{"id":"https://openalex.org/W2065382983","doi":"https://doi.org/10.1371/journal.pcbi.1002876","title":"Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics","display_name":"Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics","publication_year":2013,"publication_date":"2013-01-31","ids":{"openalex":"https://openalex.org/W2065382983","doi":"https://doi.org/10.1371/journal.pcbi.1002876","mag":"2065382983","pmid":"https://pubmed.ncbi.nlm.nih.gov/23382662"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002876","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002876","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002876&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.1002876&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056419497","display_name":"Gkikas Magiorkinis","orcid":"https://orcid.org/0000-0002-0141-4753"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]},{"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"]},{"id":"https://openalex.org/I72702400","display_name":"Athens State University","ror":"https://ror.org/01zx16v02","country_code":"US","type":"education","lineage":["https://openalex.org/I72702400"]}],"countries":["GB","GR","US"],"is_corresponding":true,"raw_author_name":"Gkikas Magiorkinis","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece. gkikas.magiorkinis@zoo.ox.ac.uk","Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Zoology, University of Oxford, Oxford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece. gkikas.magiorkinis@zoo.ox.ac.uk","institution_ids":["https://openalex.org/I72702400"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Zoology, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044857284","display_name":"Vana Sypsa","orcid":"https://orcid.org/0000-0002-9430-7614"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Vana Sypsa","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032109599","display_name":"Emmanouil Magiorkinis","orcid":"https://orcid.org/0000-0001-8883-7275"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Emmanouil Magiorkinis","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088996103","display_name":"Dimitrios Paraskevis","orcid":"https://orcid.org/0000-0001-6167-7152"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Dimitrios Paraskevis","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111573925","display_name":"Antigoni Katsoulidou","orcid":null},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Antigoni Katsoulidou","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022569324","display_name":"Robert Belshaw","orcid":"https://orcid.org/0000-0001-6234-3947"},"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":"Robert Belshaw","raw_affiliation_strings":["Department of Zoology, University of Oxford, Oxford, United Kingdom","Department of Zoology, University of Oxford , Oxford , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Zoology, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Zoology, University of Oxford , Oxford , United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027792801","display_name":"Christophe Fraser","orcid":"https://orcid.org/0000-0003-2399-9657"},"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":"Christophe Fraser","raw_affiliation_strings":["School of Public Health, Imperial College, London, United Kingdom","School of Public Health, Imperial College London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Public Health, Imperial College, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"School of Public Health, Imperial College London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061658598","display_name":"Oliver G. Pybus","orcid":"https://orcid.org/0000-0002-8797-2667"},"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":"Oliver George Pybus","raw_affiliation_strings":["Department of Zoology, University of Oxford, Oxford, United Kingdom","Department of Zoology, University of Oxford , Oxford , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Zoology, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Zoology, University of Oxford , Oxford , United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043868687","display_name":"Angelos Hatzakis","orcid":"https://orcid.org/0000-0001-8420-3830"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Angelos Hatzakis","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5043868687","https://openalex.org/A5056419497"],"corresponding_institution_ids":["https://openalex.org/I200777214","https://openalex.org/I40120149","https://openalex.org/I72702400"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.1949,"has_fulltext":true,"cited_by_count":68,"citation_normalized_percentile":{"value":0.96330695,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"e1002876","last_page":"e1002876"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"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/T10112","display_name":"HIV Research and Treatment","score":0.9801999926567078,"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/T10351","display_name":"Liver Disease Diagnosis and Treatment","score":0.9519000053405762,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/viral-phylodynamics","display_name":"Viral