{"id":"https://openalex.org/W1582237080","doi":"https://doi.org/10.1186/1471-2105-12-477","title":"A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes","display_name":"A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes","publication_year":2011,"publication_date":"2011-12-01","ids":{"openalex":"https://openalex.org/W1582237080","doi":"https://doi.org/10.1186/1471-2105-12-477","mag":"1582237080","pmid":"https://pubmed.ncbi.nlm.nih.gov/22172090"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-477","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-477","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-477","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-477","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061214521","display_name":"Kathleen M Doherty","orcid":null},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kathleen M Doherty","raw_affiliation_strings":["Department of Chemistry, Wellesley College, MA 02481, USA","Department of Chemistry, Wellesley College, Wellesley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Wellesley College, MA 02481, USA","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Department of Chemistry, Wellesley College, Wellesley, USA","institution_ids":["https://openalex.org/I189731429"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084547559","display_name":"Priyanka Nakka","orcid":"https://orcid.org/0000-0002-6572-0338"},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Priyanka Nakka","raw_affiliation_strings":["Department of Chemistry, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA","Department of Chemistry, Wellesley College, Wellesley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Department of Chemistry, Wellesley College, Wellesley, USA","institution_ids":["https://openalex.org/I189731429"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025170622","display_name":"Bracken M. King","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bracken M King","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA","Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004821374","display_name":"Soo\u2010Yon Rhee","orcid":"https://orcid.org/0000-0002-1231-6542"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soo-Yon Rhee","raw_affiliation_strings":["Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA","Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003674456","display_name":"Susan Holmes","orcid":"https://orcid.org/0000-0002-2208-8168"},"institutions":[{"id":"https://openalex.org/I4210151112","display_name":"Sequoia (United States)","ror":"https://ror.org/05y5sz883","country_code":"US","type":"company","lineage":["https://openalex.org/I4210151112"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan P Holmes","raw_affiliation_strings":["Department of Statistics, Stanford University, Sequoia Hall, Stanford, CA, 94305, USA","Department of Statistics, Stanford University, Stanford, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Stanford University, Sequoia Hall, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I4210151112","https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Statistics, Stanford University, Stanford, USA#TAB#","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066628402","display_name":"Robert W. Shafer","orcid":"https://orcid.org/0000-0003-2513-2643"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert W Shafer","raw_affiliation_strings":["Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA","Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074623322","display_name":"Mala L. Radhakrishnan","orcid":"https://orcid.org/0000-0002-5434-3696"},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mala L Radhakrishnan","raw_affiliation_strings":["Department of Chemistry, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA","Department of Chemistry, Wellesley College, Wellesley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Department of Chemistry, Wellesley College, Wellesley, USA","institution_ids":["https://openalex.org/I189731429"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074623322"],"corresponding_institution_ids":["https://openalex.org/I189731429"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.03923112,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"12","issue":"1","first_page":"477","last_page":"477"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9818999767303467,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9818999767303467,"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/T10112","display_name":"HIV Research and Treatment","score":0.009200000204145908,"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/T14065","display_name":"Biological Research and Disease Studies","score":0.0010000000474974513,"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/phenotype","display_name":"Phenotype","score":0.6880929470062256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6300647258758545},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.5884790420532227},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5539259314537048},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.4971168339252472},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.47844862937927246},{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.47346416115760803},{"id":"https://openalex.org/keywords/drug-resistance","display_name":"Drug resistance","score":0.4313977360725403},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4205301105976105},{"id":"https://openalex.org/keywords/multiple-drug-resistance","display_name":"Multiple