{"id":"https://openalex.org/W4413140828","doi":"https://doi.org/10.1186/s12859-025-06189-y","title":"HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data","display_name":"HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data","publication_year":2025,"publication_date":"2025-08-14","ids":{"openalex":"https://openalex.org/W4413140828","doi":"https://doi.org/10.1186/s12859-025-06189-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/40813968"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06189-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06189-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06189-y","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/s12859-025-06189-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055232452","display_name":"Tanya Golubchik","orcid":"https://orcid.org/0000-0003-2765-9828"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I2802952180","display_name":"Open Data Institute","ror":"https://ror.org/02hr72y72","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802952180"]}],"countries":["AU","GB"],"is_corresponding":true,"raw_author_name":"Tanya Golubchik","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK. tanya.golubchik@sydney.edu.au","Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia. tanya.golubchik@sydney.edu.au"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK. tanya.golubchik@sydney.edu.au","institution_ids":["https://openalex.org/I2802952180"]},{"raw_affiliation_string":"Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia. tanya.golubchik@sydney.edu.au","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060057242","display_name":"Lucie Abeler\u2010D\u00f6rner","orcid":"https://orcid.org/0000-0003-3662-4192"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lucie Abeler-D\u00f6rner","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107909588","display_name":"Matthew Hall","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew Hall","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014107408","display_name":"Chris Wymant","orcid":"https://orcid.org/0000-0002-9847-8226"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chris Wymant","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051261004","display_name":"David R. Bonsall","orcid":"https://orcid.org/0000-0002-2542-7559"},"institutions":[{"id":"https://openalex.org/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Bonsall","raw_affiliation_strings":["Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK","Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022974280","display_name":"George MacIntyre-Cockett","orcid":null},"institutions":[{"id":"https://openalex.org/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"George Macintyre-Cockett","raw_affiliation_strings":["Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK","Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Laura Thomson","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Laura Thomson","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064486492","display_name":"Jared M. Baeten","orcid":"https://orcid.org/0000-0001-8242-8438"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared M. Baeten","raw_affiliation_strings":["Department of Global Health, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090773831","display_name":"Connie Celum","orcid":"https://orcid.org/0000-0002-8813-3419"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210126592","display_name":"National Clinical Research","ror":"https://ror.org/03ddkvp86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210126592"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Connie L. Celum","raw_affiliation_strings":["Department of Global Health, University of Washington, Seattle, WA, USA","Department of Medicine, University of Washington, Seattle, WA, USA","International Clinical Research Center, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"International Clinical Research Center, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210126592","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035796355","display_name":"Ronald M. Galiwango","orcid":"https://orcid.org/0000-0003-3702-5722"},"institutions":[{"id":"https://openalex.org/I4210119732","display_name":"Rakai Health Sciences Program","ror":"https://ror.org/0315hfb21","country_code":"UG","type":"nonprofit","lineage":["https://openalex.org/I4210119732"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Ronald M. Galiwango","raw_affiliation_strings":["Rakai Health Sciences Program, Kalisizo, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rakai Health Sciences Program, Kalisizo, Uganda","institution_ids":["https://openalex.org/I4210119732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048330282","display_name":"Barry Kosloff","orcid":"https://orcid.org/0000-0002-8074-2586"},"institutions":[{"id":"https://openalex.org/I33278361","display_name":"University of Zambia","ror":"https://ror.org/03gh19d69","country_code":"ZM","type":"education","lineage":["https://openalex.org/I33278361"]},{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]},{"id":"https://openalex.org/I4210138699","display_name":"Zambart","ror":"https://ror.org/04p54bb05","country_code":"ZM","type":"facility","lineage":["https://openalex.org/I4210138699"]}],"countries":["GB","ZM"],"is_corresponding":false,"raw_author_name":"Barry Kosloff","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine, London, UK","Zambart, University of Zambia, Lusaka, Zambia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine, London, UK","institution_ids":["https://openalex.org/I4210089966"]},{"raw_affiliation_string":"Zambart, University