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Proceedings of the National Academy of Sciences of the United States of America|March 19, 2013
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknotsChristine E Hajdin, Stanislav Bellaousov, Wayne Huggins, et al.Bioinformatics (Oxford, England)|September 13, 2019
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam searchLiang Huang, He Zhang, Dezhong Deng, et al.Biochemistry|October 13, 2007
NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNANeelaabh Shankar, Tianbing Xia, Scott D Kennedy, et al.Nature Communications|March 12, 2022
Secondary structure prediction for RNA sequences including N6-methyladenosineElzbieta Kierzek, Xiaoju Zhang, Richard M Watson, et al.Arxiv|July 7, 2022
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA AlignmentsApoorv Malik, Liang Zhang, Milan Gautam, et al.Journal of Molecular Biology|July 6, 2024
LinearAlifold: Linear-time consensus structure prediction for RNA alignmentsApoorv Malik, Liang Zhang, Milan Gautam, et al.Proceedings of the National Academy of Sciences of the United States of America|May 5, 2004
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structureDavid H Mathews, Matthew D Disney, Jessica L Childs, et al.RNA (New York, N.Y.)|February 14, 2018
Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformationAleksandar Spasic, Scott D Kennedy, Laura Needham, et al.Nucleic Acids Research|May 3, 2018
Improving RNA nearest neighbor parameters for helices by going beyond the two-state modelAleksandar Spasic, Kyle D Berger, Jonathan L Chen, et al.Nature Communications|January 12, 2022
A small RNA that cooperatively senses two stacked metabolites in one pocket for gene controlGriffin M Schroeder, Chapin E Cavender, Maya E Blau, et al.Pageof 20