Topological classification and enumeration of RNA structures by genus
The authors study the association between RNA pseudoknot structures and topological surfaces, and the classification of the former by the genus of the latter. On the basis of earlier work [\textit{J. Harer} and \textit{D. Zagier}, Invent. Math. 85, 457--485 (1986; Zbl 0616.14017)], they calculate the generating function for the number of structures with a fixed genus and number of nucleotides, and given minimum stack size so that no two consecutive nucleotides are base-paired. In particular, they show that the generating function is algebraic, and they prove that for stack size at least two, the genus of the surface only enters sub-exponentially; hence, they argue that, for any genus, the resulting slow growth rates with respect to RNA molecule numbers imply the existence of neutral networks [\textit{C. Reidys} et al., Bull. Math. Biol. 59, No. 2, 339--397 (1997; Zbl 0925.92006)]. Specific structures known as shapes are shown to be in a one-to-one correspondence with cells in the Penner-Strebel decomposition [\textit{R.C. Penner}, Commun. Math. Phys. 113, 299--339 (1987; Zbl 0642.32012)] of Riemann's moduli space of a surface with a given genus and one boundary component.
- A direct bijection for the Harer-Zagier formula
- Analytic combinatorics
- Combinatorial aspects of continued fractions
- Combinatorial Computational Biology of RNA
- Combinatorial landscapes
- Combinatorics of RNA Hairpins and Cloverleaves
- Computation of Generating Functions for Biological Molecules
- Factoring \(n\)-cycles and counting maps of given genus
- Fatgraph models of proteins
- Finite type invariants and fatgraphs
- Generic properties of combinatory maps: Neutral networks of RNA secondary structures
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- Invariant tensor formulas via chord diagrams
- Large components in random induced subgraphs of \(n\)-cubes
- Lie algebras and the four color theorem
- Linear trees and RNA secondary structure
- Modular, \(k\)-noncrossing diagrams
- On the Vassiliev knot invariants
- Perturbative series and the moduli space of Riemann surfaces
- Quantization of the algebra of chord diagrams
- Random induced subgraphs of Cayley graphs induced by transpositions
- Replication and mutation on neutral networks
- RNA folding and large \(N\) matrix theory
- RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
- Sequence of operations analysis for dynamic data structures
- Spaces of RNA secondary structures
- The asymptotic number of tree-rooted maps on a surface
- The decorated Teichmüller space of punctured surfaces
- The Euler characteristic of the moduli space of curves
- The Poisson structure on the moduli space of flat connections and chord diagrams
- Weil-Petersson volumes
- Spaces of RNA secondary structures
- Loop homology of bi-secondary structures
- Loop homology of bi-secondary structures. II
- The block spectrum of RNA pseudoknot structures
- On RNA-RNA interaction structures of fixed topological genus
- Statistics of topological RNA structures
- Regular simple queues of protein contact maps
- On a uniformly random chord diagram and its intersection graph
- Generation of RNA pseudoknot structures with topological genus filtration
- Topological recursion for Gaussian means and cohomological field theories
- Moduli spaces and macromolecules
- Plane permutations and applications to a result of Zagier-Stanley and distances of permutations
- Topological language for RNA
- Topological Classification of RNA Structures via Intersection Graph
- Enumeration of 4-regular one-face maps
- Genus ranges of chord diagrams
- Central limit theorem for crossings in randomly embedded graphs
- Hamiltonian sets of polygonal paths in assembly graphs
- Models of discretized moduli spaces, cohomological field theories, and Gaussian means
- Shapes of topological RNA structures
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