相关论文: The Expected Order of Saturated RNA Secondary Stru…
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…
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…
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 consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…
An ordered matching of size $n$ is a graph on a linearly ordered vertex set $V$, $|V|=2n$, consisting of $n$ pairwise disjoint edges. There are three different ordered matchings of size two on $V=\{1,2,3,4\}$: an alignment…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
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…
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…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
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…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
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…
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
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…
Researchers have repeatedly found that the ends of an RNA sequence are significantly closer than expected for a random linear chain. However, we prove that the ends of a branched structure are almost certainly close. Our results are…