{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T09:12:39Z","timestamp":1744189959340,"version":"3.37.3"},"reference-count":37,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002491","name":"Bristol-Myers Squibb Co","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002491","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000104","name":"National Aeronautics and Space Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.fr","clinicalkey.jp","clinicalkey.com.au","clinicalkey.es","clinicalkey.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computers in Biology and Medicine"],"published-print":{"date-parts":[[2021,4]]},"DOI":"10.1016\/j.compbiomed.2021.104264","type":"journal-article","created":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T20:31:52Z","timestamp":1614025912000},"page":"104264","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":68,"special_numbering":"C","title":["UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets"],"prefix":"10.1016","volume":"131","author":[{"given":"Yuta","family":"Hozumi","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7402-6372","authenticated-orcid":false,"given":"Rui","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Changchuan","family":"Yin","sequence":"additional","affiliation":[]},{"given":"Guo-Wei","family":"Wei","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"unstructured":"COVID19 Weekly Epidemiological Update, 19 January 2021, 2021.","key":"10.1016\/j.compbiomed.2021.104264_bib1"},{"key":"10.1016\/j.compbiomed.2021.104264_bib2","doi-asserted-by":"crossref","first-page":"405","DOI":"10.3389\/fcimb.2020.00405","article-title":"Functional pangenome analysis shows key features of e protein are preserved in SARS and SARS-CoV-2","volume":"10","author":"Alam","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"10.1016\/j.compbiomed.2021.104264_bib3","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.ijid.2020.08.066","article-title":"Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends","author":"Bai","year":"2020","journal-title":"Int. J. Infect. Dis."},{"issue":"1","key":"10.1016\/j.compbiomed.2021.104264_bib4","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using umap","volume":"37","author":"Becht","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.compbiomed.2021.104264_bib5","first-page":"585","article-title":"Laplacian eigenmaps and spectral techniques for embedding and clustering","volume":"14","author":"Belkin","year":"2001","journal-title":"Adv. Neural Inf. Process. Syst."},{"key":"10.1016\/j.compbiomed.2021.104264_bib6","doi-asserted-by":"crossref","first-page":"5212","DOI":"10.1016\/j.jmb.2020.07.009","article-title":"Mutations strengthened SARS-CoV-2 infectivity","volume":"432","author":"Chen","year":"2020","journal-title":"J. Mol. Biol."},{"year":"2019","author":"Chen","series-title":"Evolutionary de rham-hodge method","key":"10.1016\/j.compbiomed.2021.104264_bib7"},{"key":"10.1016\/j.compbiomed.2021.104264_bib8","series-title":"Handbook of Data Visualization","first-page":"315","article-title":"Multidimensional scaling","author":"Cox","year":"2008"},{"key":"10.1016\/j.compbiomed.2021.104264_bib9","first-page":"9241","article-title":"Phylogenetic network analysis of sars-cov-2 genomes","volume":"vol. 117","author":"Forster","year":"2020"},{"issue":"1","key":"10.1016\/j.compbiomed.2021.104264_bib10","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1080\/22221751.2020.1782271","article-title":"SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East","volume":"9","author":"Gong","year":"2020","journal-title":"Emerg. Microb. Infect."},{"key":"10.1016\/j.compbiomed.2021.104264_bib11","article-title":"Principal component analysis: a review and recent developments","volume":"374","author":"Jolliffe","year":"2016","journal-title":"Phil. Trans. Math. Phys. Eng. Sci."},{"issue":"10","key":"10.1016\/j.compbiomed.2021.104264_bib12","doi-asserted-by":"crossref","DOI":"10.1002\/jmv.25909","article-title":"Understanding evolution of SARS-CoV-2: A perspective from analysis of genetic diversity of RdRp gene","volume":"92","author":"Kasibhatla","year":"2020","journal-title":"J. Med. Virol."},{"issue":"4","key":"10.1016\/j.compbiomed.2021.104264_bib13","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.cell.2020.06.043","article-title":"Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus","volume":"182","author":"Korber","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.compbiomed.2021.104264_bib14","first-page":"2278","article-title":"Gradient-based learning applied to document recognition","volume":"vol. 86","author":"LeCun","year":"1998"},{"issue":"5323","key":"10.1016\/j.compbiomed.2021.104264_bib15","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/234034a0","article-title":"Distance between sets","volume":"234","author":"Levandowsky","year":"1971","journal-title":"Nature"},{"issue":"6","key":"10.1016\/j.compbiomed.2021.104264_bib16","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1002\/jmv.25731","article-title":"Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2","volume":"92","author":"Li","year":"2020","journal-title":"J. Med. Virol."