相关论文: Relation between Insertion Sequences and Genome Re…
Insertion Sequences (ISs) are small DNA segments that have the ability of moving themselves into genomes. These types of mobile genetic elements (MGEs) seem to play an essential role in genomes rearrangements and evolution of prokaryotic…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
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…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
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…
The Cancer Genome Atlas project was initiated by the National Cancer Institute in order to characterize the genomes of hundreds of tumors of various cancer types. While much effort has been put into detecting somatic genomic variation in…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…