Related papers: Statistical analysis of Gene and Intergenic DNA Se…
DNA databases are widely used in forensic science to identify unknown offenders. When no exact match is found, familial DNA searches can help by identifying first-degree relatives using likelihood ratios. If multiple subpopulations are…
Spatial transcriptomics studies are becoming increasingly large and commonplace, necessitating simultaneous analysis of a large number of spatially resolved variables. Correspondingly, a diverse range of methodologies have been proposed to…
It is becoming routine to obtain datasets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study…
Time series measured from real-world systems are generally noisy, complex and display statistical properties that evolve continuously over time. Here, we present a method that combines wavelet analysis and non-stationary surrogates to…
Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i)…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
The aim of this paper is to describe new statistical methods for determination of the correlations among and distributions of physical parameters from a multivariate data with general and arbitrary truncations and selection biases. These…
Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…
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…
Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to…
We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting,…
A rigorous methodology is proposed to study cell division data consisting in several observed genealogical trees of possibly different shapes. The procedure takes into account missing observations, data from different trees, as well as the…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous…
We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known…
Gene-gene interactions are often regarded as playing significant roles in influencing variabilities of complex traits. Although much research has been devoted to this area, to date a comprehensive statistical model that addresses the…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…