相关论文: A family of metrics on contact structures based on…

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…

An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…

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 study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…

Accurate RNA secondary structure prediction is vital for understanding cellular regulation and disease mechanisms. Deep learning (DL) methods have surpassed traditional algorithms by predicting complex features like pseudoknots and…

Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1.…

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…

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…

Single-cell omics enable the profiles of cells, which contain large numbers of biological features, to be quantified. Cluster analysis, a dimensionality reduction process, is used to reduce the dimensions of the data to make it…

On a manifold with an almost contact metric structure $(\varphi,\vec\xi,\eta,g,X,D)$ the notions of the interior and the $N$-prolonged connections are introduced. Using the $N$-prolonged connection, a new almost contact metric structure is…

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 approach to the detection and characterization of edges, ridges, and blobs in two-dimensional images which exploits the symmetry properties of directionally sensitive analyzing functions in multiscale systems that are…

In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…

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…

RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…

It is acknowledged that co-evolutionary nucleotide-nucleotide interactions are essential for RNA structures and functions. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence…

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe…

The present paper studies multiple failure and signature analysis of coherent systems using the theory of monomial ideals. While system reliability has been studied using Hilbert series of monomial ideals, this is not enough to understand…

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…

Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…