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Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
We propose and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We previously proposed the existence of DNA to DNA transcription in eukaryotic cells, but the mechanism by which single-stranded DNA (ssDNA) transcript is produced and released from the genome remains unknown. We once speculated that the…
There are a number of vectors for attack when trying to link an individual to a certain DNA sequence. Phenotypic prediction is one such vector; linking DNA to an individual based on their traits. Current approaches are not overly effective,…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Ancient mitochondrial DNA has been used in a wide variety of palaeontological and archaeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…