{"id":"https://openalex.org/W2060582828","doi":"https://doi.org/10.1371/journal.pcbi.1001022","title":"The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time\u2014An Ultra-Deep Approach","display_name":"The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time\u2014An Ultra-Deep Approach","publication_year":2010,"publication_date":"2010-12-16","ids":{"openalex":"https://openalex.org/W2060582828","doi":"https://doi.org/10.1371/journal.pcbi.1001022","mag":"2060582828","pmid":"https://pubmed.ncbi.nlm.nih.gov/21187908"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1001022","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001022","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001022&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001022&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071433093","display_name":"John Archer","orcid":"https://orcid.org/0000-0001-6212-0962"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John Archer","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083534383","display_name":"Andrew Rambaut","orcid":"https://orcid.org/0000-0003-4337-3707"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew Rambaut","raw_affiliation_strings":["Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070980138","display_name":"Bruce E. Taillon","orcid":"https://orcid.org/0000-0002-2124-7921"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bruce E. Taillon","raw_affiliation_strings":["454 Life Sciences, Branford, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"454 Life Sciences, Branford, Connecticut, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036502017","display_name":"P. Richard Harrigan","orcid":"https://orcid.org/0000-0003-2631-3390"},"institutions":[{"id":"https://openalex.org/I4210131951","display_name":"AIDS Vancouver","ror":"https://ror.org/02mgny734","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210131951"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"P. Richard Harrigan","raw_affiliation_strings":["British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada","Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210131951"]},{"raw_affiliation_string":"Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111807565","display_name":"Marilyn Lewis","orcid":null},"institutions":[{"id":"https://openalex.org/I189718659","display_name":"Pfizer (United Kingdom)","ror":"https://ror.org/04x4v8p40","country_code":"GB","type":"company","lineage":["https://openalex.org/I180857899","https://openalex.org/I189718659"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marilyn Lewis","raw_affiliation_strings":["Pfizer Global Research and Development, Sandwich, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Pfizer Global Research and Development, Sandwich, United Kingdom","institution_ids":["https://openalex.org/I189718659"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082064376","display_name":"David L. Robertson","orcid":"https://orcid.org/0000-0001-6338-0221"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"David L. Robertson","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082064376"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.2129,"has_fulltext":false,"cited_by_count":81,"citation_normalized_percentile":{"value":0.92558414,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"6","issue":"12","first_page":"e1001022","last_page":"e1001022"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9991000294685364,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9929999709129333,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9835000038146973,"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/maraviroc","display_name":"Maraviroc","score":0.9163728952407837},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6533591151237488},{"id":"https://openalex.org/keywords/tropism","display_name":"Tropism","score":0.6376069784164429},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5959861278533936},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5796272158622742},{"id":"https://openalex.org/keywords/pyrosequencing","display_name":"Pyrosequencing","score":0.4925445020198822},{"id":"https://openalex.org/keywords/tissue-tropism","display_name":"Tissue tropism","score":0.47148510813713074},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.39576801657676697},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39187127351760864},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2982136607170105},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.29498887062072754},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.19694200158119202},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1369069516658783},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11896941065788269}],"concepts":[{"id":"https://openalex.org/C2778899366","wikidata":"https://www.wikidata.org/wiki/Q421369","display_name":"Maraviroc","level":3,"score":0.9163728952407837},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6533591151237488},{"id":"https://openalex.org/C35693153","wikidata":"https://www.wikidata.org/wiki/Q239762","display_name":"Tropism","level":3,"score":0.6376069784164429},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5959861278533936},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5796272158622742},{"id":"https://openalex.org/C125009961","wikidata":"https://www.wikidata.org/wiki/Q2342248","display_name":"Pyrosequencing","level":3,"score":0.4925445020198822},{"id":"https://openalex.org/C33602714","wikidata":"https://www.wikidata.org/wiki/Q7809666","display_name":"Tissue