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Nucleic Acids Research|March 24, 2017
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure predictionJeffrey Zuber, Hongying Sun, Xiaoju Zhang, et al.Nucleic Acids Research|November 19, 2022
LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2He Zhang, Sizhen Li, Liang Zhang, et al.Biorxiv : the Preprint Server for Biology|January 5, 2021
LazySampling and LinearSampling: Fast Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2He Zhang, Liang Zhang, Sizhen Li, et al.Journal of Chemical Theory and Computation|August 20, 2014
Influence of Sequence and Covalent Modifications on Yeast tRNA DynamicsXiaoju Zhang, Ross C Walker, Eric M Phizicky, et al.Biophysical Journal|November 20, 2025
NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preferenceOlayinka Akinyemi, Scott D Kennedy, James P McSally, et al.Bioinformatics (Oxford, England)|June 24, 2022
Deep learning models for RNA secondary structure prediction (probably) do not generalize across familiesMarcell Szikszai, Michael Wise, Amitava Datta, et al.Biochemistry|December 8, 2010
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parametersBiao Liu, Joshua M Diamond, David H Mathews, et al.RNA (New York, N.Y.)|September 16, 2015
Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamicsAsaminew H Aytenfisu, Joseph A Liberman, Joseph E Wedekind, et al.Proceedings of the National Academy of Sciences of the United States of America|December 26, 2008
Accurate SHAPE-directed RNA structure determinationKatherine E Deigan, Tian W Li, David H Mathews, et al.Journal of the American Chemical Society|July 11, 2008
NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposonJames M Hart, Scott D Kennedy, David H Mathews, et al.Pageof 18