ArticleGenes2018
Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.
Article in Genes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Viral RNAs as Dual Graphs: Extending the Motif Universe of RNAs.bioRxiv : the preprint server for biology · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element.International journal of molecular sciences · 2025Article
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Nature communications · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Research square · 2022Article
- Diagrammatic approaches to RNA structures with trinucleotide repeats.Biophysical journal · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.Biochimica et biophysica acta. General subjects · 2020Article
- Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.Journal of structural biology · 2020Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks up to nine vertices; among them, 22 are frequently occurring, 15 of which contain pseudoknots. We then catalog atomic fragments corresponding to the subgraph blocks to define a library of building blocks that can be used for RNA design, which we call
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.