Publications
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If you are publishing figures or analyses made with RNAvigate, I would
appreciate a citation! I will add your paper to this list.

RNAvigate: Efficient exploration of RNA chemical probing datasets
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- `Nucleic Acids Research <https://doi.org/10.1093/nar/gkae089>`_
- `figure notebooks <https://github.com/Weeks-UNC/RNAvigate_figures>`_

Papers that use RNAvigate in their analyses and figures
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#. Bair,C.R., VanInsberghe,D., Lowen,A.C., Conn,G.L. and Neufeldt,C.J. (2026) Comparative analysis of flavivirus sfRNA dynamics and secondary structure. 10.64898/2026.04.07.716965.
#. Ehrhardt,J.E., Qiu,D.Y., Jin,S., Boerneke,M.A., Aufgebauer,C.J., Horner,S.M. and Weeks,K.M. (2025) A Small Cationic Probe for Accurate, Punctate Discovery of RNA Tertiary Structure. JACS Au, 5, 6287–6297.
#. Allen,S.R., Schlick,T. and Laederach,A. (2025) RNA Structural Ensemble Determinants of −1 Programmed Ribosomal Frameshifting Efficiency Across Coronavirus Evolution. Journal of Molecular Biology, 437, 169512.
#. Hatfield,B.M., Weidmann,C.A., McCutchin,C.A., Irving,P.S., Nelson,I.M., Felder,S. and Weeks,K.M. (2025) Functional Proximity across an mRNA. Biochemistry, 64, 3854–3865.
#. Waldern,J.M., Taylor,C., Giannetti,C.A., Irving,P.S., Allen,S.R., Zhu,M., Backofen,R., Mathews,D.H., Weeks,K.M. and Laederach,A. (2025) Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP. Nucleic Acids Res, 53, gkaf433.
#. Veenbaas,S.D., Koehn,J.T., Irving,P.S., Lama,N.N. and Weeks,K.M. (2025) Ligand-binding pockets in RNA and where to find them. Proceedings of the National Academy of Sciences, 122, e2422346122.
#. Wang,J. (2025) Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics. Biochemistry, 64, 1817–1827.
#. Kim,J.Y., Furney,A., Benner,B. and Sengupta,A. (2025) Stress-induced changes in endogenous TP53 mRNA 5′ regulatory region. Journal of Biological Chemistry, 301.
#. Dey,A., Yan,S., Schlick,T. and Laederach,A. (2024) Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses. RNA, 30, 1437–1450.
#. Tan,A.C., Irving,P.S., Koehn,J.T., Jin,S., Qiu,D.Y. and Weeks,K.M. (2024) Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing. Biochemistry, 63, 2648–2657.
#. Dey,A. (2023) Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675—Explaining Its Regulatory Mechanism in Carcinogenesis. Non-Coding RNA, 9, 45.