{"id":"https://openalex.org/W1809466148","doi":"https://doi.org/10.1186/s13015-016-0064-x","title":"Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage","display_name":"Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage","publication_year":2016,"publication_date":"2016-03-11","ids":{"openalex":"https://openalex.org/W1809466148","doi":"https://doi.org/10.1186/s13015-016-0064-x","mag":"1809466148","pmid":"https://pubmed.ncbi.nlm.nih.gov/26973707"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-016-0064-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-016-0064-x","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0064-x","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0064-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jean P. Zukurov","orcid":null},"institutions":[{"id":"https://openalex.org/I88273585","display_name":"Universidade Federal de S\u00e3o Paulo","ror":"https://ror.org/02k5swt12","country_code":"BR","type":"education","lineage":["https://openalex.org/I88273585"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jean P. Zukurov","raw_affiliation_strings":["Departmento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I88273585"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sieberth do Nascimento-Brito","orcid":null},"institutions":[{"id":"https://openalex.org/I88273585","display_name":"Universidade Federal de S\u00e3o Paulo","ror":"https://ror.org/02k5swt12","country_code":"BR","type":"education","lineage":["https://openalex.org/I88273585"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Sieberth do Nascimento-Brito","raw_affiliation_strings":["Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Departamento de Microbiologia e Imunologia Veterin\u00e1ria, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Departamento de Microbiologia e Imunologia Veterin\u00e1ria, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I88273585"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Angela C. Volpini","orcid":"https://orcid.org/0000-0003-1513-9278"},"institutions":[{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Angela C. Volpini","raw_affiliation_strings":["Genomics and Computational Biology Group, Centro de Pesquisas Ren\u00e9 Rachou (CPqRR), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-1513-9278","affiliations":[{"raw_affiliation_string":"Genomics and Computational Biology Group, Centro de Pesquisas Ren\u00e9 Rachou (CPqRR), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Guilherme C. Oliveira","orcid":null},"institutions":[{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Guilherme C. Oliveira","raw_affiliation_strings":["Genomics and Computational Biology Group, Centro de Pesquisas Ren\u00e9 Rachou (CPqRR), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics and Computational Biology Group, Centro de Pesquisas Ren\u00e9 Rachou (CPqRR), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Luiz Mario R. Janini","orcid":null},"institutions":[{"id":"https://openalex.org/I88273585","display_name":"Universidade Federal de S\u00e3o Paulo","ror":"https://ror.org/02k5swt12","country_code":"BR","type":"education","lineage":["https://openalex.org/I88273585"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Luiz Mario R. Janini","raw_affiliation_strings":["Departmento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I88273585"]}]},{"author_position":"last","author":{"id":null,"display_name":"Fernando Antoneli","orcid":null},"institutions":[{"id":"https://openalex.org/I88273585","display_name":"Universidade Federal de S\u00e3o Paulo","ror":"https://ror.org/02k5swt12","country_code":"BR","type":"education","lineage":["https://openalex.org/I88273585"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Fernando Antoneli","raw_affiliation_strings":["Departmento de Inform\u00e1tica em Sa\u00fade, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Laborat\u00f3rio de de Biocomplexidade e Gen\u00f4mica Evolutiva, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departmento de Inform\u00e1tica em Sa\u00fade, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil ; Laborat\u00f3rio de de Biocomplexidade e Gen\u00f4mica Evolutiva, Escola Paulista de Medicina (EPM), Universidade Federal de S\u00e3o Paulo (UNIFESP), S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I88273585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I52325"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.5342,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67717718,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.39559999108314514,"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":0.39559999108314514,"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/T10112","display_name":"HIV Research and Treatment","score":0.2996000051498413,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.09860000014305115,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.6280999779701233},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6211000084877014},{"id":"https://openalex.org/keywords/genetic-diversity","display_name":"Genetic