Related papers: A combinatorial framework for RNA tertiary interac…
In this paper we enumerate $k$-noncrossing tangled-diagrams. A tangled-diagram is a labeled graph whose vertices are $1,...,n$ have degree $\le 2$, and are arranged in increasing order in a horizontal line. Its arcs are drawn in the upper…
We give recurrence relations for the enumeration of symmetric elements within four classes of arc diagrams corresponding to certain involutions and set partitions whose blocks contain no consecutive integers. These arc diagrams are…
A k-noncrossing RNA pseudoknot structure is a graph over $\{1,...,n\}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
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…
In this paper we compute the generating function of modular, $k$-noncrossing diagrams. A $k$-noncrossing diagram is called modular if it does not contains any isolated arcs and any arc has length at least four. Modular diagrams represent…
In this paper we study $k$-noncrossing RNA structures with arc-length $\ge 3$, i.e. RNA molecules in which for any $i$, the nucleotides labeled $i$ and $i+j$ ($j=1,2$) cannot form a bond and in which there are at most $k-1$ mutually…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum arc- and stack-length. That is, we study the numbers of RNA pseudoknot structures with arc-length $\ge 3$, stack-length $\ge \sigma$ and in which there…
In this work, we propose a comprehensive theoretical framework combining percolation theory with nonlinear dynamics in order to study hypergraphs with a time-varying giant component. We consider in particular hypergraphs with higher-order…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all…
A tangled-diagram over $[n]=\{1,...,n\}$ is a graph of degree less than two whose vertices $1,...,n$ are arranged in a horizontal line and whose arcs are drawn in the upper halfplane with a particular notion of crossings and nestings.…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
In this paper we study $k$-noncrossing matchings. A $k$-noncrossing matching is a labeled graph with vertex set $\{1,...,2n\}$ arranged in increasing order in a horizontal line and vertex-degree 1. The $n$ arcs are drawn in the upper…
We develop a manifestly microscopic method to deal with strongly interacting nuclear systems that have different interactions in spin-singlet and spin-triplet states. In a first step we analyze variational wave functions that have been…
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…
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…
Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…