Related papers: Exploring the Multifractal Behavior of the Human G…
This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a…
This study proposes CGRclust, a novel combination of unsupervised twin contrastive clustering of Chaos Game Representations (CGR) of DNA sequences, with convolutional neural networks (CNNs). To the best of our knowledge, CGRclust is the…
This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is…
Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-RCGR), that transforms biological sequences into…
The chaos game representation (CGR) is an interesting method to visualize one-dimensional sequences. In this paper, we show how to construct a chaos game representation. The applications mentioned here are biological, in which CGR was able…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
A new three dimensional approach to the chaos game representation of protein sequences is explored in this thesis. The basics of DNA, the synthesis of proteins from DNA, protein structure and functionality and sequence alignment techniques…
DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed…
Symbolic sequences generated by coupled map lattices (CMLs) can be used to model the chaotic-like structure of genomic sequences. In this study it is shown that diffusively coupled Chebyshev maps of order 4 (corresponding to a shift of 4…
From its first emergence in Wuhan, China in December, 2019 the COVID-19 pandemic has caused unprecedented health crisis throughout the world. The novel coronavirus disease is caused by severe acute respiratory syndrome coronavirus 2…
Nowadays, studying introns is becoming a very promising field in the genomics. Even though they play a role in the dynamic regulation of gene and in the organism's evolution, introns have not attracted enough attention like exons did;…
The spatial distribution of DNA base sequence A, C, G and T exhibit selfsimilar fractal fluctuations and the corresponding power spectra follow inverse power law form, which implies the following: (1) A scale invariant eddy continuum,…
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be…
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…
Cancer is a complex disease characterized by uncontrolled cell growth. T cell receptors (TCRs), crucial proteins in the immune system, play a key role in recognizing antigens, including those associated with cancer. Recent advancements in…
Compositional spectra (CS) analysis based on k-mer scoring of DNA sequences was employed in this study for dot-plot comparison of human and primate genomes. The detection of extended conserved synteny regions was based on continuous fuzzy…
This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…
We present a novel information-preserving Chaos Game Representation (CGR) method, also called Reverse-CGR (R-CGR), for biological sequence analysis that addresses the fundamental limitation of traditional CGR approaches - the loss of…
In medical genetics, each genetic variant is evaluated as an independent entity regarding its clinical importance. However, in most complex diseases, variant combinations in specific gene networks, rather than the presence of a particular…
We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the…