{"id":"https://openalex.org/W2040838139","doi":"https://doi.org/10.1371/journal.pcbi.1003842","title":"IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform","display_name":"IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform","publication_year":2014,"publication_date":"2014-09-25","ids":{"openalex":"https://openalex.org/W2040838139","doi":"https://doi.org/10.1371/journal.pcbi.1003842","mag":"2040838139","pmid":"https://pubmed.ncbi.nlm.nih.gov/25254639"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003842&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.1003842&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063261412","display_name":"N. Lance Hepler","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. Lance Hepler","raw_affiliation_strings":["Interdisciplinary Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060811249","display_name":"Konrad Scheffler","orcid":"https://orcid.org/0000-0002-6041-8367"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Konrad Scheffler","raw_affiliation_strings":["Department of Medicine, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058260003","display_name":"Steven Weaver","orcid":"https://orcid.org/0000-0002-6931-7191"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Weaver","raw_affiliation_strings":["Department of Medicine, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033401033","display_name":"Ben Murrell","orcid":"https://orcid.org/0000-0002-0393-4445"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Murrell","raw_affiliation_strings":["Department of Medicine, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073322790","display_name":"Douglas D. Richman","orcid":"https://orcid.org/0000-0003-0962-9254"},"institutions":[{"id":"https://openalex.org/I4210099595","display_name":"VA San Diego Healthcare System","ror":"https://ror.org/00znqwq11","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210099595","https://openalex.org/I4210138663"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas D. Richman","raw_affiliation_strings":["Department of Pathology, University of California San Diego, La Jolla, California, United States of America; San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","Department of Pathology, University of California San Diego, La Jolla, California, United States of America","San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of California San Diego, La Jolla, California, United States of America; San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Pathology, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","institution_ids":["https://openalex.org/I4210099595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058546353","display_name":"Dennis R. Burton","orcid":"https://orcid.org/0000-0001-6711-9864"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]},{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dennis R. Burton","raw_affiliation_strings":["The Scripps Research Institute, La Jolla, California, United States of America; Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, United States of America","Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, United States of America","The Scripps Research Institute, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, California, United States of America; Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024254197","display_name":"Pascal Poignard","orcid":"https://orcid.org/0000-0002-0021-7192"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pascal Poignard","raw_affiliation_strings":["The Scripps Research Institute, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044677503","display_name":"Davey M. Smith","orcid":"https://orcid.org/0000-0003-3603-1733"},"institutions":[{"id":"https://openalex.org/I4210099595","display_name":"VA San Diego Healthcare System","ror":"https://ror.org/00znqwq11","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210099595","https://openalex.org/I4210138663"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Davey M. Smith","raw_affiliation_strings":["Department of Medicine, University of California San Diego, La Jolla, California, United States of America; San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","Department of Medicine, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America; San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","institution_ids":[]},{"raw_affiliation_string":"San Diego Veterans Affairs Healthcare System, San Diego, California, United States of America","institution_ids":["https://openalex.org/I4210099595"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011410563","display_name":"Sergei L. Kosakovsky Pond","orcid":"https://orcid.org/0000-0003-4817-4029"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sergei L. Kosakovsky Pond","raw_affiliation_strings":["Department of