{"id":"https://openalex.org/W2003478689","doi":"https://doi.org/10.1371/journal.pcbi.1002525","title":"Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase","display_name":"Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase","publication_year":2012,"publication_date":"2012-05-24","ids":{"openalex":"https://openalex.org/W2003478689","doi":"https://doi.org/10.1371/journal.pcbi.1002525","mag":"2003478689","pmid":"https://pubmed.ncbi.nlm.nih.gov/22654656"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002525","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002525","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002525&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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002525&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062645497","display_name":"Rafal Mostowy","orcid":"https://orcid.org/0000-0002-4557-3748"},"institutions":[{"id":"https://openalex.org/I4210090941","display_name":"Institute for Biomedical Engineering","ror":"https://ror.org/00baskk38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I202697423","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210090941"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Rafal Mostowy","raw_affiliation_strings":["Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland. rafal.mostowy@gmail.com","Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland. rafal.mostowy@gmail.com","institution_ids":["https://openalex.org/I4210090941","https://openalex.org/I35440088"]},{"raw_affiliation_string":"Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069244385","display_name":"Roger D. Kouyos","orcid":"https://orcid.org/0000-0002-9220-8348"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roger D. Kouyos","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America","Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004763412","display_name":"Ilka Hoof","orcid":"https://orcid.org/0000-0003-3827-7227"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ilka Hoof","raw_affiliation_strings":["Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085794325","display_name":"Trevor Hinkley","orcid":"https://orcid.org/0000-0002-4834-7631"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Trevor Hinkley","raw_affiliation_strings":["Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland","Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063681285","display_name":"Mojgan Haddad","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mojgan Haddad","raw_affiliation_strings":["Monogram Biosciences, South San Francisco, California, Unites States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences, South San Francisco, California, Unites States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109338840","display_name":"Jeannette M. Whitcomb","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeannette M. Whitcomb","raw_affiliation_strings":["Monogram Biosciences, South San Francisco, California, Unites States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences, South San Francisco, California, Unites States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042931433","display_name":"Christos J. Petropoulos","orcid":"https://orcid.org/0000-0001-5496-8090"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christos J. Petropoulos","raw_affiliation_strings":["Monogram Biosciences, South San Francisco, California, Unites States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences, South San Francisco, California, Unites States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073950969","display_name":"Can Ke\u015fmir","orcid":"https://orcid.org/0000-0002-8756-1171"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Can Ke\u015fmir","raw_affiliation_strings":["Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054236642","display_name":"Sebastian Bonhoeffer","orcid":"https://orcid.org/0000-0001-8052-3925"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sebastian Bonhoeffer","raw_affiliation_strings":["Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland","Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Institute for Integrative Biology, ETH Z\u00fcrich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5062645497"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I4210090941"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.9168,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71367139,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"5","first_page":"e1002525","last_page":"e1002525"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"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":0.9998999834060669,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9957000017166138,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9800999760627747,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.7720537185668945},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6501169800758362},{"id":"https://openalex.org/keywords/reverse-transcriptase","display_name":"Reverse transcriptase","score":0.6269210577011108},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.5301156044006348},{"id":"https://openalex.org/keywords/hla-b","display_name":"HLA-B","score":0.48140954971313477},{"id":"https://openalex.org/keywords/antigen-presentation","display_name":"Antigen presentation","score":0.4590747058391571},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.4544331431388855},{"id":"https://openalex.org/keywords/viral-replication","display_name":"Viral