of Zambia, Lusaka, Zambia","institution_ids":["https://openalex.org/I33278361","https://openalex.org/I4210138699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002501531","display_name":"Mohammed Limbada","orcid":"https://orcid.org/0000-0002-3736-1462"},"institutions":[{"id":"https://openalex.org/I33278361","display_name":"University of Zambia","ror":"https://ror.org/03gh19d69","country_code":"ZM","type":"education","lineage":["https://openalex.org/I33278361"]},{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]},{"id":"https://openalex.org/I4210138699","display_name":"Zambart","ror":"https://ror.org/04p54bb05","country_code":"ZM","type":"facility","lineage":["https://openalex.org/I4210138699"]}],"countries":["GB","ZM"],"is_corresponding":false,"raw_author_name":"Mohammed Limbada","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine, London, UK","Zambart, University of Zambia, Lusaka, Zambia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine, London, UK","institution_ids":["https://openalex.org/I4210089966"]},{"raw_affiliation_string":"Zambart, University of Zambia, Lusaka, Zambia","institution_ids":["https://openalex.org/I33278361","https://openalex.org/I4210138699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088742451","display_name":"Andrew Mujugira","orcid":"https://orcid.org/0000-0001-6646-6733"},"institutions":[{"id":"https://openalex.org/I4210116188","display_name":"Infectious Diseases Institute","ror":"https://ror.org/02caa0269","country_code":"UG","type":"nonprofit","lineage":["https://openalex.org/I4210116188"]},{"id":"https://openalex.org/I72227227","display_name":"Makerere University","ror":"https://ror.org/03dmz0111","country_code":"UG","type":"education","lineage":["https://openalex.org/I72227227"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Andrew Mujugira","raw_affiliation_strings":["Infectious Diseases Institute, Makerere University, Kampala, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Diseases Institute, Makerere University, Kampala, Uganda","institution_ids":["https://openalex.org/I72227227","https://openalex.org/I4210116188"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035859750","display_name":"Nelly Mugo","orcid":"https://orcid.org/0000-0002-2347-006X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I2841861","display_name":"Kenya Medical Research Institute","ror":"https://ror.org/04r1cxt79","country_code":"KE","type":"facility","lineage":["https://openalex.org/I2841861","https://openalex.org/I87048295"]}],"countries":["KE","US"],"is_corresponding":false,"raw_author_name":"Nelly R. Mugo","raw_affiliation_strings":["Department of Global Health, University of Washington, Seattle, WA, USA","Kenya Medical Research Institute (KEMRI), Nairobi, Kenya"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Kenya Medical Research Institute (KEMRI), Nairobi, Kenya","institution_ids":["https://openalex.org/I2841861"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053575511","display_name":"Astrid Gall","orcid":"https://orcid.org/0000-0001-6452-5816"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Astrid Gall","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102811171","display_name":"Fran\u00e7ois Blanquart","orcid":"https://orcid.org/0000-0003-3208-6665"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I187986737","display_name":"Coll\u00e8ge de France","ror":"https://ror.org/04ex24z53","country_code":"FR","type":"education","lineage":["https://openalex.org/I187986737"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I4210113621","display_name":"Centre Interdisciplinaire de Recherche en Biologie","ror":"https://ror.org/01mvzn566","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I187986737","https://openalex.org/I4210096427","https://openalex.org/I4210113621"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois Blanquart","raw_affiliation_strings":["Centre for Interdisciplinary Research in Biology (CIRB), Coll\u00e8ge de France, CNRS, INSERM, PSL Research University, Paris, France","IAME, UMR 1137, INSERM, Universit\u00e9 de Paris, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Interdisciplinary Research in Biology (CIRB), Coll\u00e8ge de France, CNRS, INSERM, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I4210113621","https://openalex.org/I154526488","https://openalex.org/I187986737","https://openalex.org/I2746051580","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IAME, UMR 1137, INSERM, Universit\u00e9 de Paris, Paris, France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040038561","display_name":"Margreet Bakker","orcid":"https://orcid.org/0000-0002-3803-3380"},"institutions":[{"id":"https://openalex.org/I4210151833","display_name":"Amsterdam University Medical Centers","ror":"https://ror.org/05grdyy37","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210151833"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Margreet Bakker","raw_affiliation_strings":["Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210151833"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103138084","display_name":"Daniela Bezemer","orcid":"https://orcid.org/0000-0001-9304-0877"},"institutions":[{"id":"https://openalex.org/I4210120830","display_name":"Stichting HIV Monitoring","ror":"https://ror.org/02w6k4f12","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210120830"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Daniela