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RNA (New York, N.Y.)|August 12, 2018
Accelerated RNA secondary structure design using preselected sequences for helices and loopsStanislav Bellaousov, Mohammad Kayedkhordeh, Raymond J Peterson, et al.RNA (New York, N.Y.)|August 28, 2012
Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillanceKaryn Schmidt, Zhenjiang Xu, David H Mathews, et al.Nucleic Acids Research|November 22, 2018
Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental studyRyota Yamagami, Mohammad Kayedkhordeh, David H Mathews, et al.Methods in Molecular Biology (Clifton, N.J.)|July 27, 2020
Inverse RNA Folding Workflow to Design and Test Ribozymes that Include PseudoknotsMohammad Kayedkhordeh, Ryota Yamagami, Philip C Bevilacqua, et al.Wiley Interdisciplinary Reviews. RNA|August 18, 2017
Physics-based all-atom modeling of RNA energetics and structureLouis G Smith, Jianbo Zhao, David H Mathews, et al.Nucleic Acids Research|November 28, 2017
Modeling RNA secondary structure folding ensembles using SHAPE mapping dataAleksandar Spasic, Sarah M Assmann, Philip C Bevilacqua, et al.Bioinformatics (Oxford, England)|March 30, 2019
Determining parameters for non-linear models of multi-loop free energy changeMax Ward, Hongying Sun, Amitava Datta, et al.Biorxiv : the Preprint Server for Biology|October 28, 2024
DecoyFinder: Identification of Contaminants in Sets of Homologous RNA SequencesMingyi Zhu, Jeffrey Zuber, Zhen Tan, et al.Nature Structural & Molecular Biology|December 8, 2009
A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transferDorota Piekna-Przybylska, Laura DiChiacchio, David H Mathews, et al.Journal of Molecular Biology|May 19, 2022
A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N<sup>6</sup>-MethyladenosineMarta Szabat, Martina Prochota, Ryszard Kierzek, et al.Pageof 18