{"id":"https://openalex.org/W2950407147","doi":"https://doi.org/10.1371/journal.pcbi.1005316","title":"Inference of Transmission Network Structure from HIV Phylogenetic Trees","display_name":"Inference of Transmission Network Structure from HIV Phylogenetic Trees","publication_year":2017,"publication_date":"2017-01-13","ids":{"openalex":"https://openalex.org/W2950407147","doi":"https://doi.org/10.1371/journal.pcbi.1005316","mag":"2950407147","pmid":"https://pubmed.ncbi.nlm.nih.gov/28085876"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005316","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005316","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005316&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005316&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088481980","display_name":"Federica Giardina","orcid":"https://orcid.org/0000-0002-3710-0940"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE","US"],"is_corresponding":true,"raw_author_name":"Federica Giardina","raw_affiliation_strings":["Department of Mathematics, Stockholm University, Stockholm, Sweden","Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3710-0940","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081272194","display_name":"Ethan Romero-Severson","orcid":"https://orcid.org/0000-0002-8082-1225"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ethan Obie Romero-Severson","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8082-1225","affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"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 Institute, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0001-9020-0521","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 Institute, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068540962","display_name":"Tom Britton","orcid":"https://orcid.org/0000-0002-9228-7357"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Tom Britton","raw_affiliation_strings":["Department of Mathematics, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023859958","display_name":"Thomas Leitner","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Leitner","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5088481980"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I161593684"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2055,"currency":"EUR","value_usd":2216},"fwci":2.9494,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.91494217,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"e1005316","last_page":"e1005316"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9854999780654907,"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/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.9617000222206116,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6784942150115967},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6486622095108032},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6022306680679321},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5372668504714966},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5357073545455933},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5013577938079834},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.47421979904174805},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.45519790053367615},{"id":"https://openalex.org/keywords/approximate-bayesian-computation","display_name":"Approximate Bayesian computation","score":0.43873143196105957},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3191491365432739},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2761390805244446},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18344587087631226},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14577844738960266}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6784942150115967},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6486622095108032},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6022306680679321},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5372668504714966},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5357073545455933},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5013577938079834},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.47421979904174805},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.45519790053367615},{"id":"https://openalex.org/C2779377595","wikidata":"https://www.wikidata.org/wiki/Q21045424","display_name":"Approximate Bayesian computation","level":3,"score":0.43873143196105957},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3191491365432739},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2761390805244446},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18344587087631226},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14577844738960266},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013548","descriptor_name":"Sweden","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013548","descriptor_name":"Sweden","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013548","descriptor_name":"Sweden","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013548","descriptor_name":"Sweden","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":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1005316","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005316","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005316&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:28085876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28085876","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:osti.gov:1360708","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1360708","pdf_url":"https://www.osti.gov/servlets/purl/1360708","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:doaj.org/article:a5f84043a024439db9b0e3657bb14cb9","is_oa":true,"landing_page_url":"https://doaj.org/article/a5f84043a024439db9b0e3657bb14cb9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 13, Iss 1, p e1005316 (2017)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/4552975","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Inference_of_Transmission_Network_Structure_from_HIV_Phylogenetic_Trees/4552975","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:5279806","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5279806","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005316","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005316","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005316&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1747536516","display_name":null,"funder_award_id":"340-2013-5003","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G40015477","display_name":null,"funder_award_id":"R01AI087520","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4927543450","display_name":null,"funder_award_id":"RO1AI087520","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950407147.pdf","grobid_xml":"https://content.openalex.org/works/W2950407147.