Bezemer","raw_affiliation_strings":["Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210120830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019231020","display_name":"Swee Hoe Ong","orcid":"https://orcid.org/0000-0002-3629-5387"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Swee Hoe Ong","raw_affiliation_strings":["Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061200353","display_name":"Jan Albert","orcid":"https://orcid.org/0000-0001-9020-0521"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jan Albert","raw_affiliation_strings":["Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden","Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111457482","display_name":"Norbert Bannert","orcid":null},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Norbert Bannert","raw_affiliation_strings":["Division for HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division for HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany","institution_ids":["https://openalex.org/I24359323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089009771","display_name":"Jacques Fellay","orcid":"https://orcid.org/0000-0002-8240-939X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jacques Fellay","raw_affiliation_strings":["Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland","School of Life Sciences, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"School of Life Sciences, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112413422","display_name":"Barbara Gunsenheimer\u2010Bartmeyer","orcid":null},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Barbara Gunsenheimer-Bartmeyer","raw_affiliation_strings":["Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany","institution_ids":["https://openalex.org/I24359323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060727664","display_name":"Huldrych F. G\u00fcnthard","orcid":"https://orcid.org/0000-0002-1142-6723"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Huldrych F. G\u00fcnthard","raw_affiliation_strings":["Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland","Institute of Medical Virology, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]},{"raw_affiliation_string":"Institute of Medical Virology, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008974627","display_name":"Pia Kivel\u00e4","orcid":"https://orcid.org/0000-0002-0678-2694"},"institutions":[{"id":"https://openalex.org/I2800394112","display_name":"Helsinki University Hospital","ror":"https://ror.org/02e8hzf44","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2800394112","https://openalex.org/I4210166427"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Pia Kivel\u00e4","raw_affiliation_strings":["Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland","institution_ids":["https://openalex.org/I2800394112"]}]},{"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/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Roger D. Kouyos","raw_affiliation_strings":["Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland","Institute of Medical Virology, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]},{"raw_affiliation_string":"Institute of Medical Virology, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108631029","display_name":"Laurence Meyer","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210097159","display_name":"Assistance Publique \u2013 H\u00f4pitaux de Paris","ror":"https://ror.org/00pg5jh14","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210097159"]},{"id":"https://openalex.org/I4210103698","display_name":"Centre de recherche en Epid\u00e9miologie et Sant\u00e9 des Populations","ror":"https://ror.org/01ed4t417","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I195731000","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210097159","https://openalex.org/I4210097159","https://openalex.org/I4210103698","https://openalex.org/I4210164847","https://openalex.org/I4405259118"]},{"id":"https://openalex.org/I4210162942","display_name":"Bic\u00eatre Hospital","ror":"https://ror.org/05c9p1x46","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210097159","https://openalex.org/I4210162942","https://openalex.org/I4405259118"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurence Meyer","raw_affiliation_strings":["INSERM CESP U1018, APHP, Service de Sant\u00e9 Publique, H\u00f4pital de Bic\u00eatre, Universit\u00e9 Paris Saclay, Le Kremlin-Bic\u00eatre, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM CESP U1018, APHP, Service de Sant\u00e9 Publique, H\u00f4pital de Bic\u00eatre, Universit\u00e9 Paris Saclay, Le Kremlin-Bic\u00eatre, France","institution_ids":["https://openalex.org/I4210097159","https://openalex.org/I4210103698","https://openalex.org/I154526488","https://openalex.org/I277688954","https://openalex.org/I4210162942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053100916","display_name":"Kholoud Porter","orcid":"https://orcid.org/0000-0002-9226-6206"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kholoud Porter","raw_affiliation_strings":["Institute for Global Health, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Global Health, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107885086","display_name":"Ard van Sighem","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120830","display_name":"Stichting HIV Monitoring","ror":"https://ror.org/02w6k4f12","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210120830"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ard van Sighem","raw_affiliation_strings":["Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210120830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081970249","display_name":"Mark