Related papers: Non-alignment comparison of human and high primate…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Mapping human genetic variation is fundamentally interesting in fields such as anthropology and forensic inference. At the same time patterns of genetic diversity confound efforts to determine the genetic basis of complex disease. Due to…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
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…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
The compressive sensing (CS) and 1-bit CS demonstrate superior efficiency in signal acquisition and resource conservation, while 1-bit CS achieves maximum resource efficiency through sign-only measurements. With the emergence of massive…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Signal processing (SP) techniques convert DNA and protein sequences into information that lead to successful drug discovery. One must, however, be aware about the difference between information and entropy1. Eight other physical properties…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
The usefulness of a `total-evidence' approach to human population genetics was assessed through a clustering analysis of combined genome-wide SNP datasets. The combination contained only 3146 SNPs. Detailed examination of the results…
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…