Related papers: Valid plane trees: Combinatorial models for RNA se…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
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…
Packing graphs is a combinatorial problem where several given graphs are being mapped into a common host graph such that every edge is used at most once. In the planar tree packing problem we are given two trees T1 and T2 on n vertices and…
We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
An elimination tree for a connected graph $G$ is a rooted tree on the vertices of $G$ obtained by choosing a root $x$ and recursing on the connected components of $G-x$ to produce the subtrees of $x$. Elimination trees appear in many guises…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
Consider a random word $X^n=(X_1,\ldots ,X_n)$ in an alphabet consisting of $4$ letters, with the letters viewed either as $A$, $U$, $G$ and $C$ (i.e., nucleotides in an RNA sequence) or $\alpha$, $\bar{\alpha}$, $\beta$ and $\bar{\beta}$…
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 construct a strict pivotal monoidal category $\mathcal{D}_{\mathrm{DNA}}$ whose objects are DNA sequences (words over $\{A,C,G,T\}$) and whose morphisms are isotopy classes of typed noncrossing planar matchings, composed of…
Automata-logic connections are pillars of the theory of regular languages. Such connections are harder to obtain for transducers, but important results have been obtained recently for word-to-word transformations, showing that the three…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
We introduce a monoid structure on the set of binary search trees, by a process very similar to the construction of the plactic monoid, the Robinson-Schensted insertion being replaced by the binary search tree insertion. This leads to a new…
The computational complexity of the isomorphism problem for regular trees, regular linear orders, and regular words is analyzed. A tree is regular if it is isomorphic to the prefix order on a regular language. In case regular languages are…
Plane increasing trees are rooted labeled trees embedded into the plane such that the sequence of labels is increasing on any branch starting at the root. Relaxed binary trees are a subclass of unlabeled directed acyclic graphs. We…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…