Related papers: Central and Local Limit Theorems for RNA Structure…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
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…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
Nonparametric detection of existence of an anomalous structure over a network is investigated. Nodes corresponding to the anomalous structure (if one exists) receive samples generated by a distribution q, which is different from a…
We show the expected order of RNA saturated secondary structures of size $n$ is $\log_4n(1+O(\frac{\log_2n}{n}))$, if we select the saturated secondary structure uniformly at random. Furthermore, the order of saturated secondary structures…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.
We have examined extended structures, bridges and arches, in computer generated, non-sequentially stabilized, hard sphere deposits. The bridges and arches have well defined distributions of sizes and shapes. The distribution functions…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
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…
Networks of silicon nanowires possess intriguing electronic properties surpassing the predictions based on quantum confinement of individual nanowires. Employing large-scale atomistic pseudopotential computations, as yet unexplored branched…
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 establish a multivariate local limit theorem for the order and size as well as several other parameters of the k-core of the Erdos-Renyi graph. The proof is based on a novel approach to the k-core problem that replaces the meticulous…
Let $\mathrm{PG}(k-1,q)$ be the $(k-1)$-dimensional projective space over the finite field $\mathbb{F}_q$. An arc in $\mathrm{PG}(k-1,q)$ is a set of points with the property that any $k$ of them span the entire space. The notion of…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the unfolded states is Gaussian, which follows from central…
The concept of $k$-planarity is extensively studied in the context of Beyond Planarity. A graph is $k$-planar if it admits a drawing in the plane in which each edge is crossed at most $k$ times. The local crossing number of a graph is the…
The $k$-core of a graph is the largest subgraph of minimum degree at least $k$. We show that for $k$ sufficiently large, the $(k + 2)$-core of a random graph $\G(n,p)$ asymptotically almost surely has a spanning $k$-regular subgraph. Thus…
A {\it stuck knot} is a knot diagram containing designated crossings, called {\it stuck crossings}, whose incident strands are required to remain locally non-separable. These rigidity constraints restrict the allowable ambient isotopies and…