tropism","level":4,"score":0.47148510813713074},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.39576801657676697},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39187127351760864},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2982136607170105},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.29498887062072754},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.19694200158119202},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1369069516658783},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11896941065788269},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077592","descriptor_name":"Maraviroc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077592","descriptor_name":"Maraviroc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077592","descriptor_name":"Maraviroc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077592","descriptor_name":"Maraviroc","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":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D003510","descriptor_name":"Cyclohexanes","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D014230","descriptor_name":"Triazoles","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019718","descriptor_name":"Receptors, CXCR4","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019718","descriptor_name":"Receptors, CXCR4","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019718","descriptor_name":"Receptors, CXCR4","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019718","descriptor_name":"Receptors, CXCR4","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D023581","descriptor_name":"HIV Fusion Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D056189","descriptor_name":"Viral Tropism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056189","descriptor_name":"Viral Tropism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056189","descriptor_name":"Viral Tropism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056189","descriptor_name":"Viral Tropism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1001022","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001022","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001022&type=printable","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:21187908","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21187908","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:pure.atira.dk:openaire_cris_publications/f0b0f5c0-3084-445d-99ba-39571ebfaa0c","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/f0b0f5c0-3084-445d-99ba-39571ebfaa0c","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Archer, J, Rambaut, A, Taillon, B E, Richard Harrigan, P, Lewis, M & Robertson, D L 2010, 'The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach', PL o S Computational Biology, vol. 6, no. 12, e1001022. https://doi.org/10.1371/journal.pcbi.1001022","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/4b11cb48-e478-41ab-a8aa-8c6b8ffdfa12","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/4b11cb48-e478-41ab-a8aa-8c6b8ffdfa12","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Archer, J, Rambaut, A, Taillon, B E, Harrigan, P R, Lewis, M & Robertson, D L 2010, 'The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time-An Ultra-Deep Approach', PLoS Computational Biology, vol. 6, no. 12, e1001022, pp. -. https://doi.org/10.1371/journal.pcbi.1001022","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:eprints.gla.ac.uk:152140","is_oa":false,"landing_page_url":"http://eprints.gla.ac.uk/view/author/39082.html>","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.803.332","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.803.332","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/0f/46/pcbi.1001022.PMC3002995.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:563373be130342a0aeaf3c792c520439","is_oa":true,"landing_page_url":"https://doaj.org/article/563373be130342a0aeaf3c792c520439","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 6, Iss 12, p e1001022 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/140027","is_oa":true,"landing_page_url":"https://figshare.com/articles/The_Evolutionary_Analysis_of_Emerging_Low_Frequency_HIV_1_CXCR4_Using_Variants_through_Time_An_Ultra_Deep_Approach/140027","pdf_url":null,"source":{"id":"https://openalex.org/S4306400572","display_name":"OPAL (Open@LaTrobe) (La Trobe University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I196829312","host_organization_name":"La Trobe University","host_organization_lineage":["https://openalex.org/I196829312"],"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":"","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3002995","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3002995","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"},{"id":"pmh:oai:pure.atira.dk:publications/f0b0f5c0-3084-445d-99ba-39571ebfaa0c","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/the-evolutionary-analysis-of-emerging-low-frequency-hiv1-cxcr4-using-variants-through-timean-ultradeep-approach(f0b0f5c0-3084-445d-99ba-39571ebfaa0c).