao, Tomasz Zok, and Eric Westhof (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA, 21:1-19. [PDF]

Zhu, YH, He, ZJ., Chen, SJ. (2015) TBI server: a web server for predicting ion effects in RNA folding. PLoS ONE doi: 10.1371/journal.pone.0119705. [PDF]

Shi-Jie Chen and Donald Burke (ed) (2015) Computational Methods for Understanding Riboswitches, Volume 553, Methods in Enzymology, Academic Press. ISBN-13: 978-0128014295, ISBN-10: 0128014296. [Elsevier Link]; [Amazon Link]

Xu, XJ., Chen, SJ. (2015) A Method to Predict the 3D Structure of an RNA Scaffold. Methods Mol Biol. 1316: 1-11. doi: 10.1007/978-1-4939-2730-2_1. [PDF]

Xu, XJ., Zhao, PN., Chen, SJ. (2014) Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS ONE doi: 10.1371/journal.pone.0107504. [PDF]

Zhu, YH., Chen, SJ. (2014) Many-body effect in ion binding to RNA. J. Chem. Phys. [Featured article], 141, 055101 (2014); http://dx.doi.org/10.1063/1.489065 [PDF]

Cao, S*, Xu, XJ,*, Chen, SJ. (2014) Predicting Structure and Stability for RNA Complexes with Intermolecular Loop-loop Base Pairing. RNA, 20:835-45. doi: 10.1261/rna.043976.113. *Equal first author. [PDF]

He, ZJ., Zhu, YH., Chen, SJ. (2014) Exploring Electrostatic Energy Landscape for Tetraloop-Receptor Docking. Phys. Chem. Chem. Phys., 16 (14), 6367-6375. http://xlink.rsc.org/?doi=C3CP53655F . [PDF]

K Tian, Z He, Y Wang, SJ Chen, LQ Gu (2013) Designing a Polycationic Probe for Simultaneous Enrichment and Detection of microRNAs in a Nanopore. ACS Nano, 2013, 7 (5), pp 3962–3969. DOI: 10.1021/nn305789z. http://pubs.acs.org/doi/abs/10.1021/nn305789z [PDF]

He, ZJ., Chen, SJ. (2013) Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices. J. Phys. Chem. B, 117 (24), pp 7221-7227. DOI: 10.1021/jp4010955. http://pubs.acs.org/doi/abs/10.1021/jp4010955 [PDF]

Liu, L, Chen, SJ. (2012) Coarse-grained prediction of RNA loop structures. PLoS ONE. http://dx.plos.org/10.1371/journal.pone.0048460 [PDF]

Xu, XJ, Chen, SJ. (2012) Kinetic mechanism of conformational switch between bistable RNA hairpins. Journal of the American Chemical Society, 134 (30), pp 12499-12507 DOI: 10.1021/ja3013819 . [PDF]

Tan, ZJ, Chen, SJ. (2012) Ion-mediated RNA structural collapse: effect of spatial confinement. Biophysical Journal, 103 (4), 827-836. [PDF]

He, ZJ., Chen, SJ. (2012) Predicting ion-nucleic acid interactions by energy landscape-guided sampling. Journal of Chemical Theory and Computation, 8 (6), pp 2095-2102. DOI: 10.1021/ct300227a [PDF]

Jose Almeida Cruz, Marc-Frederick Blanchet, Michal Boniecki, Janusz M. Bujnick, Shi-Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Samuel Coulbourn Flores, Lili Huang, Christopher A. Lavender, Veronique Lisi, Francois Major, Katarzyna Mikolajczak, Dinshaw J. Patel, Anna Philips, Tomasz Puton, John Santalucia, Fredrick Sijenyi, Thomas Hermann, Kristian Rother, Magdalena Rother, Alexander Serganov, Marcin Skorupski, Tomasz Soltysinski, Parin Sripakdeevong, Irina Tuszynska, Kevin M. Weeks, Christina Waldsich, Michael Wildauer, Neocles B. Leontis, and Eric Westhof (2012) RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA. 18 (4) doi: 10.1261/rna.031054.111 [PDF]

Cao, S, Chen, SJ. (2012) Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol. 27: 185-212. [link]

Cao, S., Chen, SJ. (2012) A domain-based model for predicting large and complex pseudoknotted structures. RNA Biology. 9: 201-212. [PDF]

Cao, S., Chen, SJ. (2012) Predicting kissing interactions in microRNA–target complex and assessment of microRNA activity. Nucleic Acids Research doi: 10.1093/nar/gks052 [PDF]