diversity","score":0.5741000175476074},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.48669999837875366},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.4828000068664551},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.38440001010894775},{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.3612000048160553}],"concepts":[{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.6280999779701233},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6211000084877014},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6078000068664551},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.5741000175476074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5098999738693237},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.48669999837875366},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.4828000068664551},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47909998893737793},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.38440001010894775},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.3612000048160553},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35670000314712524},{"id":"https://openalex.org/C40583040","wikidata":"https://www.wikidata.org/wiki/Q1502105","display_name":"Human genetic variation","level":5,"score":0.3391000032424927},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3183000087738037},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.31459999084472656},{"id":"https://openalex.org/C2994067223","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"Genomic sequencing","level":4,"score":0.30300000309944153},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.2833999991416931},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C142462285","wikidata":"https://www.wikidata.org/wiki/Q2528140","display_name":"Viral load","level":3,"score":0.2572999894618988},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.25589999556541443}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.1186/s13015-016-0064-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-016-0064-x","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0064-x","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:26973707","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26973707","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:www.arca.fiocruz.br:icict/15354","is_oa":true,"landing_page_url":"https://www.arca.fiocruz.br/handle/icict/15354","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da FIOCRUZ (ARCA)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:www.arca.fiocruz.br:icict/20404","is_oa":true,"landing_page_url":"https://www.arca.fiocruz.br/handle/icict/20404","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da FIOCRUZ","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:1405.2044","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1405.2044","pdf_url":"https://arxiv.org/pdf/1405.2044","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:arca.fiocruz.br:icict/15354","is_oa":true,"landing_page_url":"https://arca.fiocruz.br/handle/icict/15354","pdf_url":null,"source":{"id":"https://openalex.org/S7407055450","display_name":"Arca - Reposit\u00f3rio Institucional da Fiocruz","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4788855","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4788855","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":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:repositorio.unifesp.br:11600/57793","is_oa":true,"landing_page_url":"https://repositorio.unifesp.br/handle/11600/57793","pdf_url":null,"source":{"id":"https://openalex.org/S4377196380","display_name":"UNIFESP Institutional Repository (Universidade Federal de S\u00e3o Paulo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I88273585","host_organization_name":"Universidade Federal de S\u00e3o Paulo","host_organization_lineage":["https://openalex.org/I88273585"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"instacron:UNIFESP","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1186/s13015-016-0064-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-016-0064-x","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0064-x","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1062955537","display_name":null,"funder_award_id":"2009/14543-0","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G2886234109","display_name":null,"funder_award_id":"309312/2012-4, 306362/2012-0","funder_id":"https://openalex.org/F4320322980","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais"},{"id":"https://openalex.org/G3003150400","display_name":null,"funder_award_id":"309312/2012-4","funder_id":"https://openalex.org/F4320322980","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais"},{"id":"https://openalex.org/G3349972184","display_name":null,"funder_award_id":"D43 TW007012","funder_id":"https://openalex.org/F4320337356","funder_display_name":"Fogarty International Center"},{"id":"https://openalex.org/G4454945259","display_name":null,"funder_award_id":"306362/2012-0","funder_id":"https://openalex.org/F4320322980","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais"},{"id":"https://openalex.org/G7418945092","display_name":null,"funder_award_id":"PQ-306362/2012-0","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G7965537521","display_name":null,"funder_award_id":"306362/2012-0","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322980","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","ror":"https://ror.org/00nc55f03"},{"id":"https://openalex.org/F4320337356","display_name":"Fogarty International Center","ror":"https://ror.org/02xey9a22"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1809466148.pdf","grobid_xml":"https://content.openalex.org/works/W1809466148.