{"id":"https://openalex.org/W4392529729","doi":"https://doi.org/10.1093/bioinformatics/btae093","title":"ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment","display_name":"ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment","publication_year":2024,"publication_date":"2024-02-19","ids":{"openalex":"https://openalex.org/W4392529729","doi":"https://doi.org/10.1093/bioinformatics/btae093","pmid":"https://pubmed.ncbi.nlm.nih.gov/38374486"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae093/56832253/btae093.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae093/56832253/btae093.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063430171","display_name":"Zuher Jahshan","orcid":"https://orcid.org/0000-0003-4333-1718"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Zuher Jahshan","raw_affiliation_strings":["EnICS Labs, Engineering Department, Bar-Ilan University , Ramat Gan, Tel Aviv 5290002, Israel"],"raw_orcid":"https://orcid.org/0000-0003-4333-1718","affiliations":[{"raw_affiliation_string":"EnICS Labs, Engineering Department, Bar-Ilan University , Ramat Gan, Tel Aviv 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007161424","display_name":"Leonid Yavits","orcid":"https://orcid.org/0000-0001-5248-3997"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Leonid Yavits","raw_affiliation_strings":["EnICS Labs, Engineering Department, Bar-Ilan University , Ramat Gan, Tel Aviv 5290002, Israel"],"raw_orcid":"https://orcid.org/0000-0001-5248-3997","affiliations":[{"raw_affiliation_string":"EnICS Labs, Engineering Department, Bar-Ilan University , Ramat Gan, Tel Aviv 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063430171"],"corresponding_institution_ids":["https://openalex.org/I13955877"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9331,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.72288917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6851000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6851000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.1647000014781952,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.06069999933242798,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.6832655668258667},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6161203384399414},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5795300602912903},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45200014114379883},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44018277525901794},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.42529192566871643},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3080676794052124},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2038554847240448},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.19608837366104126},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13246390223503113},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.08258253335952759},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07639965415000916}],"concepts":[{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6832655668258667},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6161203384399414},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5795300602912903},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45200014114379883},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44018277525901794},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.42529192566871643},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3080676794052124},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2038554847240448},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.19608837366104126},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13246390223503113},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.08258253335952759},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07639965415000916},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae093/56832253/btae093.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38374486","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38374486","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10913383","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10913383","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10913383/pdf/btae093.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae093/56832253/btae093.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G2342797219","display_name":null,"funder_award_id":"101047160","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392529729.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1601795611","https://openalex.org/W1979543168","https://openalex.org/W2025720061","https://openalex.org/W2083239248","https://openalex.org/W2095705004","https://openalex.org/W2105368763","https://openalex.org/W2138398659","https://openalex.org/W2157539385","https://openalex.org/W2259815689","https://openalex.org/W2618398196","https://openalex.org/W2889664156","https://openalex.org/W2950150251","https://openalex.org/W2950266744","https://openalex.org/W2990618091","https://openalex.org/W3088711112","https://openalex.org/W3119770574","https://openalex.org/W3127482714","https://openalex.org/W3160568774","https://openalex.org/W4224436915","https://openalex.org/W4225524232","https://openalex.org/W4385245566","https://openalex.org/W6674330103","https://openalex.org/W6738373677","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W4382894326","https://openalex.org/W3035105474","https://openalex.org/W4205698903","https://openalex.org/W2506149209","https://openalex.org/W4294968941","https://openalex.org/W2352153050","https://openalex.org/W4283819461","https://openalex.org/W4390279739","https://openalex.org/W4205413867","https://openalex.org/W2053972265"],"abstract_inverted_index":{"MOTIVATION:":[0],"Rapid":[1],"spread":[2],"of":[3,19,85,93,141,168,191],"viral":[4,31],"diseases":[5],"such":[6,133],"as":[7,134],"Coronavirus":[8],"disease":[9],"2019":[10],"(COVID-19)":[11],"highlights":[12],"an":[13],"urgent":[14],"need":[15],"for":[16,95,102],"efficient":[17],"surveillance":[18],"virus":[20],"mutation":[21],"and":[22,29,53,99,106,136,143,206],"transmission":[23],"dynamics,":[24],"which":[25,46],"requires":[26],"fast,":[27],"inexpensive":[28],"accurate":[30,65],"lineage":[32,66,83,107,124],"assignment.":[33,108],"The":[34,197],"first":[35],"two":[36],"goals":[37],"might":[38],"be":[39,185,208],"achieved":[40],"through":[41],"low-coverage":[42],"whole-genome":[43],"sequencing":[44,50],"(LC-WGS)":[45],"enables":[47],"rapid":[48],"genome":[49,104],"at":[51,54,127],"scale":[52],"reduced":[55],"costs.":[56],"Unfortunately,":[57],"LC-WGS":[58],"significantly":[59],"diminishes":[60],"the":[61,139,166,173],"genomic":[62,96],"details,":[63],"rendering":[64],"assignment":[67,84,125],"very":[68],"challenging.":[69],"RESULTS:":[70],"We":[71,109,160,180],"present":[72],"ViTAL,":[73],"a":[74,91],"novel":[75,169,192],"deep":[76],"learning":[77],"algorithm":[78],"specifically":[79],"designed":[80],"to":[81,122,153,164,187],"perform":[82],"low":[86],"coverage-sequenced":[87],"genomes.":[88],"ViTAL":[89,112,146,183],"utilizes":[90],"combination":[92],"MinHash":[94],"feature":[97],"extraction":[98],"Vision":[100,174],"Transformer":[101,175],"fine-grain":[103],"classification":[105],"show":[110,181],"that":[111],"outperforms":[113],"state-of-the-art":[114,131,158],"tools":[115,132],"across":[116],"diverse":[117],"coverage":[118,129,156],"levels,":[119],"reaching":[120],"up":[121,152],"87.7%":[123],"accuracy":[126,140,149],"1\u00d7":[128],"where":[130],"UShER":[135],"Kraken2":[137],"achieve":[138],"5.4%":[142],"27.4%":[144],"respectively.":[145],"achieves":[147],"comparable":[148],"results":[150],"with":[151,210],"8\u00d7":[154],"lower":[155],"than":[157],"tools.":[159],"explore":[161],"ViTAL's":[162],"ability":[163],"identify":[165],"lineages":[167],"genomes,":[170],"i.e.":[171],"genomes":[172],"was":[176],"not":[177],"trained":[178],"on.":[179],"how":[182],"can":[184,207],"applied":[186],"preliminary":[188],"phylogenetic":[189],"placement":[190],"variants.":[193],"AVAILABILITY":[194],"AND":[195],"IMPLEMENTATION:":[196],"data":[198],"underlying":[199],"this":[200],"article":[201],"are":[202],"available":[203],"in":[204],"https://github.com/zuherJahshan/vital":[205],"accessed":[209],"10.5281/zenodo.10688110.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":5}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
