Related papers: Understanding Long-range Correlations in DNA Seque…
Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
DNA replication fidelity is a critical issue in molecular biology. Biochemical experiments have provided key insights on the mechanism of fidelity control by DNAP in the past decades, whereas systematic theoretical studies on this issue…
Starting with the results of Li et al. in 1992 there is valuable interest in finding long range correlations in dna sequences since it raises questions about the role of introns and intron-containing genes. In the present paper we studied…
We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
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…
We investigate the relationship between the frequency spectrum of image data and the generalization behavior of convolutional neural networks (CNN). We first notice CNN's ability in capturing the high-frequency components of images. These…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah. Interacting vortices between pillars lead to long-range order…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Several recent studies have dealt with the effects of short range correlations on the momentum distribution of nucleons in nuclei. Here we investigate the correlation effects on the density and spectral distribution in coordinate space. A…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…