Zhao, PN., Zhang, WB., Chen, SJ. (2011) Cotranscriptional folding kinetics of RNA secondary structures. Journal of Chemical Physics, 135, 245101 (2011); http://dx.doi.org/10.1063/1.3671644 (10 pages) [PDF]

Chen, GS, Chen, SJ. (2011) Quantitative analysis of the ion-dependent folding stability of DNA triplexes. Physical Biology. 8: 066006 (9pp) [PDF]

Cao, S., Chen, SJ. (2011) Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA. 17: 2130-2143. [PDF]

Rockey, W.M., Hernandez, F.J., Huang, S.Y., Cao, S., Howell, C.A., Thomas, G.S., Liu, X.Y., Lapteva, N., Spencer, D.M., McNamara II, J.O., Zou, X., Chen, SJ., Giangrande, P.H. (2011) Rational truncation of an RNA aptamer to prostate specific membrane antigen using computational structural modeling. Nucleic Acid Therapeutic, 21: 299-314. [PDF]

Stammler, S.N., Cao, S., Chen, SJ, Giedroc, D.P. (2011) A conserved RNA pseudoknot in a putative molecular switch domain of the 3' untranslated region of coronaviruses is only marginally stable. RNA, 17: 1747-1759. [PDF]

Tan, ZJ, Chen, SJ. (2011) Salt contribution to RNA tertiary structure folding stability. Biophysical Journal, 101: 176-187. [PDF]

Cao, S., Chen, SJ. (2011) Physics-based de novo prediction of RNA 3D structures. The Journal of Physical Chemistry B, 115:4216-26. [PDF]

Cao, S., Fuertig, B., Schwalbe, Harald., Chen, SJ. (2010) Folding Kinetics for the Conformational Switch between Alternative RNA Structures. The Journal of Physical Chemistry B, 114: 13609-13615. [PDF]

Tan, ZJ., Chen, SJ. (2010) Predicting ion binding properties for RNA tertiary structures. Biophysical Journal, 99: 1565-1576 [PDF]

Liu, L., Chen, SJ. (2010) Computing the conformational entropy for RNA folds. Journal of Chemical Physics, 132, 235104; doi:10.1063/1.3447385 (12 pages) [PDF]

Zhao, PN., Zhang, WB., Chen, SJ. (2010) Predicting Secondary Structural Folding Kinetics for Nucleic Acids. Biophysical Journal, 98: 1617-1625. [PDF]

Cao, S., Giedroc, DP., Chen, SJ. (2010) Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA, 16: 538-552. [PDF]

Chen, GS., Tan, ZJ., Chen, SJ. (2010) Salt dependent folding energy landscape of RNA three-way junction. Biophysical Journal, 98: 111-120. [PDF]

Tan, ZJ, Chen, SJ. (2010) Importance of Diffuse Metal Ion Binding to RNA, Chapter 3 in "Structural and Catalytic Roles of Metal Ions in RNA" (volume of METAL IONS IN LIFE SCIENCES), edited by Astrid Sigel, Helmut Sigel, and Roland K. O. Sigel. Royal Society of Chemistry Publishing. [PDF]

Cao, S., Chen, SJ. (2009) Predicting structures and stabilities for H-type pseudoknots with inter-helix loop. RNA, 15: 696-706. [PDF] [Faculty of 1000 Recommended]

Cao, S., Chen, SJ. (2009) A new computational approach for mechanical folding kinetics of RNA hairpins. Biophysical Journal, 96: 4024-4034 [PDF]

Tan, ZJ, Chen, SJ. (2009) Predicting electrostatic forces in RNA folding, 465: 465-487, Chapter 22 in "Biophysical Approaches to RNA Structure and Folding" (volume of Methods in Enzymology), edited by Daniel Herschlag. [PDF]

Chen, SJ. (2008) RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics. Annual Review of Biophysics 37: 197-214. (NIHMSID: 55566)[PDF]

Cao, S., Chen, SJ. (2008) Predicting ribosomal frameshifting efficiency. Physical Biology 5, 016002: 1-10. (NIHMSID: 55567)[PDF]

Tan, ZJ., Chen, SJ. (2008) Electrostatic free energy landscapes for DNA helix bending. Biophysical Journal 94: 3137-3149. (NIHMSID: 55573)[PDF]

Tan, ZJ., Chen, SJ. (2008) Salt dependence of nucleic acid hairpin stability. Biophysical Journal 95: 738-752. (NIHMSID: 55574)[PDF]

Chen, SJ., Cao, S., Kopeikin, Z., Zhang, WB. Polymer Statistical Mechanics for RNA Folding. In "Concepts in Protein Computations", (Ed. Robert L. Jernigan, Andrzej Kloczkowski), Cambridge University Press. To be published.