phylodynamics","score":0.9208536148071289},{"id":"https://openalex.org/keywords/epidemiology","display_name":"Epidemiology","score":0.6984015703201294},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.6713674664497375},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5809383988380432},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.5734668374061584},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.505174458026886},{"id":"https://openalex.org/keywords/hepatitis-c-virus","display_name":"Hepatitis C virus","score":0.4644615054130554},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"Viral evolution","score":0.46012282371520996},{"id":"https://openalex.org/keywords/viral-hepatitis","display_name":"Viral hepatitis","score":0.4523908793926239},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.31911516189575195},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.29160594940185547},{"id":"https://openalex.org/keywords/environmental-health","display_name":"Environmental health","score":0.28053146600723267},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18780165910720825},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.10090059041976929},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.0707070529460907},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.05760091543197632}],"concepts":[{"id":"https://openalex.org/C21833749","wikidata":"https://www.wikidata.org/wiki/Q7189431","display_name":"Viral phylodynamics","level":4,"score":0.9208536148071289},{"id":"https://openalex.org/C107130276","wikidata":"https://www.wikidata.org/wiki/Q133805","display_name":"Epidemiology","level":2,"score":0.6984015703201294},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.6713674664497375},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5809383988380432},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5734668374061584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.505174458026886},{"id":"https://openalex.org/C2776408679","wikidata":"https://www.wikidata.org/wiki/Q708693","display_name":"Hepatitis C virus","level":3,"score":0.4644615054130554},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.46012282371520996},{"id":"https://openalex.org/C2777072776","wikidata":"https://www.wikidata.org/wiki/Q1983841","display_name":"Viral hepatitis","level":2,"score":0.4523908793926239},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.31911516189575195},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.29160594940185547},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.28053146600723267},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18780165910720825},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.10090059041976929},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.0707070529460907},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.05760091543197632},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D006526","descriptor_name":"Hepatitis C","qualifier_ui":"Q000635","qualifier_name":"transmission","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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","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":"D016021","descriptor_name":"Epidemiologic Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016021","descriptor_name":"Epidemiologic Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016021","descriptor_name":"Epidemiologic Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016021","descriptor_name":"Epidemiologic Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1002876","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002876","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002876&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:23382662","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23382662","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.712.5800","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.712.5800","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://evolve.zoo.ox.ac.uk/Evolve/Oliver_Pybus_files/IntegratingPhylodynamics%26Epidemiology.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:d902ab94cbea4c66ac5cb93764719725","is_oa":false,"landing_page_url":"https://doaj.org/article/d902ab94cbea4c66ac5cb93764719725","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 9, Iss 1, p e1002876 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2564862","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3561042","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/155147","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Integrating_Phylodynamics_and_Epidemiology_to_Estimate_Transmission_Diversity_in_Viral_Epidemics__/155147","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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:ora.ox.ac.uk:uuid:67798702-b402-44a4-8b96-8389dd54657d","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:67798702-b402-44a4-8b96-8389dd54657d","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3561042","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3561042","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002876","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002876","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002876&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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8700000047683716}],"awards":[{"id":"https://openalex.org/G1313656976","display_name":null,"funder_award_id":"MR/K010174/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065382983.pdf","grobid_xml":"https://content.openalex.org/works/W2065382983.