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1487612538","https://openalex.org/W1565354039","https://openalex.org/W1968225289","https://openalex.org/W1968381465","https://openalex.org/W1976927254","https://openalex.org/W1983249544","https://openalex.org/W1986420798","https://openalex.org/W2000894445","https://openalex.org/W2010880827","https://openalex.org/W2020939898","https://openalex.org/W2021724381","https://openalex.org/W2024585092","https://openalex.org/W2026721694","https://openalex.org/W2027969303","https://openalex.org/W2037113830","https://openalex.org/W2037953066","https://openalex.org/W2038810697","https://openalex.org/W2043380577","https://openalex.org/W2055043387","https://openalex.org/W2061680337","https://openalex.org/W2063176128","https://openalex.org/W2073918065","https://openalex.org/W2079054072","https://openalex.org/W2082555199","https://openalex.org/W2087839385","https://openalex.org/W2092772380","https://openalex.org/W2094979163","https://openalex.org/W2098439468","https://openalex.org/W2103441770","https://openalex.org/W2104720574","https://openalex.org/W2105757606","https://openalex.org/W2106578604","https://openalex.org/W2108234281","https://openalex.org/W2111098905","https://openalex.org/W2111283804","https://openalex.org/W2112113834","https://openalex.org/W2127504354","https://openalex.org/W2134053782","https://openalex.org/W2134941776","https://openalex.org/W2135631383","https://openalex.org/W2146396346","https://openalex.org/W2147413871","https://openalex.org/W2151265018","https://openalex.org/W2152241467","https://openalex.org/W2155943701","https://openalex.org/W2161724277","https://openalex.org/W2163314170","https://openalex.org/W2164762627","https://openalex.org/W2170551349","https://openalex.org/W2170765088","https://openalex.org/W2336208944","https://openalex.org/W4230900352","https://openalex.org/W4231539689","https://openalex.org/W6600179900","https://openalex.org/W6701575323"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1],"this":[2,34,298],"paper":[3,299],"we":[4],"propose":[5,167],"a":[6,83,173,177,213,236,269],"method":[7,96,206],"and":[8,53,110,163,267,284,317,355],"discuss":[9],"its":[10,137],"computational":[11],"implementation":[12,203],"as":[13,51,303],"an":[14,304],"integrated":[15,305],"tool":[16,306],"for":[17,33,57,250,310],"the":[18,40,70,89,92,105,118,133,185,188,194,202,205,220,223,229,232,251,260,264,287,351],"analysis":[19],"of":[20,43,48,69,85,91,104,121,136,157,172,179,187,196,204,222,227,231,263,289,312],"viral":[21,58,174,340],"genetic":[22,41,170],"diversity":[23,42,59,90,171],"on":[24,208,320,332,350],"data":[25],"generated":[26],"by":[27,74,184],"high-throughput":[28],"sequencing.":[29],"The":[30,95,243,294],"main":[31,119,210],"motivation":[32],"work":[35],"is":[36,99,344],"to":[37,66,81,101,132,147,153,168,256,272],"better":[38],"understand":[39],"viruses":[44],"with":[45,239],"high":[46],"rates":[47],"nucleotide":[49],"substitution,":[50],"HIV-1":[52,324],"Influenza.":[54],"Most":[55],"methods":[56,295],"estimation":[60],"proposed":[61,97],"so":[62],"far":[63],"are":[64,117],"intended":[65],"take":[67,102,257],"benefit":[68],"longer":[71],"reads":[72],"produced":[73],"some":[75,122,149],"next-generation":[76],"sequencing":[77],"platforms":[78],"in":[79,235,297,314,337,346],"order":[80],"estimate":[82],"population":[84,175],"haplotypes":[86],"which":[87,116,139],"represent":[88],"original":[93],"population.":[94],"here":[98],"custom-made":[100],"advantage":[103],"very":[106],"low":[107],"error":[108,161,291],"rate":[109],"extremely":[111],"deep":[112],"coverage":[113],"per":[114,199],"site,":[115],"features":[120],"neglected":[123],"technologies":[124],"that":[125,217],"have":[126,300],"not":[127],"received":[128],"much":[129],"attention":[130],"due":[131],"short":[134],"length":[135],"reads,":[138,159],"precludes":[140],"haplotype":[141,154],"estimation.":[142,242],"This":[143],"approach":[144,245],"allowed":[145],"us":[146],"avoid":[148],"hard":[150],"problems":[151],"related":[152],"reconstruction":[155],"(need":[156],"long":[158],"preliminary":[160,290],"filtering":[162],"assembly).":[164],"RESULTS:":[165],"We":[166],"measure":[169],"through":[176],"family":[178],"multinomial":[180,233,252],"probability":[181,248],"distributions":[182,249],"indexed":[183],"sites":[186],"virus":[189],"genome,":[190],"each":[191],"one":[192,255],"representing":[193],"distribution":[195],"nucleic":[197],"bases":[198],"site.":[200],"Moreover,":[201],"focuses":[207],"two":[209],"optimization":[211],"strategies:":[212],"read":[214],"mapping/alignment":[215],"procedure":[216],"aims":[218],"at":[219],"recovery":[221],"maximum":[224],"possible":[225],"number":[226],"short-reads;":[228],"inference":[230],"parameters":[234,253],"Bayesian":[237,244,281],"framework":[238],"smoothed":[240],"Dirichlet":[241],"provides":[246],"conditional":[247],"allowing":[254],"into":[258],"account":[259],"prior":[261],"information":[262],"control":[265],"experiment":[266],"providing":[268],"natural":[270],"way":[271],"separate":[273],"signal":[274],"from":[275,323],"noise,":[276],"since":[277],"it":[278],"automatically":[279],"furnishes":[280],"confidence":[282],"intervals":[283],"thus":[285],"avoids":[286],"drawbacks":[288],"filtering.":[292],"CONCLUSIONS:":[293],"described":[296],"been":[301],"implemented":[302],"called":[307],"Tanden":[308,343],"(Tool":[309],"Analysis":[311],"Diversity":[313],"Viral":[315],"Populations)":[316],"successfully":[318],"tested":[319],"samples":[321],"obtained":[322],"strain":[325],"NL4-3":[326],"(group":[327],"M,":[328],"subtype":[329],"B)":[330],"cultivations":[331],"primary":[333],"human":[334],"cell":[335],"cultures":[336],"many":[338],"distinct":[339],"propagation":[341],"conditions.":[342],"written":[345],"C#":[347],"(Microsoft),":[348],"runs":[349],"Windows":[352],"operating":[353],"system,":[354],"can":[356],"be":[357],"downloaded":[358],"from:":[359],"http://tanden.url.ph/.":[360]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2016-06-24T00:00:00"}
