Related papers: Using Ciliate Operations to construct Chromosome P…
Determination of functions for poorly characterized genes is crucial for understanding biological processes and studying human diseases. Functionally associated genes are often gained and lost together through evolution. Therefore…
In this paper we consider the fundamental operations dilation and erosion of mathematical morphology. Many powerful image filtering operations are based on their combinations. We establish homomorphism between max-plus semi-ring of integers…
Tumor cells acquire different genetic alterations during the course of evolution in cancer patients. As a result of competition and selection, only a few subgroups of cells with distinct genotypes survive. These subgroups of cells are often…
This work discusses single-objective constrained genetic algorithm with floating-point, integer, binary and permutation representation. Floating-point genetic algorithm tuning with use of test functions is done and leads to a…
Combinatorial designs provide an interesting source of optimization problems. Among them, permutation codes are particularly interesting given their applications in powerline communications, flash memories, and block ciphers. This paper…
We consider the optimization problem of constructing a binary orthogonal array (OA) starting from a bigger one, by removing a specified amount of lines. In particular, we develop a genetic algorithm (GA) where the underlying chromosomes are…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
The {\em double-cut-and-join} (DCJ) operation, introduced by Yancopoulos \emph{et al.}, allows minimum edit distance to be computed by modeling all possible classical rearrangement operations, such as inversions, fusions, fissions,…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Choosing which properties of the data to use as input to multivariate decision algorithms -- a.k.a. feature selection -- is an important step in solving any problem with machine learning. While there is a clear trend towards training…
The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…
Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
With the rapid development of the satellite industry, the information transmission network based on communication satellites has gradually become a major and important part of the future satellite ground integration network. However, the…
A cascaded iterative Fourier transform (CIFT) algorithm is presented for optical security applications. Two phase-masks are designed and located in the input and the Fourier domains of a 4-f correlator respectively, in order to implement…
Stemmatology is a subfield of philology where one approach to understand the copy-history of textual variants of a text (witnesses of a tradition) is to generate an evolutionary tree. Computational methods are partly shared between the…