相关论文: Long range correlations in DNA sequences
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
Sophisticated high-energy and large momentum-transfer scattering experiments combined with ab-initio calculations can reveal the short-distance behavior of nucleon pairs in nuclei. On an opposite energy and resolution scale, elastic…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
Normal and anomalous diffusion are ubiquitous in many complex systems [1] . Here, we define a time and space generalized diffusion equation (GDE), which uses fractional-time derivatives and transformed d-path Laplacian operators on…
Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS)…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We perform an analytical analysis of the long-range degree correlation of the giant component in an uncorrelated random network by employing generating functions. By introducing a characteristic length, we find that a pair of nodes in the…
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such…
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is…
Physics has been transforming our view of nature for centuries. While combining physical knowledge with computational approaches has enabled detailed modeling of physical systems' evolution, understanding the emergence of patterns and…
In many longitudinal microarray studies, the gene expression levels in a random sample are observed repeatedly over time under two or more conditions. The resulting time courses are generally very short, high-dimensional, and may have…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…