Related papers: Statistical analysis of Gene and Intergenic DNA Se…
Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties…
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…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Processing of symbolic sequences represented by mapping of symbolic data into numerical signals is commonly used in various applications. It is a particularly popular approach in genomic and proteomic sequence analysis. Numerous mappings of…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Analyzing time series in the frequency domain enables the development of powerful tools for investigating the second-order characteristics of multivariate processes. Parameters like the spectral density matrix and its inverse, the coherence…
Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information…
Tumor samples are heterogeneous. They consist of different subclones that are characterized by differences in DNA nucleotide sequences and copy numbers on multiple loci. Heterogeneity can be measured through the identification of the…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…
The method of constrained randomisation is applied to three-dimensional simulated galaxy distributions. With this technique we generate for a given data set surrogate data sets which have the same linear properties as the original data…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
A novel non-linear approach to fast and effective comparison of sequences is presented, compared to the traditional cross-correlation operator, and illustrated with respect to DNA sequences.
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
Identifying the risk factors for mental illnesses is of significant public health importance. Diagnosis, stigma associated with mental illnesses, comorbidity, and complex etiologies, among others, make it very challenging to study mental…
When a defendant's DNA matches a sample found at a crime scene, how compelling is the match? To answer this question, DNA analysts typically use relative frequencies, random-match probabilities or likelihood ratios. They compute these…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…