{"id":"https://openalex.org/W2059041686","doi":"https://doi.org/10.1371/journal.pcbi.1002768","title":"A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data","display_name":"A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data","publication_year":2012,"publication_date":"2012-11-15","ids":{"openalex":"https://openalex.org/W2059041686","doi":"https://doi.org/10.1371/journal.pcbi.1002768","mag":"2059041686","pmid":"https://pubmed.ncbi.nlm.nih.gov/23166481"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002768","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002768","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002768&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.1002768&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007690571","display_name":"Marco J. Morelli","orcid":"https://orcid.org/0000-0003-1862-667X"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marco J. Morelli","raw_affiliation_strings":["Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Glasgow , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Glasgow , United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090719715","display_name":"Ga\u00ebl Th\u00e9baud","orcid":"https://orcid.org/0000-0002-2987-4997"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I24906876","display_name":"Institut Agro Montpellier","ror":"https://ror.org/03rnk6m14","country_code":"FR","type":"education","lineage":["https://openalex.org/I24906876","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210087514","display_name":"Biologie et G\u00e9n\u00e9tique des Interactions Plante-Parasite","ror":"https://ror.org/0026vdt21","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I24906876","https://openalex.org/I4210087514","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ga\u00ebl Th\u00e9baud","raw_affiliation_strings":["INRA, UMR BGPI, Cirad TA A-54/K, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, UMR BGPI, Cirad TA A-54/K, Montpellier, France","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I24906876","https://openalex.org/I4210087514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028597798","display_name":"Jo\u00ebl Chad\u0153uf","orcid":"https://orcid.org/0000-0001-8755-7116"},"institutions":[{"id":"https://openalex.org/I4210121908","display_name":"Biostatistique et processus spatiaux","ror":"https://ror.org/02d898a89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210121908"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jo\u00ebl Chad\u0153uf","raw_affiliation_strings":["INRA, UR546 Biostatistics and Spatial Processes, Avignon, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, UR546 Biostatistics and Spatial Processes, Avignon, France","institution_ids":["https://openalex.org/I4210121908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073483634","display_name":"Donald P. King","orcid":"https://orcid.org/0000-0002-6959-2708"},"institutions":[{"id":"https://openalex.org/I1287548271","display_name":"The Pirbright Institute","ror":"https://ror.org/04xv01a59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1287548271","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Donald P. King","raw_affiliation_strings":["Institute for Animal Health, Pirbright, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Animal Health, Pirbright, United Kingdom","institution_ids":["https://openalex.org/I1287548271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014427910","display_name":"Daniel T. Haydon","orcid":"https://orcid.org/0000-0002-1240-1886"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Daniel T. Haydon","raw_affiliation_strings":["Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Glasgow , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Glasgow , United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006060184","display_name":"Samuel Soubeyrand","orcid":"https://orcid.org/0000-0003-2447-3067"},"institutions":[{"id":"https://openalex.org/I4210121908","display_name":"Biostatistique et processus spatiaux","ror":"https://ror.org/02d898a89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210121908"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Samuel Soubeyrand","raw_affiliation_strings":["INRA, UR546 Biostatistics and Spatial Processes, Avignon, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, UR546 Biostatistics and Spatial Processes, Avignon, France","institution_ids":["https://openalex.org/I4210121908"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5014427910"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":13.1642,"has_fulltext":true,"cited_by_count":124,"citation_normalized_percentile":{"value":0.9912141,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"8","issue":"11","first_page":"e1002768","last_page":"e1002768"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11560","display_name":"Animal Disease Management and Epidemiology","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1102","display_name":"Agronomy and Crop Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11560","display_name":"Animal Disease Management and Epidemiology","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1102","display_name":"Agronomy and Crop Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10199","display_name":"Wildlife Ecology and Conservation","score":0.9776999950408936,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10838","display_name":"Animal Behavior and Welfare Studies","score":0.9775999784469604,"subfield":{"id":"https://openalex.org/subfields/3404","display_name":"Small Animals"},"field":{"id":"https://openalex.org/fields/34","display_name":"Veterinary"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6888434290885925},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6247421503067017},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.6093527674674988},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5011324882507324},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.49319523572921753},{"id":"https://openalex.org/keywords/genetic-epidemiology","display_name":"Genetic epidemiology","score":0.460584819316864},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.45098552107810974},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4375796318054199},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.42460396885871887},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3563578724861145},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3531854748725891},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2785930633544922},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14600247144699097}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6888434290885925},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6247421503067017},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.6093527674674988},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5011324882507324},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.49319523572921753},{"id":"https://openalex.org/C177860879","wikidata":"https://www.wikidata.org/wiki/Q5532897","display_name":"Genetic