drug resistance","score":0.4159614145755768},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3689362108707428},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16270896792411804},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13316336274147034},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.06843045353889465}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.6880929470062256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6300647258758545},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.5884790420532227},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5539259314537048},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.4971168339252472},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.47844862937927246},{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.47346416115760803},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.4313977360725403},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4205301105976105},{"id":"https://openalex.org/C133936738","wikidata":"https://www.wikidata.org/wiki/Q643839","display_name":"Multiple drug resistance","level":3,"score":0.4159614145755768},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3689362108707428},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16270896792411804},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13316336274147034},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.06843045353889465},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D018432","descriptor_name":"Drug Resistance, Multiple","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018432","descriptor_name":"Drug Resistance, Multiple","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018432","descriptor_name":"Drug Resistance, Multiple","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-12-477","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-477","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-477","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22172090","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22172090","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:dspace.mit.edu:1721.1/70131","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/70131","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioMed Central Ltd","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3305535","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3305535","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"},{"id":"mag:1582237080","is_oa":false,"landing_page_url":"http://dspace.mit.edu/handle/1721.1/70131","pdf_url":null,"source":{"id":"https://openalex.org/S4306504412","display_name":"BioMed Central Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"BioMed Central Ltd","raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-477","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-477","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-477","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G1996860710","display_name":null,"funder_award_id":"R01GM086884","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2119659357","display_name":null,"funder_award_id":"R01 GM086884","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2534655269","display_name":null,"funder_award_id":"P01GM066524-06","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2714060006","display_name":null,"funder_award_id":"AI068581","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3906500218","display_name":null,"funder_award_id":"AI068581","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5992084012","display_name":null,"funder_award_id":"R01 AI068581","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8005353130","display_name":null,"funder_award_id":"GM82209","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320308518","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1582237080.pdf","grobid_xml":"https://content.openalex.org/works/W1582237080.grobid-xml"},"referenced_works_count":96,"referenced_works":["https://openalex.org/W56727962","https://openalex.org/W325597738","https://openalex.org/W1491468287","https://openalex.org/W1496518737","https://openalex.org/W1533957288","https://openalex.org/W1975552235","https://openalex.org/W1976295381","https://openalex.org/W1981651833","https://openalex.org/W1981719094","https://openalex.org/W1982694918","https://openalex.org/W1984399867","https://openalex.org/W1988215875","https://openalex.org/W2000176602","https://openalex.org/W2001897216","https://openalex.org/W2004800530","https://openalex.org/W2004827391","https://openalex.org/W2007788465","https://openalex.org/W2008105864","https://openalex.org/W2009467617","https://openalex.org/W2023158628","https://openalex.org/W2029534465","https://openalex.org/W2029777156","https://openalex.org/W2030284869","https://openalex.org/W2035210758","https://openalex.org/W2040305511","https://openalex.org/W2052505662","https://openalex.org/W2054688372","https://openalex.org/W2055698455","https://openalex.org/W2058616175","https://openalex.org/W2058950377","https://openalex.org/W2059684559","https://openalex.org/W2060969737","https://openalex.org/W2067419109","https://openalex.org/W2071949631","https://openalex.org/W2074877586","https://openalex.org/W2080878445","https://openalex.org/W2087730348","https://openalex.org/W2091110992","https://openalex.org/W2096933078","https://openalex.org/W2097008764","https://openalex.org/W2097544439","https://openalex.org/W2097847166","https://openalex.org/W2100173291","https://openalex.org/W2101654079","https://openalex.org/W2102