ArticleComputational and structural biotechnology journal2021
Geometric construction of viral genome space and its applications.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms.Briefings in bioinformatics · 2026Article
- Genomic similarity to quantitatively evaluate the reassortment potential of H7N9 with other subtypes of avian influenza viruses.Frontiers in cellular and infection microbiology · 2026Article
- The grand biological universe: A comprehensive geometric construction of genome space.Innovation (Cambridge (Mass.)) · 2025Article
- Reconstruction of masked sequencesPeerJ · 2025Article
- The optimal metric for viral genome space.Computational and structural biotechnology journal · 2024Article
- Article
- Automated recognition of chromosome fusion using an alignment-free natural vector method.Frontiers in genetics · 2024Article
- Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms.Genes · 2023Article
- How the latent geometry of a biological network provides information on its dynamics: the case of the gene network of chronic myeloid leukaemia.Frontiers in cell and developmental biology · 2023Article
- Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time.Genes · 2022Article
- In-depth investigation of the point mutation pattern of HIV-1.Frontiers in cellular and infection microbiology · 2022Article
- An efficient numerical representation of genome sequence: natural vector with covariance component.PeerJ · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the relationships between genomic sequences is essential to the classification and characterization of living beings. The classes and characteristics of an organism can be identified in the corresponding genome space. In the genome space, the natural metric is important to describe the distribution of genomes. Therefore, the similarity of two biological sequences can be measured. Here, we report that all of the viral genomes are in 32-dimensional Euclidean space, in which the natural metric is the weighted summation of Euclidean distance of k-mer natural vectors. The classification of viral genomes in the constructed genome space further proves the convex hull principle of taxonomy, which states that convex hulls of different families are mutually disjoint. This study provides a novel geometric perspective to describe the genome sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.