Medicine, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5011410563"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.5169,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.81821277,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"9","first_page":"e1003842","last_page":"e1003842"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9983999729156494,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9980999827384949,"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/epitope","display_name":"Epitope","score":0.6660440564155579},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5817846655845642},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5506470203399658},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5068214535713196},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.493843138217926},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48583242297172546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.464526504278183},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4518508315086365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3844239115715027},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3318871557712555},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3276306986808777},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3260765075683594},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20639732480049133},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.16482830047607422},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16001027822494507}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.6660440564155579},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5817846655845642},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5506470203399658},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5068214535713196},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.493843138217926},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48583242297172546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.464526504278183},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4518508315086365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3844239115715027},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3318871557712555},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3276306986808777},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3260765075683594},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20639732480049133},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.16482830047607422},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16001027822494507},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015526","descriptor_name":"AIDS Dementia Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015526","descriptor_name":"AIDS Dementia Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015526","descriptor_name":"AIDS Dementia Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054298","descriptor_name":"Human Immunodeficiency Virus Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1003842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003842&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:25254639","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25254639","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:CiteSeerX.psu:10.1.1.785.667","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.785.667","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/1c/a8/pcbi.1003842.PMC4177671.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003842","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003842","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:68f8c9d0586541d3b58b57af20d44a30","is_oa":true,"landing_page_url":"https://doaj.org/article/68f8c9d0586541d3b58b57af20d44a30","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-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 10, Iss 9, p e1003842 (2014)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt7f54475z","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7f54475z","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3156112","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4177671","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1182885","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_IDEPI_Rapid_Prediction_of_HIV_1_Antibody_Epitopes_and_Other_Phenotypic_Features_from_Sequence_Data_Using_a_Flexible_Machine_Learning_Platform_/1182885","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:scholarshare.temple.edu:20.500.12613/5333","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12613/5333","pdf_url":null,"source":{"id":"https://openalex.org/S4306402624","display_name":"TUScholarShare (Temple University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84392919","host_organization_name":"Temple University","host_organization_lineage":["https://openalex.org/I84392919"],"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":"Journal Article"},{"id":"pmh:qt7f54475z","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/7f54475z","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Hepler, Lance; Scheffler, Konrad; Weaver, Steven; Murrell, Ben; Richman, Douglas; Burton, Dennis; \u00c2\u00a0et al.(2014). IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. Plos Comp Biol. UC Office of the President: UC Lab Fees Research Program (LFRP); a funding opportunity through UC Research Initiatives (UCRI). Retrieved from: http://www.escholarship.org/uc/item/7f54475z","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003842&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":[{"score":0.7900000214576721,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1317008451","display_name":null,"funder_award_id":"AI100665","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1755511917","display_name":null,"funder_award_id":"AI36214","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2225737672","display_name":null,"funder_award_id":"U54HL108460","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2980349986","display_name":null,"funder_award_id":"AI090970","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3136917840","display_name":null,"funder_award_id":"U54HL10846","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G619170566","display_name":null,"funder_award_id":"36617","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6720438208","display_name":null,"funder_award_id":"DA034978","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6807754532","display_name":null,"funder_award_id":"GM093939","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306138","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203"},{"id":"https://openalex.org/F4320311932","display_name":"James