replication","score":0.4494105577468872},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.4277046024799347},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4138268828392029},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.4135659635066986},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40365317463874817},{"id":"https://openalex.org/keywords/cytotoxic-t-cell","display_name":"Cytotoxic T cell","score":0.37335312366485596},{"id":"https://openalex.org/keywords/in-vitro","display_name":"In vitro","score":0.3379770517349243},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.3247554898262024},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.322543740272522},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.27669548988342285},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22177010774612427},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.1687702238559723},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.13928154110908508},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08888620138168335}],"concepts":[{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.7720537185668945},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6501169800758362},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.6269210577011108},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.5301156044006348},{"id":"https://openalex.org/C41007239","wikidata":"https://www.wikidata.org/wiki/Q18026920","display_name":"HLA-B","level":4,"score":0.48140954971313477},{"id":"https://openalex.org/C83464605","wikidata":"https://www.wikidata.org/wiki/Q575296","display_name":"Antigen presentation","level":4,"score":0.4590747058391571},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.4544331431388855},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.4494105577468872},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.4277046024799347},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4138268828392029},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.4135659635066986},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40365317463874817},{"id":"https://openalex.org/C154317977","wikidata":"https://www.wikidata.org/wiki/Q376266","display_name":"Cytotoxic T cell","level":3,"score":0.37335312366485596},{"id":"https://openalex.org/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.3379770517349243},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.3247554898262024},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.322543740272522},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.27669548988342285},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22177010774612427},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.1687702238559723},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.13928154110908508},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08888620138168335}],"mesh":[{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","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":"D016333","descriptor_name":"HIV Protease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054303","descriptor_name":"HIV Reverse Transcriptase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054303","descriptor_name":"HIV Reverse Transcriptase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054303","descriptor_name":"HIV Reverse Transcriptase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1002525","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002525","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002525&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:22654656","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22654656","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:doaj.org/article:8f3336575b1246d68a87fa26b3fd2722","is_oa":true,"landing_page_url":"https://doaj.org/article/8f3336575b1246d68a87fa26b3fd2722","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 8, Iss 5, p e1002525 (2012)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/124603","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Estimating_the_Fitness_Cost_of_Escape_from_HLA_Presentation_in_HIV_1_Protease_and_Reverse_Transcriptase/124603","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:3359966","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3359966","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/53094","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/53094","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"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":"e1002525","raw_type":"Journal Article"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/51356","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/51356","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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 Computational Biology, 8 (5)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000051356","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000051356","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002525","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002525","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002525&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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8399999737739563}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003478689.pdf","grobid_xml":"https://content.openalex.org/works/W2003478689.grobid-xml"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W1502370146","https://openalex.org/W1564673741","https://openalex.org/W1963813930","https://openalex.org/W1965167575","https://openalex.org/W1969057879","https://openalex.org/W1971877271","https://openalex.org/W1976608858","