Related papers: Embedded transfer RNA Genes
In eukaryotic cells, KDEL receptors (KDELRs) facilitate the retrieval of endoplasmic reticulum (ER) luminal proteins from the Golgi compartment back to the ER. Apart from the well-documented retention function, recent findings reveal that…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
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…
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
Networks are abundant in the life sciences. Outstanding challenges include how to characterize similarities between networks, and in extension how to integrate information across networks. Yet, network alignment remains a core algorithmic…
DNA monolayers with inherent chirality play a pivotal role across various domains, including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA)…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are…
Neural networks (NNs) have become the state of the art in many machine learning applications, especially in image and sound processing [1]. The same, although to a lesser extent [2,3], could be said in natural language processing (NLP)…
When an external field is applied across a liquid-crystal cell, the twist and tilt distributions cannot be calculated analytically and must be extracted numerically. In the standard approach, the Euler-Lagrange equations are derived from…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…