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1001022","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001022","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001022&type=printable","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":[],"awards":[{"id":"https://openalex.org/G1329556879","display_name":null,"funder_award_id":"BB/H012419/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5282413452","display_name":null,"funder_award_id":"BB/H011285/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7122601629","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"}],"funders":[{"id":"https://openalex.org/F4320307765","display_name":"Pfizer","ror":"https://ror.org/01xdqrp08"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2060582828.pdf","grobid_xml":"https://content.openalex.org/works/W2060582828.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1597858674","https://openalex.org/W1664573657","https://openalex.org/W1973398091","https://openalex.org/W1995198826","https://openalex.org/W1999048558","https://openalex.org/W2018808081","https://openalex.org/W2037113830","https://openalex.org/W2051445869","https://openalex.org/W2053485968","https://openalex.org/W2058079473","https://openalex.org/W2059670608","https://openalex.org/W2061680337","https://openalex.org/W2064541590","https://openalex.org/W2067391188","https://openalex.org/W2082555199","https://openalex.org/W2084454379","https://openalex.org/W2087064593","https://openalex.org/W2098448352","https://openalex.org/W2099172313","https://openalex.org/W2103546861","https://openalex.org/W2104275641","https://openalex.org/W2108256128","https://openalex.org/W2109034006","https://openalex.org/W2109093556","https://openalex.org/W2110917275","https://openalex.org/W2111283804","https://openalex.org/W2112113834","https://openalex.org/W2119951120","https://openalex.org/W2124985265","https://openalex.org/W2128114769","https://openalex.org/W2132926880","https://openalex.org/W2133233128","https://openalex.org/W2136145671","https://openalex.org/W2147064797","https://openalex.org/W2151292912","https://openalex.org/W2152365654","https://openalex.org/W2153527981","https://openalex.org/W2158266834","https://openalex.org/W2158714788","https://openalex.org/W2160230582","https://openalex.org/W2164631357","https://openalex.org/W2164762627","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W1953735714","https://openalex.org/W2121566985","https://openalex.org/W2020056247","https://openalex.org/W2790559265","https://openalex.org/W4383426296","https://openalex.org/W1888155289","https://openalex.org/W2103138322","https://openalex.org/W2105516881","https://openalex.org/W2147544546","https://openalex.org/W2128056683"],"abstract_inverted_index":{"Large-scale":[0],"parallel":[1],"pyrosequencing":[2,45],"produces":[3],"unprecedented":[4],"quantities":[5],"of":[6,26,50,60,82,94,112,143,154,164,228,235,246,252],"sequence":[7,63,166],"data.":[8,64,167],"However,":[9],"when":[10],"generated":[11],"from":[12,78,135,260],"viral":[13,51,102,186,248],"populations":[14],"current":[15],"mapping":[16,149],"software":[17,56,69,180,239],"is":[18,99,258],"inadequate":[19],"for":[20,33,57,243],"dealing":[21],"with":[22,171],"the":[23,31,41,48,58,87,95,110,119,141,152,162,185,226,233,244],"high":[24],"levels":[25],"variation":[27],"present,":[28],"resulting":[29],"in":[30,159,169,232],"potential":[32],"biased":[34],"data":[35],"loss.":[36],"In":[37,192],"order":[38],"to":[39,47,100,121,131,161,183,203,212],"apply":[40],"454":[42],"Life":[43],"Sciences'":[44],"system":[46],"study":[49,81,245],"populations,":[52],"we":[53,66],"have":[54,241],"developed":[55],"processing":[59],"highly":[61],"variable":[62],"Here":[65],"demonstrate":[67,151],"our":[68,179],"by":[70],"analyzing":[71],"two":[72],"temporally":[73],"sampled":[74],"HIV-1":[75,92],"intra-patient":[76],"datasets":[77],"a":[79,122],"clinical":[80],"maraviroc.":[83],"This":[84],"drug":[85],"binds":[86],"CCR5":[88],"coreceptor,":[89],"thus":[90,224],"preventing":[91],"infection":[93],"cell.":[96],"The":[97,238],"objective":[98],"determine":[101],"tropism":[103],"(CCR5":[104],"versus":[105],"CXCR4":[106],"usage)":[107],"and":[108,150,190,250,257],"track":[109],"evolution":[111,251],"minority":[113],"CXCR4-using":[114,197,230],"variants":[115,198,209],"that":[116,175,217],"may":[117],"limit":[118],"response":[120],"maraviroc-containing":[123],"treatment":[124],"regimen.":[125],"Five":[126],"time":[127],"points":[128],"(two":[129],"prior":[130,202],"treatment)":[132],"were":[133,200,210,218],"available":[134,259],"each":[136],"patient.":[137],"We":[138],"first":[139],"quantify":[140,184],"effects":[142],"divergence":[144],"on":[145],"initial":[146],"read":[147],"k-mer":[148],"importance":[153],"utilizing":[155],"population-specific":[156],"template":[157],"sequences":[158],"relation":[160],"analysis":[163],"next-generation":[165],"Then,":[168],"conjunction":[170],"coreceptor":[172],"prediction":[173],"algorithms":[174],"infer":[176],"HIV":[177],"tropism,":[178],"was":[181],"used":[182],"population":[187],"structure":[188],"pre-":[189],"post-treatment.":[191],"both":[193],"cases,":[194],"low":[195],"frequency":[196],"(2.5-15%)":[199],"detected":[201],"treatment.":[204],"Following":[205],"phylogenetic":[206],"inference,":[207],"these":[208],"observed":[211],"exist":[213],"as":[214],"distinct":[215],"lineages":[216],"maintained":[219],"through":[220],"time.":[221],"Our":[222],"analysis,":[223],"confirms":[225],"role":[227],"pre-existing":[229],"virus":[231],"emergence":[234],"maraviroc-insensitive":[236],"HIV.":[237],"will":[240],"utility":[242],"intra-host":[247],"diversity":[249],"other":[253],"fast":[254],"evolving":[255],"viruses,":[256],"http://www.bioinf.manchester.ac.uk/segminator/.":[261]},"counts_by_year":[{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":16}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