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W167782390","https://openalex.org/W229097380","https://openalex.org/W803982123","https://openalex.org/W1499965417","https://openalex.org/W1606697907","https://openalex.org/W1749900216","https://openalex.org/W1970472356","https://openalex.org/W1989741819","https://openalex.org/W1992908338","https://openalex.org/W2001657177","https://openalex.org/W2006961590","https://openalex.org/W2022101730","https://openalex.org/W2026042206","https://openalex.org/W2034670909","https://openalex.org/W2034795216","https://openalex.org/W2037782528","https://openalex.org/W2038990588","https://openalex.org/W2041936375","https://openalex.org/W2045973738","https://openalex.org/W2048343560","https://openalex.org/W2048596679","https://openalex.org/W2060811492","https://openalex.org/W2064766914","https://openalex.org/W2073627497","https://openalex.org/W2091556805","https://openalex.org/W2096039030","https://openalex.org/W2097487570","https://openalex.org/W2100378151","https://openalex.org/W2102187991","https://openalex.org/W2112090702","https://openalex.org/W2113258333","https://openalex.org/W2122337420","https://openalex.org/W2124637492","https://openalex.org/W2126141460","https://openalex.org/W2130362098","https://openalex.org/W2133979592","https://openalex.org/W2135267747","https://openalex.org/W2142773663","https://openalex.org/W2148870302","https://openalex.org/W2150646850","https://openalex.org/W2151409320","https://openalex.org/W2151729750","https://openalex.org/W2152246075","https://openalex.org/W2155418451","https://openalex.org/W2164787828","https://openalex.org/W2199500517","https://openalex.org/W2280931876","https://openalex.org/W2294528210","https://openalex.org/W2314461521","https://openalex.org/W2331613197","https://openalex.org/W2342485906","https://openalex.org/W2402980652","https://openalex.org/W2427536221","https://openalex.org/W2511343380","https://openalex.org/W2525716265","https://openalex.org/W2582743722","https://openalex.org/W2754580359","https://openalex.org/W3122602071","https://openalex.org/W4205814206","https://openalex.org/W4245053866","https://openalex.org/W4290200829","https://openalex.org/W4312512934"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2949296710","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"Phylogenetic":[0],"inference":[1,104,254],"is":[2,14],"an":[3,103,234,247],"attractive":[4],"means":[5],"to":[6,112,212,226],"reconstruct":[7],"transmission":[8,20,43,168,200],"histories":[9],"and":[10,22,28,41,58,85,94,119,125,140,148,205],"epidemics.":[11],"However,":[12],"there":[13],"not":[15],"a":[16,51,156,179],"perfect":[17],"correspondence":[18],"between":[19,37,146,214],"history":[21],"virus":[23,157],"phylogeny.":[24],"Both":[25],"node":[26],"height":[27],"topological":[29,139],"differences":[30,79],"may":[31,161],"occur,":[32],"depending":[33],"on":[34,86,107,231,255],"the":[35,61,87,95,98,131,166,175,183,194,199,202,224,260],"interaction":[36],"within-host":[38,52,195],"evolutionary":[39,53,196],"dynamics":[40,207],"between-host":[42,167],"patterns.":[44],"To":[45,71],"investigate":[46],"these":[47],"interactions,":[48],"we":[49,75,90,101,190,250],"added":[50],"model":[54],"in":[55,80,246],"epidemiological":[56,127],"simulations":[57,153],"examined":[59],"if":[60],"resulting":[62],"phylogeny":[63,159,180],"could":[64],"recover":[65],"different":[66,164,215,257],"types":[67,216],"of":[68,97,177,217],"contact":[69,186,218,228],"networks.":[70,219],"further":[72],"improve":[73],"realism,":[74],"also":[76,208,221],"introduced":[77],"patient-specific":[78],"infectivity":[81,206],"across":[82],"disease":[83],"stages,":[84],"epidemic":[88,185,235],"level":[89],"considered":[91],"incomplete":[92],"sampling":[93],"age":[96],"epidemic.":[99,248,263],"Second,":[100],"implemented":[102],"method":[105],"based":[106],"approximate":[108],"Bayesian":[109],"computation":[110],"(ABC)":[111],"discriminate":[113],"among":[114],"three":[115],"well-studied":[116],"network":[117,123],"models":[118],"jointly":[120],"estimate":[121],"both":[122,138],"parameters":[124],"key":[126],"quantities":[128],"such":[129],"as":[130],"infection":[132],"rate.":[133],"Our":[134],"ABC":[135,253],"framework":[136],"used":[137],"distance-based":[141,239],"tree":[142,240],"statistics":[143,241],"for":[144,174],"comparison":[145],"simulated":[147],"observed":[149],"trees.":[150],"Overall,":[151],"our":[152,252],"showed":[154],"that":[155,192,223],"time-scaled":[158],"(genealogy)":[160],"be":[162],"substantially":[163],"from":[165,259],"tree.":[169],"This":[170],"has":[171,236],"important":[172],"implications":[173],"interpretation":[176],"what":[178],"reveals":[181],"about":[182],"underlying":[184],"network.":[187],"In":[188],"particular,":[189],"found":[191,222],"while":[193],"process":[197,204],"obscures":[198],"tree,":[201],"diversification":[203],"add":[209],"discriminatory":[210],"power":[211,244],"differentiate":[213,227],"We":[220],"possibility":[225],"networks":[229],"depends":[230],"how":[232],"far":[233],"progressed,":[237],"where":[238],"have":[242],"more":[243],"early":[245],"Finally,":[249],"applied":[251],"two":[256],"outbreaks":[258],"Swedish":[261],"HIV-1":[262]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}