Related papers: Irreducibility in RNA structures
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
Genetic robustness, the preservation of evolved phenotypes against genotypic mutations, is one of the central concepts in evolution. In recent years a large body of work has focused on the origins, mechanisms, and consequences of robustness…
Feedback shift registers(FSRs) are a fundamental component in electronics and secure communication. An FSR $f$ is said to be reducible if all the output sequences of another FSR $g$ can also be generated by $f$ and the FSR $g$ has less…
A sparsity pattern in $\mathbb{R}^{n \times m}$, for $m\geq n$, is a vector subspace of matrices admitting a basis consisting of canonical basis vectors in $\mathbb{R}^{n \times m}$. We represent a sparsity pattern by a matrix with…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
In this paper, we investigate the structure of the most general kind of substitution shifts, including non-minimal ones, and allowing erasing morphisms. We prove the decidability of many properties of these morphisms with respect to the…
In a previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1-55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
In large data centers, storage nodes are organized in racks, and the cross-rack transmission dominates the bandwidth cost. For the repair of single node failures, codes achieving the tradeoff between the storage redundancy and cross-rack…
Using closure concepts, we show that within every undirected network, or graph, there is a unique irreducible subgraph which we call its "spine". The chordless cycles which comprise this irreducible core effectively characterize the…
Given manifolds $M$ and $N$, with $M$ compact, we study the geometrical structure of the space of embeddings of $M$ into $N$, having less regularity than $\mathcal C^\infty$, quotiented by the group of diffeomorphisms of $M$.
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…