Related papers: Simplifying the mosaic description of DNA sequence…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
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…
Domain knowledge can often be encoded in the structure of a network, such as convolutional layers for vision, which has been shown to increase generalization and decrease sample complexity, or the number of samples required for successful…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
In view of the critical behavior exhibited by a statistical model describing a one dimensional crystal containing isotopic impurities and the fact that for impurity mass parameter 3 times the host mass the critical temperature can attain…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
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…