218736","https://openalex.org/W2103089413","https://openalex.org/W2105860794","https://openalex.org/W2106571163","https://openalex.org/W2106720283","https://openalex.org/W2109046728","https://openalex.org/W2110774309","https://openalex.org/W2113264508","https://openalex.org/W2115568737","https://openalex.org/W2116844530","https://openalex.org/W2118245054","https://openalex.org/W2118879505","https://openalex.org/W2119751130","https://openalex.org/W2120338717","https://openalex.org/W2122818068","https://openalex.org/W2124977780","https://openalex.org/W2125038904","https://openalex.org/W2125176038","https://openalex.org/W2125229283","https://openalex.org/W2125900719","https://openalex.org/W2127237622","https://openalex.org/W2127706932","https://openalex.org/W2128685318","https://openalex.org/W2129670212","https://openalex.org/W2140179827","https://openalex.org/W2140227530","https://openalex.org/W2140708560","https://openalex.org/W2143107901","https://openalex.org/W2144729871","https://openalex.org/W2144886570","https://openalex.org/W2144948767","https://openalex.org/W2148291080","https://openalex.org/W2149958386","https://openalex.org/W2154164013","https://openalex.org/W2155312822","https://openalex.org/W2157053750","https://openalex.org/W2159769151","https://openalex.org/W2160877552","https://openalex.org/W2163914644","https://openalex.org/W2168459018","https://openalex.org/W2169192079","https://openalex.org/W2171365066","https://openalex.org/W2171764043","https://openalex.org/W2172073367","https://openalex.org/W2182593161","https://openalex.org/W2318289184","https://openalex.org/W2321852728","https://openalex.org/W2335293609","https://openalex.org/W2417693750","https://openalex.org/W2787894218","https://openalex.org/W2911949936","https://openalex.org/W4297914773"],"related_works":["https://openalex.org/W2151238491","https://openalex.org/W1988215875","https://openalex.org/W2289015004","https://openalex.org/W2525062205","https://openalex.org/W2972130793","https://openalex.org/W2955517206","https://openalex.org/W3030020101","https://openalex.org/W2893446289","https://openalex.org/W2499686589","https://openalex.org/W3163336885","https://openalex.org/W2799591144","https://openalex.org/W3134631939","https://openalex.org/W3117048482","https://openalex.org/W3083934723","https://openalex.org/W2951768958","https://openalex.org/W2779995494","https://openalex.org/W2525271232","https://openalex.org/W3132716326","https://openalex.org/W2104818573","https://openalex.org/W1980560288"],"abstract_inverted_index":{"BACKGROUND:":[0],"Great":[1],"strides":[2],"have":[3,95],"been":[4,97],"made":[5],"in":[6,262],"the":[7,13,42,45,102,109,113,121,129,139,149,162,230,263],"effective":[8,22],"treatment":[9],"of":[10,15,89,112,123,128,145,161,232,265],"HIV-1":[11,26,65,91,105,152,207,217],"with":[12,209],"development":[14],"second-generation":[16],"protease":[17,92,153],"inhibitors":[18,267],"(PIs)":[19],"that":[20,31,59,94,141,190,198,251,268],"are":[21,60,155,171],"against":[23,62],"historically":[24],"multi-PI-resistant":[25],"variants.":[27,66],"Nevertheless,":[28],"mutation":[29,201],"patterns":[30,49,84,202,241,259],"confer":[32],"decreasing":[33],"susceptibility":[34,100,125,218],"to":[35,39,79,119,126,157,173,183,206,255,260],"available":[36,130],"PIs":[37,58,131],"continue":[38],"arise":[40],"within":[41],"population.":[43],"Understanding":[44],"phenotypic":[46,82,146,164,191,211,240,258],"and":[47,167,177,242],"genotypic":[48,186,196,246],"responsible":[50],"for":[51,56,99,179],"multi-PI":[52,81],"resistance":[53,83,181,235],"is":[54],"necessary":[55],"developing":[57],"active":[61],"clinically-relevant":[63,163,257],"PI-resistant":[64],"RESULTS:":[67],"In":[68],"this":[69],"work,":[70],"we":[71],"use":[72],"globally":[73],"optimal":[74],"integer":[75],"programming-based":[76],"clustering":[77],"techniques":[78],"elucidate":[80,184],"using":[85,132],"a":[86,133,143,226,249],"data":[87],"set":[88],"398":[90],"sequences":[93,176],"each":[96,127,220],"phenotyped":[98],"toward":[101,219],"nine":[103],"clinically-approved":[104],"PIs.":[106],"We":[107,137,188],"validate":[108],"information":[110],"content":[111],"clusters":[114],"by":[115,236],"evaluating":[116],"their":[117,185,243],"ability":[118],"predict":[120],"level":[122],"decreased":[124],"cross":[134,147],"validation":[135],"procedure.":[136],"demonstrate":[138],"finding":[140],"as":[142,275],"result":[144],"resistance,":[148],"considered":[150],"clinical":[151],"isolates":[154,208],"confined":[156],"~6%":[158],"or":[159],"less":[160],"space.":[165],"Clustering":[166],"feature":[168],"selection":[169],"methods":[170],"used":[172],"find":[174],"representative":[175],"mutations":[178],"major":[180,238],"phenotypes":[182],"signatures.":[187],"show":[189],"similarity":[192],"does":[193],"not":[194],"imply":[195],"similarity,":[197],"different":[199],"PI-resistance":[200],"can":[203,252],"give":[204],"rise":[205],"similar":[210],"profiles.":[212],"CONCLUSION:":[213],"Rather":[214],"than":[215],"characterizing":[216],"PI":[221,233],"individually,":[222],"our":[223],"study":[224],"offers":[225],"unique":[227],"perspective":[228],"on":[229],"phenomenon":[231],"class":[234],"uncovering":[237],"multidrug-resistant":[239],"often":[244],"diverse":[245],"determinants,":[247],"providing":[248],"methodology":[250],"be":[253],"applied":[254],"understand":[256],"aid":[261],"design":[264],"novel":[266],"target":[269],"other":[270],"rapidly":[271],"evolving":[272],"molecular":[273],"targets":[274],"well.":[276]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}