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W138424127","https://openalex.org/W212507277","https://openalex.org/W282039410","https://openalex.org/W1502700877","https://openalex.org/W1504384931","https://openalex.org/W1548037568","https://openalex.org/W1606697907","https://openalex.org/W1793259860","https://openalex.org/W1969030917","https://openalex.org/W1974464383","https://openalex.org/W1982306896","https://openalex.org/W1985482454","https://openalex.org/W1989058813","https://openalex.org/W1989741819","https://openalex.org/W2004506270","https://openalex.org/W2005674014","https://openalex.org/W2010400293","https://openalex.org/W2020004919","https://openalex.org/W2021762717","https://openalex.org/W2021831138","https://openalex.org/W2022687771","https://openalex.org/W2026112119","https://openalex.org/W2041804560","https://openalex.org/W2041903808","https://openalex.org/W2046274292","https://openalex.org/W2052402745","https://openalex.org/W2057443000","https://openalex.org/W2058538904","https://openalex.org/W2059655508","https://openalex.org/W2064551064","https://openalex.org/W2066074857","https://openalex.org/W2067309872","https://openalex.org/W2068438963","https://openalex.org/W2069251911","https://openalex.org/W2072453168","https://openalex.org/W2094427796","https://openalex.org/W2094939159","https://openalex.org/W2098062910","https://openalex.org/W2099206288","https://openalex.org/W2101285175","https://openalex.org/W2104563699","https://openalex.org/W2106551271","https://openalex.org/W2108972940","https://openalex.org/W2110835349","https://openalex.org/W2116614776","https://openalex.org/W2117002055","https://openalex.org/W2117178635","https://openalex.org/W2118726788","https://openalex.org/W2118849557","https://openalex.org/W2118935439","https://openalex.org/W2119168386","https://openalex.org/W2124352443","https://openalex.org/W2128429998","https://openalex.org/W2142773663","https://openalex.org/W2148301044","https://openalex.org/W2150482242","https://openalex.org/W2150977550","https://openalex.org/W2153750363","https://openalex.org/W2166022262","https://openalex.org/W2177170902","https://openalex.org/W2271620852","https://openalex.org/W2314619766","https://openalex.org/W2319462502","https://openalex.org/W2327525734","https://openalex.org/W2328171401","https://openalex.org/W2339016944","https://openalex.org/W2441114060","https://openalex.org/W3023906401","https://openalex.org/W4237454490","https://openalex.org/W4247464444","https://openalex.org/W4388299012"],"related_works":["https://openalex.org/W2148594363","https://openalex.org/W3187962553","https://openalex.org/W2998154928","https://openalex.org/W2018843752","https://openalex.org/W592081755","https://openalex.org/W3098202346","https://openalex.org/W2049402058","https://openalex.org/W2558781459","https://openalex.org/W2765549458","https://openalex.org/W2002169365"],"abstract_inverted_index":{"The":[0],"epidemiology":[1],"of":[2,27,37,57,65,82,105,133,148,156],"chronic":[3,157],"viral":[4,107,124,158],"infections,":[5],"such":[6],"as":[7],"those":[8],"caused":[9],"by":[10,22,35],"Hepatitis":[11],"C":[12],"Virus":[13,18],"(HCV)":[14],"and":[15,75,95,118,127,135,160],"Human":[16],"Immunodeficiency":[17],"(HIV),":[19],"is":[20,68],"affected":[21],"the":[23,28,54,63,80,101,120,146,153],"risk":[24,48],"group":[25,49],"structure":[26],"infected":[29,59],"population.":[30],"Risk":[31],"groups":[32],"are":[33],"defined":[34],"each":[36,58],"their":[38],"members":[39],"having":[40],"acquired":[41],"infection":[42],"through":[43],"a":[44,89,114,131],"specific":[45],"behavior.":[46],"However,":[47],"definitions":[50],"say":[51],"little":[52],"about":[53],"transmission":[55,154],"potential":[56],"individual.":[60],"Variation":[61],"in":[62,79,103],"number":[64],"secondary":[66],"infections":[67],"extremely":[69],"difficult":[70],"to":[71,99],"estimate":[72,100],"for":[73,119,151,161],"HCV":[74,116],"HIV":[76],"but":[77],"crucial":[78],"design":[81],"efficient":[83],"control":[84,163],"interventions.":[85],"Here":[86],"we":[87],"describe":[88],"novel":[90],"method":[91,112],"that":[92,140],"combines":[93],"epidemiological":[94,136],"population":[96],"genetic":[97],"approaches":[98],"variation":[102],"transmissibility":[104],"rapidly-evolving":[106],"epidemics.":[108],"We":[109,138],"evaluate":[110],"this":[111,141],"using":[113],"nationwide":[115],"epidemic":[117],"first":[121],"time":[122],"co-estimate":[123],"generation":[125],"times":[126],"superspreading":[128],"events":[129],"from":[130],"combination":[132],"molecular":[134],"data.":[137],"anticipate":[139],"integrated":[142],"approach":[143],"will":[144],"form":[145],"basis":[147],"powerful":[149],"tools":[150],"describing":[152],"dynamics":[155],"diseases,":[159],"evaluating":[162],"strategies":[164],"directed":[165],"against":[166],"them.":[167]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":6}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
