Related papers: Methods for Analyzing RNA Pseudoknots via Chord Di…
Classical knots in $\mathbb{R}^3$ can be represented by diagrams in the plane. These diagrams are formed by curves with a finite number of transverse crossings, where each crossing is decorated to indicate which strand of the knot passes…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
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…
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…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
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…
In this paper we analyze the length-spectrum of blocks in $\gamma$-structures. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $\gamma$-structure is…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
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 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…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
We further develop the large $ N $ formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to…
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 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 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…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
A pseudoline arrangement graph is a planar graph induced by an embedding of a (simple) pseudoline arrangement. We study the corresponding graph realization problem and properties of pseudoline arrangement graphs. In the first part, we give…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
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…
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,…