Related papers: $k$-noncrossing RNA structures with arc-length $\g…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
An $(n,k)$-perfect sequence covering array with multiplicity $\lambda$, denoted PSCA$(n,k,\lambda)$, is a multiset whose elements are permutations of the sequence $(1,2, \dots, n)$ and which collectively contain each ordered length $k$…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
The family of snarks -- connected bridgeless cubic graphs that cannot be 3-edge-coloured -- is well-known as a potential source of counterexamples to several important and long-standing conjectures in graph theory. These include the cycle…
In this paper we present three different results dealing with the number of $(\leq k)$-facets of a set of points: 1. We give structural properties of sets in the plane that achieve the optimal lower bound $3\binom{k+2}{2}$ of $(\leq…
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA…
We provide a new lower bound on the number of $(\leq k)$-edges of a set of $n$ points in the plane in general position. We show that for $0 \leq k \leq\lfloor\frac{n-2}{2}\rfloor$ the number of $(\leq k)$-edges is at least $$ E_k(S) \geq…
Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, removal or shift of a single base pair. Using context-free…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
Knots are commonly found in molecular chains such as DNA and proteins, and they have been considered to be useful models for structural analysis of these molecules. One interested quantity is the minimum number of monomers necessary to…
An orientation of a graph is semi-transitive if it is acyclic, and for any directed path $v_0\rightarrow v_1\rightarrow \cdots\rightarrow v_k$ either there is no edge between $v_0$ and $v_k$, or $v_i\rightarrow v_j$ is an edge for all…
A graph $G$ is {$k$-crossing-critical} if $cr(G)\ge k$, but $cr(G\setminus e)<k$ for each edge $e\in E(G)$, where $cr(G)$ is the crossing number of $G$. It is known that for any $k$-crossing-critical graph $G$, $cr(G)\le 2.5k+16$ holds, and…
We investigate which chordal graphs have a representation as intersection graphs of pseudosegments. For positive we have a construction which shows that all chordal graphs that can be represented as intersection graph of subpaths on a tree…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
In this paper, we present a reduction algorithm which transforms $m$-regular partitions of $[n]=\{1, 2, ..., n\}$ to $(m-1)$-regular partitions of $[n-1]$. We show that this algorithm preserves the noncrossing property. This yields a simple…
Let $n$, $r$, $k_1,\ldots,k_r$ and $t$ be positive integers with $r\geq 2$, and $\mathcal{F}_i\ (1\leq i\leq r)$ a family of $k_i$-subsets of an $n$-set $V$. The families $\mathcal{F}_1,\ \mathcal{F}_2,\ldots,\mathcal{F}_r$ are said to be…
In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
A pseudocircle is a simple closed curve on the sphere or in the plane. The study of arrangements of pseudocircles was initiated by Gr\"unbaum, who defined them as collections of simple closed curves that pairwise intersect in exactly two…
We introduce an alternative stratification of knots: by the size of lattice on which a knot can be first met. Using this classification, we find ratio of unknots and knots with more than 10 minimal crossings inside different lattices and…