{"id":"https://openalex.org/W4310433486","doi":"https://doi.org/10.1371/journal.pcbi.1010745","title":"Optimized phylogenetic clustering of HIV-1 sequence data for public health applications","display_name":"Optimized phylogenetic clustering of HIV-1 sequence data for public health applications","publication_year":2022,"publication_date":"2022-11-30","ids":{"openalex":"https://openalex.org/W4310433486","doi":"https://doi.org/10.1371/journal.pcbi.1010745","pmid":"https://pubmed.ncbi.nlm.nih.gov/36449514"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010745","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010745","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1010745","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082929859","display_name":"Connor Chato","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Connor Chato","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Western University, London, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Western University, London, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101844801","display_name":"Yi Feng","orcid":"https://orcid.org/0000-0003-4995-1440"},"institutions":[{"id":"https://openalex.org/I4210131009","display_name":"National Center for AIDS/STD Control and Prevention,China CDC","ror":"https://ror.org/02xnb4v27","country_code":"CN","type":"government","lineage":["https://openalex.org/I184490438","https://openalex.org/I4210127390","https://openalex.org/I4210131009","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Feng","raw_affiliation_strings":["Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China"],"affiliations":[{"raw_affiliation_string":"Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China","institution_ids":["https://openalex.org/I4210131009"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025217307","display_name":"Yuhua Ruan","orcid":"https://orcid.org/0000-0003-2346-9154"},"institutions":[{"id":"https://openalex.org/I4210131009","display_name":"National Center for AIDS/STD Control and Prevention,China CDC","ror":"https://ror.org/02xnb4v27","country_code":"CN","type":"government","lineage":["https://openalex.org/I184490438","https://openalex.org/I4210127390","https://openalex.org/I4210131009","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhua Ruan","raw_affiliation_strings":["Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China"],"affiliations":[{"raw_affiliation_string":"Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China","institution_ids":["https://openalex.org/I4210131009"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102836681","display_name":"Hui Xing","orcid":"https://orcid.org/0000-0002-9213-2531"},"institutions":[{"id":"https://openalex.org/I4210131009","display_name":"National Center for AIDS/STD Control and Prevention,China CDC","ror":"https://ror.org/02xnb4v27","country_code":"CN","type":"government","lineage":["https://openalex.org/I184490438","https://openalex.org/I4210127390","https://openalex.org/I4210131009","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Xing","raw_affiliation_strings":["Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China"],"affiliations":[{"raw_affiliation_string":"Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China","institution_ids":["https://openalex.org/I4210131009"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080594686","display_name":"Joshua T. Herbeck","orcid":"https://orcid.org/0000-0003-4577-7406"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Herbeck","raw_affiliation_strings":["Department of Global Health, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Global Health, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107414102","display_name":"Marcia L. Kalish","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcia Kalish","raw_affiliation_strings":["Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004110504","display_name":"Art F. Y. Poon","orcid":"https://orcid.org/0000-0003-3779-154X"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Art F. Y. Poon","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Western University, London, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Western University, London, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5004110504"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6932,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67603842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"18","issue":"11","first_page":"e1010745","last_page":"e1010745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944999814033508,"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":0.9944999814033508,"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/T10112","display_name":"HIV Research and Treatment","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9347000122070312,"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/statistics","display_name":"Statistics","score":0.6415173411369324},{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.5914206504821777},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.5593501925468445},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5533037781715393},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5330124497413635},{"id":"https://openalex.org/keywords/null-model","display_name":"Null