Cao, S., Chen, SJ. (2007) Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. Journal of Molecular Biology 367: 909-924. (PMCID: PMC1995092) [PDF]

Tan, ZJ., Chen, SJ. (2007) RNA helix stability in mixed Na+/Mg2+ solution. Biophysical Journal 92: 3615-3632. (PMCID: PMC1853146) [PDF]

Tan, ZJ., Chen, SJ. (2006) Electrostatic free energy landscape for nucleic acid helix assembly. Nucleic Acids Research 34: 6629-6639. [PDF] [Faculty of 1000 Recommended]

Cao, S., Chen, SJ. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research 34: 2634-2652, 2006. (PMCID: PMC1463895) [PDF]

Tan, ZJ., Chen, SJ. (2006) Ion-mediated nucleic acid helix-helix interactions. Biophysical Journal 91: 518-536. (PMCID: PMC1483110) [PDF]

Kopeikin, Z., Chen, SJ. (2006) Folding thermodynamics of pseudoknotted chain conformations. Journal of Chemical Physics 124, 154903: 1-13. (NIHMSID: 55563) [PDF]

Cao, S., Chen, SJ. (2006) Free energy landscapes of RNA/RNA complexes - with applications to snRNA complexes in spliceosomes. Journal of Molecular Biology 356: 292-312. (NIHMSID: 55564) [PDF]

Zhang, WB., Chen, SJ. (2006) Exploring the complex folding kinetics of RNA hairpins. 2. effect of sequence, length, and misfolded states. Biophysical Journal 90: 778-787. (PMCID: PMC1367103) [PDF]

Zhang, WB., Chen, SJ. (2006) Exploring the complex folding kinetics of RNA hairpins. 1. general folding kinetics analysis. Biophysical Journal 90: 765-777. (PMCID: PMC1367102) [PDF]

Tan, ZJ., Chen, SJ. (2006) Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophysical Journal 90: 1175-1190. (PMCID: PMC1367269) [PDF]

Chen, SJ., Tan, ZJ., Cao, S., Zhang, WB. (2006) Statistical mechanics of RNA folding. Physics (Chinese) 35: 218-229. (NIHMSID: 56190) [PDF]

Cao, S., Chen, SJ. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA 11: 1884-1897. (PMCID: PMC1370876) [PDF]

Kopeikin, Z., Chen, SJ. (2005) Statistical thermodynamics for chain molecules with simple RNA tertiary contacts. Journal of Chemical Physics 122, 094909: 1-13. (NIHMSID: 55565) [PDF]

Tan, ZJ., Chen, SJ. (2005) Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. Journal of Chemical Physics 122, 044903: 1-16. (NIHMSID: 55562) [PDF]

Zhang, WB., Chen, SJ. (2003) Analyzing the folding rates and pathways using kinetic cluster method. Journal of Chemical Physics 119: 8716-8729. (NIHMSID: 55561) [PDF]

Zhang, WB., Chen, SJ. (2003) Master equation approach to finding the rate-limiting steps in biopolymer folding. Journal of Chemical Physics 118: 3413-3420. (NIHMSID: 55560) [PDF]

Zhang, WB., Chen, SJ. (2002) RNA hairpin-folding kinetics. Proceedings of the National Academy of Sciences U.S.A. 99: 1931-1936. [PDF]

Zhang, WB., Chen, SJ. (2001) A three-dimensional statistical mechanical model of folding double-stranded chain molecules. Journal of Chemical Physics 114: 7669-7681. [PDF]

Tostesen, E., Chen, SJ., Dill, K. A. (2001) RNA folding transitions and cooperativity. Journal of Physical Chemistry B 105: 1618-1630. [PDF]

Zhang, WB., Chen, SJ. (2001) Predicting free energy landscapes for complexes of double stranded chain molecules. Journal of Chemical Physics 114: 4253-4266. [PDF]

Chen, SJ., Dill, K. A. (2000) RNA folding energy landscapes. Proceedings of the National Academy of Sciences U.S.A 97: 646-651. [PDF]