van der Valk","orcid":null},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mark van der Valk","raw_affiliation_strings":["Amsterdam UMC Location Meibergdreef, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Amsterdam UMC Location Meibergdreef, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019287445","display_name":"Ben Berkhout","orcid":"https://orcid.org/0000-0002-1905-8486"},"institutions":[{"id":"https://openalex.org/I4210151833","display_name":"Amsterdam University Medical Centers","ror":"https://ror.org/05grdyy37","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210151833"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ben Berkhout","raw_affiliation_strings":["Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210151833"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067304304","display_name":"Paul Kellam","orcid":"https://orcid.org/0000-0003-3166-4734"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul Kellam","raw_affiliation_strings":["Department of Infectious Diseases, Department of Medicine, Imperial College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Department of Medicine, Imperial College London, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085074415","display_name":"Marion Cornelissen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151833","display_name":"Amsterdam University Medical Centers","ror":"https://ror.org/05grdyy37","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210151833"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marion Cornelissen","raw_affiliation_strings":["Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210151833"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113693386","display_name":"Peter Reiss","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120830","display_name":"Stichting HIV Monitoring","ror":"https://ror.org/02w6k4f12","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210120830"]},{"id":"https://openalex.org/I4210124406","display_name":"Amsterdam Institute for Global Health and Development","ror":"https://ror.org/037n2rm85","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210124406"]},{"id":"https://openalex.org/I4210151833","display_name":"Amsterdam University Medical Centers","ror":"https://ror.org/05grdyy37","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210151833"]},{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Peter Reiss","raw_affiliation_strings":["Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands","Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands","institution_ids":["https://openalex.org/I4210124406","https://openalex.org/I4210151833","https://openalex.org/I887064364"]},{"raw_affiliation_string":"Stichting HIV Monitoring, Amsterdam UMC, Location AMC, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I4210120830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029841050","display_name":"Helen Ayles","orcid":"https://orcid.org/0000-0003-4108-2842"},"institutions":[{"id":"https://openalex.org/I33278361","display_name":"University of Zambia","ror":"https://ror.org/03gh19d69","country_code":"ZM","type":"education","lineage":["https://openalex.org/I33278361"]},{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]},{"id":"https://openalex.org/I4210138699","display_name":"Zambart","ror":"https://ror.org/04p54bb05","country_code":"ZM","type":"facility","lineage":["https://openalex.org/I4210138699"]}],"countries":["GB","ZM"],"is_corresponding":false,"raw_author_name":"Helen Ayles","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine, London, UK","Zambart, University of Zambia, Lusaka, Zambia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine, London, UK","institution_ids":["https://openalex.org/I4210089966"]},{"raw_affiliation_string":"Zambart, University of Zambia, Lusaka, Zambia","institution_ids":["https://openalex.org/I33278361","https://openalex.org/I4210138699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102994075","display_name":"David Burns","orcid":"https://orcid.org/0000-0002-3362-865X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David N. Burns","raw_affiliation_strings":["Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067056877","display_name":"Sarah Fidler","orcid":"https://orcid.org/0000-0003-1676-7583"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah Fidler","raw_affiliation_strings":["Department of Infectious Disease Epidemiology, Imperial College, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Disease Epidemiology, Imperial College, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073671389","display_name":"M. Kate Grabowski","orcid":"https://orcid.org/0000-0002-4451-3436"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Kate Grabowski","raw_affiliation_strings":["Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091777537","display_name":"Richard Hayes","orcid":"https://orcid.org/0000-0002-1729-9892"},"institutions":[{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard Hayes","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine, London, UK","institution_ids":["https://openalex.org/I4210089966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080594686","display_name":"Joshua T. Herbeck","orcid":"https://orcid.org/0000-0003-4577-7406"},"institutions":[{"id":"https://openalex.org/I4210108985","display_name":"Bellevue Hospital Center","ror":"https://ror.org/01ky34z31","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283621791","https://openalex.org/I4210086933","https://openalex.org/I4210108985"]},{"id":"https://openalex.org/I4210161647","display_name":"Institute