https://openalex.org/W1979158913","https://openalex.org/W1981710464","https://openalex.org/W1982271112","https://openalex.org/W1983890005","https://openalex.org/W1986152436","https://openalex.org/W1993846907","https://openalex.org/W1997677784","https://openalex.org/W2001999757","https://openalex.org/W2005143264","https://openalex.org/W2023897382","https://openalex.org/W2033654955","https://openalex.org/W2045551237","https://openalex.org/W2051453551","https://openalex.org/W2054798895","https://openalex.org/W2056374390","https://openalex.org/W2058248480","https://openalex.org/W2063485002","https://openalex.org/W2069926681","https://openalex.org/W2070627782","https://openalex.org/W2076006481","https://openalex.org/W2076225720","https://openalex.org/W2077596118","https://openalex.org/W2080578177","https://openalex.org/W2081825634","https://openalex.org/W2081844025","https://openalex.org/W2083522539","https://openalex.org/W2084000984","https://openalex.org/W2085096513","https://openalex.org/W2087484510","https://openalex.org/W2088129901","https://openalex.org/W2092297539","https://openalex.org/W2095855948","https://openalex.org/W2096015577","https://openalex.org/W2096130477","https://openalex.org/W2097398162","https://openalex.org/W2099182602","https://openalex.org/W2099364824","https://openalex.org/W2102421932","https://openalex.org/W2104784743","https://openalex.org/W2107186721","https://openalex.org/W2109130469","https://openalex.org/W2110802771","https://openalex.org/W2111066113","https://openalex.org/W2113613707","https://openalex.org/W2118115182","https://openalex.org/W2129222479","https://openalex.org/W2142739377","https://openalex.org/W2143210482","https://openalex.org/W2147134928","https://openalex.org/W2147403620","https://openalex.org/W2148233687","https://openalex.org/W2148291080","https://openalex.org/W2151326236","https://openalex.org/W2151651155","https://openalex.org/W2152719039","https://openalex.org/W2154981737","https://openalex.org/W2161762733","https://openalex.org/W2163591597","https://openalex.org/W2164213171","https://openalex.org/W2167155055","https://openalex.org/W2168688111","https://openalex.org/W2169629503","https://openalex.org/W2171540341","https://openalex.org/W2171752791","https://openalex.org/W2172297142","https://openalex.org/W2400580124","https://openalex.org/W2917847056","https://openalex.org/W4214514832","https://openalex.org/W4236479494","https://openalex.org/W6682978103","https://openalex.org/W6759666926","https://openalex.org/W6992945715"],"related_works":["https://openalex.org/W2601749131","https://openalex.org/W30621581","https://openalex.org/W3186489996","https://openalex.org/W2311010430","https://openalex.org/W2205639878","https://openalex.org/W2325920701","https://openalex.org/W2073266897","https://openalex.org/W2461112563","https://openalex.org/W2006475088","https://openalex.org/W2946568617"],"abstract_inverted_index":{"Human":[0],"immunodeficiency":[1],"virus":[2,199,227],"(HIV-1)":[3],"is,":[4],"like":[5],"most":[6],"pathogens,":[7],"under":[8],"selective":[9],"pressure":[10],"to":[11,38,49,53,90,121,131,135,149,178,233],"escape":[12,63,91,155,183],"the":[13,32,44,54,82,97,167,210,222,234,248,254],"immune":[14,55],"system":[15],"of":[16,35,46,85,99,112,182,212,224,245,250,256],"its":[17],"host.":[18],"In":[19,77],"particular,":[20],"HIV-1":[21,100,257],"can":[22],"avoid":[23],"recognition":[24],"by":[25,30,93],"cytotoxic":[26],"T":[27],"lymphocytes":[28],"(CTLs)":[29],"altering":[31],"binding":[33,119,130,148,173],"affinity":[34,120],"viral":[36],"peptides":[37,52],"human":[39],"leukocyte":[40],"antigen":[41],"(HLA)":[42],"molecules,":[43,151,186],"role":[45],"which":[47,87,128,144],"is":[48,58,175],"present":[50],"those":[51],"system.":[56],"It":[57],"generally":[59],"assumed":[60],"that":[61,126,153,166,237],"HLA":[62,94,122],"mutations":[64,86,127,143,156],"carry":[65,157],"a":[66,206],"replicative":[67,83,115,140],"fitness":[68,116,141,159,170],"cost,":[69],"but":[70],"these":[71,188],"costs":[72,160,189],"have":[73,136],"not":[74,146,204,219],"been":[75],"quantified.":[76],"this":[78,217,230],"study,":[79],"we":[80,106,202],"assess":[81],"cost":[84,181],"are":[88,190],"likely":[89],"presentation":[92],"molecules":[95,133,239],"in":[96,113,138,209,226,253,261],"region":[98],"protease":[101],"and":[102,117,171,187,258],"reverse":[103],"transcriptase.":[104],"Specifically,":[105],"combine":[107],"computational":[108],"approaches":[109],"for":[110,193],"prediction":[111],"vitro":[114,139],"peptide":[118],"molecules.":[123],"We":[124,164],"find":[125],"impair":[129,147],"HLA-A":[132,150,154,172,185,194,238,251],"tend":[134],"lower":[137],"than":[142,161],"do":[145,203],"suggesting":[152],"higher":[158],"non-escape":[162],"mutations.":[163],"argue":[165,220],"association":[168],"between":[169],"impairment":[174],"probably":[176],"due":[177],"an":[179],"intrinsic":[180],"from":[184],"particularly":[191],"strong":[192],"alleles":[195],"associated":[196],"with":[197],"efficient":[198],"control.":[200,228],"Counter-intuitively,":[201],"observe":[205],"significant":[207],"effect":[208],"case":[211],"HLA-B,":[213],"but,":[214],"as":[215],"discussed,":[216],"does":[218],"against":[221],"relevance":[223],"HLA-B":[225],"Overall,":[229],"article":[231],"points":[232],"intriguing":[235],"possibility":[236],"preferentially":[240],"target":[241],"more":[242],"conserved":[243],"regions":[244],"HIV-1,":[246],"emphasizing":[247],"importance":[249],"genes":[252],"evolution":[255],"RNA":[259],"viruses":[260],"general.":[262]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