B. Pendleton Charitable Trust","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2040838139.pdf","grobid_xml":"https://content.openalex.org/works/W2040838139.grobid-xml"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W1582887581","https://openalex.org/W1584323946","https://openalex.org/W1635348995","https://openalex.org/W1876598876","https://openalex.org/W1900729316","https://openalex.org/W1964441398","https://openalex.org/W1965865659","https://openalex.org/W1972341594","https://openalex.org/W1983365822","https://openalex.org/W1988719235","https://openalex.org/W1992566288","https://openalex.org/W2004414122","https://openalex.org/W2012356776","https://openalex.org/W2016582810","https://openalex.org/W2020841101","https://openalex.org/W2027074843","https://openalex.org/W2028219017","https://openalex.org/W2045949915","https://openalex.org/W2051127367","https://openalex.org/W2053088580","https://openalex.org/W2053154970","https://openalex.org/W2054331494","https://openalex.org/W2056710036","https://openalex.org/W2068732957","https://openalex.org/W2069388608","https://openalex.org/W2069441228","https://openalex.org/W2070086938","https://openalex.org/W2070220357","https://openalex.org/W2083726777","https://openalex.org/W2087179955","https://openalex.org/W2087913283","https://openalex.org/W2090763940","https://openalex.org/W2094750078","https://openalex.org/W2095472461","https://openalex.org/W2096730244","https://openalex.org/W2099308199","https://openalex.org/W2102011058","https://openalex.org/W2102254707","https://openalex.org/W2104275641","https://openalex.org/W2109102997","https://openalex.org/W2110215558","https://openalex.org/W2113236498","https://openalex.org/W2113264508","https://openalex.org/W2116273933","https://openalex.org/W2117595928","https://openalex.org/W2117671898","https://openalex.org/W2118274231","https://openalex.org/W2119704168","https://openalex.org/W2120558856","https://openalex.org/W2122617162","https://openalex.org/W2124846613","https://openalex.org/W2128819444","https://openalex.org/W2129465264","https://openalex.org/W2133758885","https://openalex.org/W2135817154","https://openalex.org/W2136431383","https://openalex.org/W2139878522","https://openalex.org/W2140227530","https://openalex.org/W2149197858","https://openalex.org/W2149451504","https://openalex.org/W2149620753","https://openalex.org/W2154053567","https://openalex.org/W2154164013","https://openalex.org/W2154728363","https://openalex.org/W2156127238","https://openalex.org/W2163192209","https://openalex.org/W2165346130","https://openalex.org/W2169725989","https://openalex.org/W3105187411"],"related_works":["https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W1978626146","https://openalex.org/W2789551765"],"abstract_inverted_index":{"Since":[0],"its":[1],"identification":[2],"in":[3,15,32],"1983,":[4],"HIV-1":[5],"has":[6],"been":[7],"the":[8,29,37,42,62,71,156,167,174,188],"focus":[9],"of":[10,28,41,53,60,65,120,147,158,166,173],"a":[11,24,76,96,132,196],"research":[12],"effort":[13],"unprecedented":[14],"scope":[16],"and":[17,23,91,123,176,195],"difficulty,":[18],"whose":[19],"ultimate":[20],"goals--a":[21],"cure":[22],"vaccine--remain":[25],"elusive.":[26],"One":[27],"fundamental":[30],"challenges":[31],"accomplishing":[33],"these":[34],"goals":[35],"is":[36],"tremendous":[38],"genetic":[39,63,171],"variability":[40],"virus,":[43,168,175],"with":[44,109],"some":[45],"genes":[46],"differing":[47],"at":[48,205],"as":[49,51],"many":[50,66],"40%":[52],"nucleotide":[54],"positions":[55],"among":[56],"circulating":[57],"strains.":[58],"Because":[59],"this,":[61],"bases":[64],"viral":[67],"phenotypes,":[68,122],"most":[69],"notably":[70],"susceptibility":[72],"to":[73,81,117,131,142],"neutralization":[74],"by":[75],"particular":[77,133],"antibody,":[78],"are":[79],"difficult":[80],"identify":[82,125],"computationally.":[83],"Drawing":[84],"upon":[85],"open-source":[86],"general-purpose":[87],"machine":[88,199],"learning":[89,103],"algorithms":[90],"libraries,":[92],"we":[93],"have":[94],"developed":[95],"software":[97],"package":[98],"IDEPI":[99,112,138,201],"(IDentify":[100],"EPItopes)":[101],"for":[102,200],"genotype-to-phenotype":[104],"predictive":[105],"models":[106,116],"from":[107],"sequences":[108,119],"known":[110],"phenotypes.":[111],"can":[113,202],"apply":[114],"learned":[115],"classify":[118],"unknown":[121],"also":[124],"specific":[126],"sequence":[127],"features":[128],"which":[129],"contribute":[130],"phenotype.":[134],"We":[135],"demonstrate":[136],"that":[137,146],"achieves":[139],"performance":[140],"similar":[141],"or":[143],"better":[144],"than":[145],"previously":[148],"published":[149],"approaches":[150],"on":[151],"four":[152],"well-studied":[153],"problems:":[154],"finding":[155],"epitopes":[157],"broadly":[159],"neutralizing":[160],"antibodies":[161],"(bNab),":[162],"determining":[163],"coreceptor":[164],"tropism":[165],"identifying":[169],"compartment-specific":[170],"signatures":[172],"deducing":[177],"drug-resistance":[178],"associated":[179],"mutations.":[180],"The":[181],"cross-platform":[182],"Python":[183],"source":[184],"code":[185],"(released":[186],"under":[187],"GPL":[189],"3.0":[190],"license),":[191],"documentation,":[192],"issue":[193],"tracking,":[194],"pre-configured":[197],"virtual":[198],"be":[203],"found":[204],"https://github.com/veg/idepi.":[206]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