},{"issue":"3","key":"10.1016\/j.compbiomed.2021.104264_bib17","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41592-018-0308-4","article-title":"Fast interpolation-based t-sne for improved visualization of single-cell rna-seq data","volume":"16","author":"Linderman","year":"2019","journal-title":"Nat. Methods"},{"issue":"Nov","key":"10.1016\/j.compbiomed.2021.104264_bib18","first-page":"2579","article-title":"Visualizing data using t-sne","volume":"9","author":"Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"year":"2018","author":"McInnes","series-title":"UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction","key":"10.1016\/j.compbiomed.2021.104264_bib19"},{"year":"1996","author":"Nene","series-title":"Columbia Object Image Library (Coil-20)","key":"10.1016\/j.compbiomed.2021.104264_bib20"},{"issue":"4","key":"10.1016\/j.compbiomed.2021.104264_bib21","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41564-020-0695-z","article-title":"The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2","volume":"5","author":"of the International","year":"2020","journal-title":"Nature Microbiol"},{"issue":"2","key":"10.1016\/j.compbiomed.2021.104264_bib22","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.tree.2011.12.002","article-title":"Space, time, form: viewing the tree of life","volume":"27","author":"Page","year":"2012","journal-title":"Trends Ecol. Evol."},{"year":"2019","author":"Rozemberczki","series-title":"Multi-scale Attributed Node Embedding","key":"10.1016\/j.compbiomed.2021.104264_bib23"},{"issue":"5","key":"10.1016\/j.compbiomed.2021.104264_bib24","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1109\/T-C.1969.222678","article-title":"A nonlinear mapping for data structure analysis","volume":"100","author":"Sammon","year":"1969","journal-title":"IEEE Trans. Comput."},{"issue":"1","key":"10.1016\/j.compbiomed.2021.104264_bib25","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.compbiomed.2021.104264_bib26","article-title":"Metric realization of fuzzy simplicial sets","author":"Spivak","year":"2012","journal-title":"Self Published Notes"},{"key":"10.1016\/j.compbiomed.2021.104264_bib27","series-title":"Proceedings of the 25th International Conference on World Wide Web","first-page":"287","article-title":"Visualizing large-scale and high-dimensional data","author":"Tang","year":"2016"},{"key":"10.1016\/j.compbiomed.2021.104264_bib28","article-title":"SARS-CoV-2 genomic variations associated with mortality rate of COVID-19","volume":"1\u20138","author":"Toyoshima","year":"2020","journal-title":"J. Hum. Genet."},{"author":"Ulyanov","key":"10.1016\/j.compbiomed.2021.104264_bib29"},{"key":"10.1016\/j.compbiomed.2021.104264_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2020.104351","article-title":"Emergence of genomic diversity and recurrent mutations in SARS-CoV-2","volume":"83","author":"van Dorp","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.compbiomed.2021.104264_bib31","article-title":"Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants","volume":"4","author":"Wang","year":"2021","journal-title":"Commun. Biol."},{"issue":"23","key":"10.1016\/j.compbiomed.2021.104264_bib32","doi-asserted-by":"crossref","first-page":"10007","DOI":"10.1021\/acs.jpclett.0c02765","article-title":"Decoding asymptomatic COVID-19 infection and transmission","volume":"11","author":"Wang","year":"2020","journal-title":"J. Phys. Chem. Lett."},{"key":"10.1016\/j.compbiomed.2021.104264_bib33","doi-asserted-by":"crossref","first-page":"5853","DOI":"10.1021\/acs.jcim.0c00501","article-title":"Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine","volume":"60","author":"Wang","year":"2020","journal-title":"J. Chem. Inf. Model."},{"issue":"47","key":"10.1016\/j.compbiomed.2021.104264_bib34","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1088\/0305-4470\/33\/47\/317","article-title":"Wavelets generated by using discrete singular convolution kernels","volume":"33","author":"Wei","year":"2000","journal-title":"J. Phys. Math. Gen."},{"issue":"6516","key":"10.1016\/j.compbiomed.2021.104264_bib35","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1126\/science.abc8169","article-title":"The emergence of SARS-CoV-2 in europe and north America","volume":"370","author":"Worobey","year":"2020","journal-title":"Science"},{"issue":"7798","key":"10.1016\/j.compbiomed.2021.104264_bib36","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.compbiomed.2021.104264_bib37","series-title":"International Symposium on Bioinformatics Research and Applications","first-page":"38","article-title":"An approach for determining evolutionary distance in network-based phylogenetic analysis","author":"Zhou","year":"2008"}],"container-title":["Computers in Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482521000585?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482521000585?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T17:26:34Z","timestamp":1671729994000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0010482521000585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4]]},"references-count":37,"alternative-id":["S0010482521000585"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiomed.2021.104264","relation":{},"ISSN":["0010-4825"],"issn-type":[{"type":"print","value":"0010-4825"}],"subject":[],"published":{"date-parts":[[2021,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets","name":"articletitle","label":"Article Title"},{"value":"Computers in Biology and Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiomed.2021.104264","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"104264"}}