model","score":0.49087005853652954},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4537898898124695},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4371863007545471},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.42747655510902405},{"id":"https://openalex.org/keywords/poisson-regression","display_name":"Poisson regression","score":0.4218202233314514},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.28842365741729736},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.24331605434417725},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.21199536323547363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18370512127876282}],"concepts":[{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.6415173411369324},{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.5914206504821777},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.5593501925468445},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5533037781715393},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5330124497413635},{"id":"https://openalex.org/C36382193","wikidata":"https://www.wikidata.org/wiki/Q7068966","display_name":"Null model","level":2,"score":0.49087005853652954},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4537898898124695},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4371863007545471},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.42747655510902405},{"id":"https://openalex.org/C73269764","wikidata":"https://www.wikidata.org/wiki/Q954529","display_name":"Poisson regression","level":3,"score":0.4218202233314514},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28842365741729736},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.24331605434417725},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.21199536323547363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18370512127876282},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010745","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010745","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36449514","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36449514","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1010745","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010745","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:67112e635a2a48d4927fd8683a38d966","is_oa":true,"landing_page_url":"https://doaj.org/article/67112e635a2a48d4927fd8683a38d966","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 11, p e1010745 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9744331","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9744331","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010745","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010745","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8100000023841858}],"awards":[{"id":"https://openalex.org/G4389354971","display_name":null,"funder_award_id":"Research","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G4515207065","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G530539032","display_name":null,"funder_award_id":"PJT-156178","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G6282788884","display_name":null,"funder_award_id":"Canadian Institutes of Health","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G6826593982","display_name":null,"funder_award_id":"(PJT-156178)","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320332582","display_name":"Center for AIDS Research, University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":85,"referenced_works":["https://openalex.org/W24778476","https://openalex.org/W1605984840","https://openalex.org/W1943089283","https://openalex.org/W1970771372","https://openalex.org/W1975375203","https://openalex.org/W1987526988","https://openalex.org/W1990653767","https://openalex.org/W2004989708","https://openalex.org/W2006617902","https://openalex.org/W2008620264","https://openalex.org/W2031611770","https://openalex.org/W2037320822","https://openalex.org/W2058815839","https://openalex.org/W2070519435","https://openalex.org/W2076169690","https://openalex.org/W2079513642","https://openalex.org/W2085326051","https://openalex.org/W2096812618","https://openalex.org/W2097278341","https://openalex.org/W2105243066","https://openalex.org/W2111647009","https://openalex.org/W2119284380","https://openalex.org/W2125230147","https://openalex.org/W2127832030","https://openalex.org/W2133979592","https://openalex.org/W2138324310","https://openalex.org/W2141877163","https://openalex.org/W2144775551","https://openalex.org/W2146397496","https://openalex.org/W2148323323","https://openalex.org/W2154331465","https://openalex.org/W2158666214","https://openalex.org/W2164582219","https://openalex.org/W2265419465","https://openalex.org/W2319514196","https://openalex.org/W2325940284","https://openalex.