相关论文: On Reidys and Stadler's metrics for RNA secondary …

The measurement of the similarity of RNA secondary structures, and in general of contact structures, of a fixed length has several specific applications. For instance, it is used in the analysis of the ensemble of suboptimal secondary…

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,…

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…

Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…

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…

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…

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…

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…

Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…

Recently Yoffe {\it et al.} observed that the average distances between $5'-3'$ ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical…

In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…

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 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…

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…

Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…

RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…

The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…

In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…