ArticleMethods (San Diego, Calif.)2019
An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.
Article in Methods (San Diego, Calif.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
14 citing papers in PubMed.
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element.International journal of molecular sciences · 2025Article
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 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
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- The Multiscale Future of RNA Modeling.Biophysical journal · 2020Article
- Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.bioRxiv : the preprint server for biology · 2020Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Exploring novel RNA topologies is imperative for understanding RNA structure and pursuing its design. Our RNA-As-Graphs (RAG) approach exploits graph theory tools and uses coarse-grained tree and dual graphs to represent RNA helices and loops by vertices and edges. Only dual graphs represent pseudoknotted RNAs fully. Here we develop a dual graph enumeration algorithm to generate an expanded library of dual graph topologies for 2-9 vertices, and extend our dual graph partitioning algorithm to identify all possible RNA subgraphs. Our enumeration algorithm connects smaller-vertex graphs, using all possible edge combinations, to build larger-vertex graphs and retain all non-isomorphic graph topologies, thereby more than doubling the size of our prior library to a total of 110,667 dual graph topologies. We apply our dual graph partitioning algorithm, which keeps pseudoknots and junctions intact, to all existing RNA structures to identify all possible substructures up to 9 vertices. In addition, our expanded dual graph library assigns graph topologies to all RNA graphs and subgraphs, rectifying prior inconsistencies. We update our RAG-3Dual database of RNA atomic fragments with all newly identified substructures and their graph IDs, increasing its size by more than 50 times. The enlarged dual graph library and RAG-3Dual database provide a comprehensive repertoire of graph topologies and atomic fragments to study yet undiscovered RNA molecules and design RNA sequences with novel topologies, including a variety of pseudoknotted RNAs.
Indexed as
Identifiers
What OpenQuestion holds
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.