org/W2339822499","https://openalex.org/W2465493330","https://openalex.org/W2549654384","https://openalex.org/W2557801288","https://openalex.org/W2564054800","https://openalex.org/W2598381200","https://openalex.org/W2598532836","https://openalex.org/W2605599004","https://openalex.org/W2763389670","https://openalex.org/W2766463782","https://openalex.org/W2782500353","https://openalex.org/W2791699957","https://openalex.org/W2793085614","https://openalex.org/W2794406673","https://openalex.org/W2883251903","https://openalex.org/W2884242568","https://openalex.org/W2884876954","https://openalex.org/W2885319825","https://openalex.org/W2889534444","https://openalex.org/W2894393582","https://openalex.org/W2896818093","https://openalex.org/W2900465010","https://openalex.org/W2901879045","https://openalex.org/W2903803722","https://openalex.org/W2912227521","https://openalex.org/W2942179837","https://openalex.org/W2949210352","https://openalex.org/W2949470996","https://openalex.org/W2950916832","https://openalex.org/W2951155461","https://openalex.org/W2951384372","https://openalex.org/W2964052890","https://openalex.org/W2969491951","https://openalex.org/W2971743870","https://openalex.org/W2979805875","https://openalex.org/W2981223466","https://openalex.org/W2997330044","https://openalex.org/W3003030812","https://openalex.org/W3011246689","https://openalex.org/W3012364352","https://openalex.org/W3017213354","https://openalex.org/W3029457766","https://openalex.org/W3032896424","https://openalex.org/W3034729528","https://openalex.org/W3038018049","https://openalex.org/W3044022174","https://openalex.org/W3046966614","https://openalex.org/W3095611768","https://openalex.org/W4286697461"],"related_works":["https://openalex.org/W2503331259","https://openalex.org/W1590941618","https://openalex.org/W3096804274","https://openalex.org/W2509788866","https://openalex.org/W3134844154","https://openalex.org/W3200250056","https://openalex.org/W2385896179","https://openalex.org/W2150462512","https://openalex.org/W2885596111","https://openalex.org/W2270206682"],"abstract_inverted_index":{"Clusters":[0,92],"of":[1,107,112,141,203,212],"genetically":[2],"similar":[3],"infections":[4],"suggest":[5,233],"rapid":[6],"transmission":[7],"and":[8,27,89,167,232],"may":[9],"indicate":[10],"priorities":[11],"for":[12,41,58,242],"public":[13,42,243],"health":[14,43,244],"action":[15],"or":[16],"reveal":[17],"underlying":[18],"epidemiological":[19],"processes.":[20],"However,":[21],"clusters":[22],"often":[23],"require":[24],"user-defined":[25],"thresholds":[26,57,144,196,205,241],"are":[28],"sensitive":[29],"to":[30,126,130],"non-epidemiological":[31],"factors,":[32],"such":[33],"as":[34,148,176],"non-random":[35],"sampling.":[36],"Consequently":[37],"the":[38,131,139,213],"ideal":[39],"threshold":[40],"applications":[44],"varies":[45],"substantially":[46],"across":[47,187,199],"settings.":[48],"Here,":[49],"we":[50,123],"show":[51],"a":[52,103,110,116,119,149,158],"method":[53,69],"which":[54],"selects":[55],"optimal":[56,191,204],"phylogenetic":[59,229],"(subset":[60],"tree)":[61],"clustering":[62,250],"based":[63],"on":[64,70,145],"population.":[65],"We":[66,137],"evaluated":[67,138],"this":[68],"HIV-1":[71],"pol":[72],"datasets":[73],"(n":[74],"=":[75,222],"14,":[76],"221":[77],"sequences)":[78],"from":[79,98,164],"four":[80],"sites":[81],"in":[82,194,239,249],"USA":[83],"(Tennessee,":[84],"Washington),":[85],"Canada":[86],"(Northern":[87],"Alberta)":[88],"China":[90],"(Beijing).":[91],"were":[93],"defined":[94],"by":[95,134,152,185,215],"tips":[96],"descending":[97],"an":[99,168,177],"ancestral":[100],"node":[101],"(with":[102],"minimum":[104],"bootstrap":[105],"support":[106],"95%)":[108],"through":[109],"series":[111],"branches,":[113],"each":[114],"with":[115,190],"length":[117],"below":[118],"given":[120],"threshold.":[121],"Next,":[122],"used":[124,248],"pplacer":[125],"graft":[127],"new":[128],"cases":[129],"fixed":[132],"tree":[133],"maximum":[135],"likelihood.":[136],"effect":[140],"varying":[142],"branch-length":[143],"cluster":[146,165,230],"growth":[147,163,231],"count":[150],"outcome":[151],"fitting":[153],"two":[154],"Poisson":[155],"regression":[156],"models:":[157],"null":[159],"model":[160,170,182],"that":[161,171,234],"predicts":[162],"size,":[166],"alternative":[169,181],"includes":[172],"mean":[173],"collection":[174],"date":[175],"additional":[178],"covariate.":[179],"The":[180,201],"was":[183,206],"favoured":[184],"AIC":[186],"most":[188],"thresholds,":[189],"(greatest":[192],"difference":[193],"AIC)":[195],"ranging":[197],"0.007-0.013":[198],"sites.":[200],"range":[202],"more":[207,237],"variable":[208],"when":[209],"re-sampling":[210],"80%":[211],"data":[214],"location":[216],"(IQR":[217],"0.008":[218],"-":[219],"0.016,":[220],"n":[221],"100":[223],"replicates).":[224],"Our":[225],"results":[226],"use":[227],"prospective":[228],"there":[235],"is":[236],"variation":[238],"effective":[240],"than":[245],"those":[246],"typically":[247],"studies.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
