Related papers: A note on some conjectures about combinatorial mod…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
Enumerative studies of RNA secondary structures were initiated four decades ago by Waterman and his coworkers. Since then, RNA secondary structures have been explored according to many different structural characteristics, for instance,…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…
We give a Large Deviation Principle (LDP) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of RNA secondary structures. We calculate the typical degree distributions based on nearest…
A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…
We extend results regarding a combinatorial model introduced by Black, Drellich, and Tymoczko (2017+) which generalizes the folding of the RNA molecule in biology. Consider a word on alphabet $\{A_1, \overline{A}_1, \ldots, A_m,…
An elementary, at the undergraduate level derivation is given of precise upper bounds of the number of various RNA secondary structures. The method works when the generating function has multiple singularities at the circle of convergence,…
In this paper, we give a simple combinatorial explanation of a formula of A. Postnikov relating bicolored rooted trees to bicolored binary trees. We also present generalized formulas for the number of labeled k-ary trees, rooted labeled…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
We consider a certain abstract of RNA secondary structures, which is closely related to RNA shapes. The generating function counting the number of the abstract structures is obtained by means of Narayana numbers and 2-Motzkin paths, through…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
We introduce the notion of doubly rooted plane trees and give a decomposition of these trees, called the butterfly decomposition which turns out to have many applications. From the butterfly decomposition we obtain a one-to-one…
In this second paper, we look at the following question: are the properties of the trees associated to the tilings $\{p,4\}$ and $\{p$+$2,3\}$ of the hyperbolic plane still true if we consider a finitely generated tree by the same rules but…
In this paper we analyse some questions concerning trees on $\kappa$, both for the countable and the uncountable case, and the connections with Cohen reals. In particular, we provide a proof for one of the implications left open in…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
We study a circular order on labelled, m-edge-coloured trees with k vertices, and show that the set of such trees with a fixed circular order is in bijection with the set of RNA m-diagrams of degree k, combinatorial objects which can be…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…