{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/revealing-the-shape-of-genome-space-via-k-mer","title":"Revealing the Shape of Genome Space via K-mer Topology","arxiv_id":"2412.20202","date":"2024-12-28","proceeding":null,"authors":["Yuta Hozumi","Guo-Wei Wei"],"abstract":"Despite decades of effort, understanding the shape of genome space in biology remains a challenge due to the similarity, variability, diversity, and plasticity of evolutionary relationships among species, genes, or other biological entities. We present a k-mer topology method, the first of its kind, to delineate the shape of the genome space. K-mer topology examines the topological persistence and the evolution of the homotopic shape of the sequences of k nucleotides in species, organisms, and genes using persistent Laplacians, a new multiscale combinatorial approach. We also propose a topological genetic distance between species by their topological invariants and non-harmonic spectra over scales. This new metric defines the topological phylogenetic trees of genomes, facilitating species classification and clustering. K-mer topology substantially outperforms state-of-the-art methods on a variety of benchmark datasets, including mammalian mitochondrial genomes, Rhinovirus, SARS-CoV-2 variants, Ebola virus, Hepatitis E virus, Influenza hemagglutinin genes, and whole bacterial genomes. K-mer topology reveals the intrinsic shapes of the genome space and can be directly applied to the rational design of viral vaccines.","url_abs":"https://arxiv.org/abs/2412.20202v1","url_pdf":"https://arxiv.org/pdf/2412.20202v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"revealing-the-shape-of-genome-space-via-k-mer","repo_url":"https://github.com/hozumiyu/KmerTopology","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"diversity","task_name":"Diversity"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}