On RNA-RNA interaction structures of fixed topological genus

DOI10.1016/J.MBS.2014.12.008zbMath1311.05020arXiv1311.0684OpenAlexW1963786121WikidataQ46779199 ScholiaQ46779199MaRDI QIDQ2344602

Benjamin M. M. Fu, Hillary S. W. Han, Christian M. Reidys

Publication date: 15 May 2015

Published in: Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1311.0684

zbMATH Keywords

decompositionnon-uniform samplingtopological genusuniform generationbicellular mapRNA-RNA interaction structure

Mathematics Subject Classification ID

Combinatorial identities, bijective combinatorics (05A19) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Uses Software

• starBase

Cites Work

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• Topological classification and enumeration of RNA structures by genus
• A new combinatorial identity for unicellular maps, via a direct bijective approach
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• Shapes of topological RNA structures
• The structure of unicellular maps, and a connection between maps of positive genus and planar labelled trees
• Modular, \(k\)-noncrossing diagrams
• Spaces of RNA secondary structures
• Generation of RNA pseudoknot structures with topological genus filtration
• Fatgraph models of proteins
• Combinatorics of RNA Hairpins and Cloverleaves
• Algorithms for Loop Matchings
• Boltzmann Samplers for the Random Generation of Combinatorial Structures
• Proportions of Irreducible Diagrams
• RNA folding and large \(N\) matrix theory

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