Related papers: Statistics of DNA sequences: a low frequency analy…
We establish the fundamental limits of DNA shotgun sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
Based on the numerical representations by T basic vectors of a symbolic sequence consisting of T symbols, first, we prove mathematical that the total Fourier spectrum of the sequence is the square of the length of the sequence. In the…
We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of random networks, including Erdoes-Renyi…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Hierarchical networks actually have many applications in the real world. Firstly, we propose a new class of hierarchical networks with scale-free and fractal structure, which are the networks with triangles compared to traditional…
The site frequency spectrum describes variation among a set of n DNA sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at which the mutant allele is present in i copies. Under selective neutrality, random mating,…
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual…
Complex networks have been mostly characterized from the point of view of the degree distribution of their nodes and a few other motifs (or modules), with a special attention to triangles and cliques. The most exotic phenomena have been…
Genomic data provides clinical researchers with vast opportunities to study various patient ailments. Yet the same data contains revealing information, some of which a patient might want to remain concealed. The question then arises: how…
Researchers have repeatedly found that the ends of an RNA sequence are significantly closer than expected for a random linear chain. However, we prove that the ends of a branched structure are almost certainly close. Our results are…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
We examine the stability of a 1D electrical transmission line in the simultaneous presence of PT-symmetry and fractionality. The array contains a binary gain/loss distribution $\gamma_{n}$ and a fractional Laplacian characterized by a…