for Disease Modeling","ror":"https://ror.org/0532gcg76","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210161647"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua T. Herbeck","raw_affiliation_strings":["Institute for Disease Modeling, Bellevue, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Disease Modeling, Bellevue, WA, USA","institution_ids":["https://openalex.org/I4210161647","https://openalex.org/I4210108985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077362439","display_name":"Joseph Kagaayi","orcid":"https://orcid.org/0000-0003-4101-3038"},"institutions":[{"id":"https://openalex.org/I4210119732","display_name":"Rakai Health Sciences Program","ror":"https://ror.org/0315hfb21","country_code":"UG","type":"nonprofit","lineage":["https://openalex.org/I4210119732"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Joseph Kagaayi","raw_affiliation_strings":["Rakai Health Sciences Program, Kalisizo, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rakai Health Sciences Program, Kalisizo, Uganda","institution_ids":["https://openalex.org/I4210119732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077833051","display_name":"Pontiano Kaleebu","orcid":null},"institutions":[{"id":"https://openalex.org/I91369620","display_name":"Uganda Virus Research Institute","ror":"https://ror.org/04509n826","country_code":"UG","type":"facility","lineage":["https://openalex.org/I91369620"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Pontiano Kaleebu","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda","Medical Research Council (MRC), Uganda Virus Research Institute (UVRI), Entebbe, Uganda","Uganda Virus Research Institute, Entebbe, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]},{"raw_affiliation_string":"Medical Research Council (MRC), Uganda Virus Research Institute (UVRI), Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]},{"raw_affiliation_string":"Uganda Virus Research Institute, Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009104193","display_name":"Jairam R. Lingappa","orcid":"https://orcid.org/0000-0001-6191-9828"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jairam R. Lingappa","raw_affiliation_strings":["Department of Global Health, University of Washington, Seattle, WA, USA","Department of Medicine, University of Washington, Seattle, WA, USA","Department of Pediatrics, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Pediatrics, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071331157","display_name":"Deogratius Ssemwanga","orcid":"https://orcid.org/0000-0001-9675-4234"},"institutions":[{"id":"https://openalex.org/I91369620","display_name":"Uganda Virus Research Institute","ror":"https://ror.org/04509n826","country_code":"UG","type":"facility","lineage":["https://openalex.org/I91369620"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Deogratius Ssemwanga","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda","Medical Research Council (MRC), Uganda Virus Research Institute (UVRI), Entebbe, Uganda","Uganda Virus Research Institute, Entebbe, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]},{"raw_affiliation_string":"Medical Research Council (MRC), Uganda Virus Research Institute (UVRI), Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]},{"raw_affiliation_string":"Uganda Virus Research Institute, Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081294489","display_name":"Susan H. Eshleman","orcid":"https://orcid.org/0000-0002-4587-791X"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan H. Eshleman","raw_affiliation_strings":["Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024262342","display_name":"Myron S. Cohen","orcid":"https://orcid.org/0000-0001-5917-9664"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Myron S. Cohen","raw_affiliation_strings":["Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075573079","display_name":"Oliver Ratmann","orcid":"https://orcid.org/0000-0001-8667-4118"},"institutions":[{"id":"https://openalex.org/I4210109636","display_name":"NIHR Imperial Biomedical Research Centre","ror":"https://ror.org/01kmhx639","country_code":"GB","type":"facility","lineage":["https://openalex.org/I34931013","https://openalex.org/I4210109636"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Oliver Ratmann","raw_affiliation_strings":["Department of Mathematics and Imperial-X, Imperial College, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Imperial-X, Imperial College, London, UK","institution_ids":["https://openalex.org/I47508984","https://openalex.org/I4210109636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002192906","display_name":"Oliver Laeyendecker","orcid":"https://orcid.org/0000-0002-6429-4760"},"institutions":[{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oliver Laeyendecker","raw_affiliation_strings":["Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210134534"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113352199","display_name":"Christophe Fraser","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christophe Fraser","raw_affiliation_strings":["Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":12,"institutions_distinct_count":49,"corresponding_author_ids":["https://openalex.org/A5055232452"],"corresponding_institution_ids":["https://openalex.org/I129604602","https://openalex.org/I2802952180"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21462303,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"212","last_page":"212"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9541000127792358,"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":0.9541000127792358,"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/T10082","display_name":"HIV/AIDS