{"id":"https://openalex.org/W4386322157","doi":"https://doi.org/10.1093/bioinformatics/btad538","title":"Tracking and curating putative SARS-CoV-2 recombinants with RIVET","display_name":"Tracking and curating putative SARS-CoV-2 recombinants with RIVET","publication_year":2023,"publication_date":"2023-08-30","ids":{"openalex":"https://openalex.org/W4386322157","doi":"https://doi.org/10.1093/bioinformatics/btad538","pmid":"https://pubmed.ncbi.nlm.nih.gov/37651464"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad538","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad538/51316862/btad538.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/advance-article-pdf/doi/10.1093/bioinformatics/btad538/51316862/btad538.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019413667","display_name":"Kyle Smith","orcid":"https://orcid.org/0000-0002-0188-8289"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle Smith","raw_affiliation_strings":["Department of Biological Sciences, University of California, San Diego , San Diego, CA 92093, United States","San Diego, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of California, San Diego , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100741784","display_name":"Cheng Ye","orcid":"https://orcid.org/0009-0003-1113-6990"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheng Ye","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California, San Diego , San Diego, CA 92093, United States","San Diego, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California, San Diego , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080797757","display_name":"Yatish Turakhia","orcid":"https://orcid.org/0000-0001-5600-2900"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yatish Turakhia","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California, San Diego , San Diego, CA 92093, United States","San Diego, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0001-5600-2900","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California, San Diego , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080797757"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.1587,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.87787064,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.7578999996185303,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.7578999996185303,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.07109999656677246,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.016899999231100082,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rivet","display_name":"Rivet","score":0.9029315710067749},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6430907249450684},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.49273398518562317},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4795496165752411},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4692668318748474},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4560328722000122},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4453299939632416},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.426670104265213},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4127092957496643},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24964585900306702},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23017403483390808},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15895289182662964},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14473751187324524}],"concepts":[{"id":"https://openalex.org/C57769158","wikidata":"https://www.wikidata.org/wiki/Q212500","display_name":"Rivet","level":2,"score":0.9029315710067749},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6430907249450684},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.49273398518562317},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4795496165752411},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4692668318748474},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4560328722000122},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4453299939632416},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.426670104265213},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4127092957496643},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24964585900306702},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23017403483390808},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15895289182662964},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14473751187324524},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"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":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad538","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad538/51316862/btad538.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:37651464","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37651464","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:escholarship.org:ark:/13030/qt5pk8w7rw","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5pk8w7rw","pdf_url":"https://escholarship.org/content/qt5pk8w7rw/qt5pk8w7rw.pdf?t=s16j7i","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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, vol 39, iss 9","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10493179","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10493179","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10493179/pdf/btad538.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/btad538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad538","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad538/51316862/btad538.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":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G675940157","display_name":null,"funder_award_id":"BAA 200-2021-11554","funder_id":"https://openalex.org/F4320332162","funder_display_name":"Centers for Disease Control and Prevention"},{"id":"https://openalex.org/G8498159171","display_name":null,"funder_award_id":"200-2021-11554","funder_id":"https://openalex.org/F4320332162","funder_display_name":"Centers for Disease Control and Prevention"}],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386322157.pdf","grobid_xml":"https://content.openalex.org/works/W4386322157.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2141008678","https://openalex.org/W2605343262","https://openalex.org/W2952045272","https://openalex.org/W3043124965","https://openalex.org/W3160568774","https://openalex.org/W3176993778","https://openalex.org/W3196426464","https://openalex.org/W4291016578","https://openalex.org/W4308963287","https://openalex.org/W4310490448","https://openalex.org/W4319066889","https://openalex.org/W4367838604"],"related_works":["https://openalex.org/W2508625793","https://openalex.org/W2061230997","https://openalex.org/W4231824373","https://openalex.org/W2168500534","https://openalex.org/W3004544189","https://openalex.org/W2387459886","https://openalex.org/W2922209186","https://openalex.org/W1992310911","https://openalex.org/W2011822696","https://openalex.org/W2956119965"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"and":[2,17,68,83,90,108,132,144,170],"tracking":[3,109],"recombinant":[4],"strains":[5],"of":[6,14,28,52,74,106,122],"SARS-CoV-2":[7,24,88,124,162],"is":[8,39,126,135,149],"critical":[9],"to":[10,45,81],"understanding":[11],"the":[12,15,92,104,118,139,145],"evolution":[13],"virus":[16],"controlling":[18],"its":[19],"spread.":[20],"But":[21],"confidently":[22],"identifying":[23,107],"recombinants":[25,44,89,125],"from":[26,50],"thousands":[27],"new":[29],"genome":[30],"sequences":[31],"that":[32,71,99],"are":[33,163],"being":[34,55],"shared":[35],"online":[36],"every":[37],"day":[38],"quite":[40],"challenging,":[41],"causing":[42],"many":[43],"be":[46],"missed":[47],"or":[48],"suffer":[49],"weeks":[51],"delay":[53],"in":[54,78,95],"formally":[56],"identified":[57],"while":[58],"undergoing":[59],"expert":[60],"curation.":[61],"RESULTS:":[62],"We":[63],"present":[64],"RIVET-a":[65],"software":[66],"pipeline":[67],"visual":[69],"platform":[70],"takes":[72],"advantage":[73],"recent":[75],"algorithmic":[76],"advances":[77],"recombination":[79],"inference":[80],"comprehensively":[82],"sensitively":[84],"search":[85],"for":[86,147,156,161],"potential":[87,123],"organize":[91],"relevant":[93],"information":[94],"a":[96,166],"web":[97,115],"interface":[98,116],"would":[100],"help":[101],"greatly":[102],"accelerate":[103],"process":[105],"recombinants.":[110],"AVAILABILITY":[111],"AND":[112],"IMPLEMENTATION:":[113],"RIVET-based":[114],"displaying":[117],"most":[119],"updated":[120,171],"analysis":[121],"available":[127,137,150,164],"at":[128,142,151],"https://rivet.ucsd.edu/.":[129],"RIVET's":[130,158],"frontend":[131],"backend":[133,159],"code":[134],"freely":[136],"under":[138],"MIT":[140],"license":[141],"https://github.com/TurakhiaLab/rivet":[143],"documentation":[146],"RIVET":[148],"https://turakhialab.github.io/rivet/.":[152],"The":[153],"inputs":[154],"necessary":[155],"running":[157],"workflow":[160],"through":[165],"public":[167],"database":[168],"maintained":[169],"daily":[172],"by":[173],"UCSC":[174],"(https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/).":[175]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
