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Biophysical Journal|May 20, 2009
A new computational approach for mechanical folding kinetics of RNA hairpinsSong Cao, Shi-Jie ChenRNA (New York, N.Y.)|February 25, 2009
Predicting structures and stabilities for H-type pseudoknots with interhelix loopsSong Cao, Shi-Jie ChenPhysical Biology|November 10, 2011
Quantitative analysis of the ion-dependent folding stability of DNA triplexesGengsheng Chen, Shi-Jie ChenThe Journal of Physical Chemistry. B|March 19, 2011
Physics-based de novo prediction of RNA 3D structuresSong Cao, Shi-Jie ChenMethods in Molecular Biology (Clifton, N.J.)|June 4, 2021
Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLAXiaojun Xu, Shi-Jie ChenJournal of Chemical Theory and Computation|September 25, 2012
Predicting ion-nucleic acid interactions by energy landscape-guided samplingZhaojian He, Shi-Jie ChenBiophysical Journal|March 25, 2026
Building RNA Coarse-Grained Force Fields: Design Principles and Training StrategiesWenfei Li, Shi-Jie ChenThe Journal of Chemical Physics|May 6, 2006
Folding thermodynamics of pseudoknotted chain conformationsZoia Kopeikin, Shi-Jie ChenPlos One|September 23, 2016
VfoldCPX Server: Predicting RNA-RNA Complex Structure and StabilityXiaojun Xu, Shi-Jie ChenNucleic Acids Research|February 7, 2012
Predicting kissing interactions in microRNA-target complex and assessment of microRNA activitySong Cao, Shi-Jie ChenPageof 18