Research and Interventions","score":0.01269999984651804,"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/T11655","display_name":"HIV-related health complications and treatments","score":0.006300000008195639,"subfield":{"id":"https://openalex.org/subfields/2711","display_name":"Emergency Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.7171846628189087},{"id":"https://openalex.org/keywords/incidence","display_name":"Incidence (geometry)","score":0.6042324304580688},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.543660044670105},{"id":"https://openalex.org/keywords/cross-sectional-study","display_name":"Cross-sectional study","score":0.5167012214660645},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4585338532924652},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.44428551197052},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3879600167274475},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3167567551136017},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20917215943336487},{"id":"https://openalex.org/keywords/environmental-health","display_name":"Environmental health","score":0.16223973035812378},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10517841577529907},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.09273037314414978}],"concepts":[{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.7171846628189087},{"id":"https://openalex.org/C61511704","wikidata":"https://www.wikidata.org/wiki/Q1671857","display_name":"Incidence (geometry)","level":2,"score":0.6042324304580688},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.543660044670105},{"id":"https://openalex.org/C142052008","wikidata":"https://www.wikidata.org/wiki/Q954027","display_name":"Cross-sectional study","level":2,"score":0.5167012214660645},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4585338532924652},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.44428551197052},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3879600167274475},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3167567551136017},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20917215943336487},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.16223973035812378},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10517841577529907},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.09273037314414978},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003430","descriptor_name":"Cross-Sectional Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003430","descriptor_name":"Cross-Sectional Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003430","descriptor_name":"Cross-Sectional Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003430","descriptor_name":"Cross-Sectional Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015994","descriptor_name":"Incidence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015994","descriptor_name":"Incidence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015994","descriptor_name":"Incidence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015994","descriptor_name":"Incidence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1186/s12859-025-06189-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06189-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06189-y","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:40813968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40813968","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:researchonline.lshtm.ac.uk:4677392","is_oa":false,"landing_page_url":"https://orcid.org/0000-0002-2671-3864>;","pdf_url":null,"source":{"id":"https://openalex.org/S4306402527","display_name":"LSHTM Research Online (London School of Hygiene and Tropical Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210089966","host_organization_name":"London School of Hygiene & Tropical Medicine","host_organization_lineage":["https://openalex.org/I4210089966"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:iris.unil.ch:iris/275175","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/275175","pdf_url":"https://iris.unil.ch/bitstreams/bd1da696-d198-419b-80ed-312ed526ec12/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pure.amsterdamumc.nl:openaire_cris_publications/fb4af2c9-22e5-4b47-bec3-c6c61417b1f5","is_oa":true,"landing_page_url":"https://pure.amsterdamumc.nl/en/publications/fb4af2c9-22e5-4b47-bec3-c6c61417b1f5","pdf_url":"https://pure.amsterdamumc.nl/ws/files/155929541/Hiv-phylotsi.pdf","source":{"id":"https://openalex.org/S7407055222","display_name":"Pure Amsterdam UMC","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"the HPTN 071 (PopART) Phylogenetics protocol team, the BEEHIVE consortium and the PANGEA consortium 2025, 'HIV-phyloTSI : subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data', BMC bioinformatics, vol. 26, no. 1, 212. https://doi.org/10.1186/s12859-025-06189-y","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:HAL:hal-05386814v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05386814","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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, 2025, 26, pp.212. &#x27E8;10.1186/s12859-025-06189-y&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:d0cd34dad9aa4ecb9eede01d14c17bbd","is_oa":true,"landing_page_url":"https://doaj.org/article/d0cd34dad9aa4ecb9eede01d14c17bbd","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":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-21 (2025)","raw_type":"article"},{"id":"pmh:oai:infoscience.epfl.ch:20.500.14299/252992","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/252992","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"research article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12351810","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12351810","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06189-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06189-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06189-y","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":0.8700000047683716}],"awards":[{"id":"https://openalex.org/G3400668103","display_name":null,"funder_award_id":"GNT2025445","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G5756016161","display_name":null,"funder_award_id":"PBDR-339251","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G7673395723","display_name":null,"funder_award_id":"UM1-AI068619, UM1-AI068617, UM1-AI068613","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8729917560","display_name":null,"funder_award_id":"OPP1175094","funder_id":"https://openalex.org/F4320306137","funder_display_name":"Bill and Melinda Gates Foundation"}],"funders":[{"id":"https://openalex.org/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413140828.pdf","grobid_xml":"https://content.openalex.org/works/W4413140828.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1859373664","https://openalex.org/W1970870597","https://openalex.org/W1983238746","https://openalex.org/W2042009035","https://openalex.org/W2061474260","https://openalex.org/W2109992855","https://openalex.org/W2111647009","https://openalex.org/W2115606439","https://openalex.org/W2116279310","https://openalex.org/W2117057469","https://openalex.org/W2117211286","https://openalex.org/W2121597235","https://openalex.org/W2126515754","https://openalex.org/W2134476478","https://openalex.org/W2145441111","https://openalex.org/W2154556944","https://openalex.org/W2159954944","https://openalex.org/W2160376658","https://openalex.org/W2164977615","https://openalex.org/W2165659928","https://openalex.org/W2167069127","https://openalex.org/W2167836864","https://openalex.org/W2167876918","https://openalex.org/W2170614926","https://openalex.org/W2171750584","https://openalex.org/W2326200534","https://openalex.org/W2326243398","https://openalex.org/W2469408700","https://openalex.org/W2509607956","https://openalex.org/W2602322060","https://openalex.org/W2626453821","https://openalex.org/W2744072791","https://openalex.org/W2773402514","https://openalex.org/W2791212039","https://openalex.org/W2804624135","https://openalex.org/W2918580560","https://openalex.org/W2927292733","https://openalex.org/W2950424777","https://openalex.org/W2957405671","https://openalex.org/W2961360820","https://openalex.org/W2980190037","https://openalex.org/W3006940104","https://openalex.org/W3042341244","https://openalex.org/W3043181818","https://openalex.org/W3047978686","https://openalex.org/W3164049327","https://openalex.org/W3168121242","https://openalex.org/W3174432009","https://openalex.org/W3202405895","https://openalex.org/W4200334485","https://openalex.org/W4232173555","https://openalex.org/W4293795531","https://openalex.org/W6677493503","https://openalex.org/W6685352449"],"related_works":["https://openalex.org/W4310894029","https://openalex.org/W2007075040","https://openalex.org/W4399033476","https://openalex.org/W2434162981","https://openalex.org/W4291398414","https://openalex.org/W2363171232","https://openalex.org/W4385684794","https://openalex.org/W1489156230","https://openalex.org/W2805384219","https://openalex.org/W2100632149"],"abstract_inverted_index":{"BACKGROUND:":[0],"Estimating":[1],"the":[2,17,45],"time":[3],"since":[4],"HIV":[5,19,128],"infection":[6],"(TSI)":[7],"at":[8],"population":[9,151],"level":[10],"is":[11],"essential":[12],"for":[13,23,81,111,125,146],"tracking":[14],"changes":[15],"in":[16],"global":[18],"epidemic.":[20],"Most":[21],"methods":[22],"determining":[24],"TSI":[25,71,90,115],"give":[26],"a":[27,37,54,86,96,114,119,150],"binary":[28],"classification":[29],"of":[30,39,48,63,89,100,116],"infections":[31,112],"as":[32],"recent":[33],"or":[34],"non-recent":[35],"within":[36],"window":[38],"several":[40],"months,":[41],"and":[42,66,106,135],"cannot":[43],"assess":[44],"cumulative":[46],"impact":[47],"an":[49],"intervention.":[50],"RESULTS:":[51],"We":[52,139],"developed":[53],"Random":[55],"Forest":[56],"Regression":[57],"model,":[58],"HIV-phyloTSI,":[59],"which":[60],"combines":[61],"measures":[62],"within-host":[64],"diversity":[65],"divergence":[67],"to":[68,92,118],"generate":[69],"continuous":[70,87],"estimates":[72,148],"directly":[73],"from":[74,133],"viral":[75],"deep-sequencing":[76],"data,":[77],"with":[78,95,113],"no":[79],"need":[80],"additional":[82],"variables.":[83],"HIV-phyloTSI":[84,142],"provides":[85],"measure":[88],"up":[91,117],"9":[93],"years,":[94],"mean":[97],"absolute":[98],"error":[99],"less":[101,107],"than":[102,108],"12":[103],"months":[104,110],"overall":[105],"5":[109],"year.":[120],"It":[121],"performs":[122],"equally":[123],"well":[124],"all":[126],"major":[127],"subtypes":[129],"based":[130],"on":[131,149],"data":[132],"African":[134],"European":[136],"cohorts.":[137],"CONCLUSIONS:":[138],"demonstrate":[140],"how":[141],"can":[143],"be":[144],"used":[145],"incidence":[147],"level.":[152]},"counts_by_year":[],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