epidemiology","level":3,"score":0.460584819316864},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.45098552107810974},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4375796318054199},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.42460396885871887},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3563578724861145},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3531854748725891},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2785930633544922},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14600247144699097},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","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":"D004812","descriptor_name":"Epidemiologic Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004812","descriptor_name":"Epidemiologic Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004812","descriptor_name":"Epidemiologic Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004812","descriptor_name":"Epidemiologic Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D005536","descriptor_name":"Foot-and-Mouth Disease","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D006113","descriptor_name":"United Kingdom","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006113","descriptor_name":"United Kingdom","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006113","descriptor_name":"United Kingdom","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006113","descriptor_name":"United Kingdom","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":"D012756","descriptor_name":"Sheep","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012756","descriptor_name":"Sheep","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012756","descriptor_name":"Sheep","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012756","descriptor_name":"Sheep","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018562","descriptor_name":"Disease Transmission, Infectious","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D018562","descriptor_name":"Disease Transmission, Infectious","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D018562","descriptor_name":"Disease Transmission, Infectious","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D018562","descriptor_name":"Disease Transmission, Infectious","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058872","descriptor_name":"Epidemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058872","descriptor_name":"Epidemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058872","descriptor_name":"Epidemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058872","descriptor_name":"Epidemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1002768","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002768","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002768&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:23166481","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23166481","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:eprints.gla.ac.uk:76828","is_oa":false,"landing_page_url":"https://eprints.gla.ac.uk/view/author/9808.html>,","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Articles"},{"id":"pmh:oai:europepmc.org:2499414","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3499255","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.776.7887","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.776.7887","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/3e/7c/pcbi.1002768.PMC3499255.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:hal-02652392v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-02652392","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ploscompbiol.org/","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1002768","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002768","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:deff33e7175e46c597a439e10038273e","is_oa":true,"landing_page_url":"https://doaj.org/article/deff33e7175e46c597a439e10038273e","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 8, Iss 11, p e1002768 (2012)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/117235","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_Bayesian_Inference_Framework_to_Reconstruct_Transmission_Trees_Using_Epidemiological_and_Genetic_Data__/117235","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002768","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002768","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002768&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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8600000143051147}],"awards":[{"id":"https://openalex.org/G1459213601","display_name":null,"funder_award_id":"BB/I014314/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5164097158","display_name":"Beyond the consensus: defining the significance of foot-and-mouth disease viral sequence diversity","funder_award_id":"BB/I014314/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5907576401","display_name":"A systems biology approach to integrating pathogen evolution and epidemiology","funder_award_id":"BB/F005733/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6052374112","display_name":null,"funder_award_id":"BB/F005733/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6105055101","display_name":"Beyond the consensus: defining the significance of foot and mouth disease viral sequence diversity","funder_award_id":"BB/I013784/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6266957294","display_name":null,"funder_award_id":"KBBE 2007-1-4-10","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6450324582","display_name":null,"funder_award_id":"SE2938","funder_id":"https://openalex.org/F4320319995","funder_display_name":"Department for Environment, Food and Rural Affairs, UK Government"},{"id":"https://openalex.org/G8769888314","display_name":null,"funder_award_id":"BB/I013784/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320319995","display_name":"Department for Environment, Food and Rural Affairs, UK Government","ror":"https://ror.org/00tnppw48"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2059041686.pdf","grobid_xml":"https://content.openalex.org/works/W2059041686.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W625640516","https://openalex.org/W1501586228","https://openalex.org/W1980099211","https://openalex.org/W1984841045","https://openalex.org/W1986090465","https://openalex.org/W2009678335","https://openalex.org/W2010615067","https://openalex.org/W2017984345","https://openalex.org/W2032460042","https://openalex.org/W2052708825","https://openalex.org/W2060919531","https://openalex.org/W2071827932","https://openalex.org/W2088267428","https://openalex.org/W2100995977","https://openalex.org/W2101372412","https://openalex.org/W2118526609","https://openalex.org/W2118780696","https://openalex.org/W2122919191","https://openalex.org/W2124851014","https://openalex.org/W2125454666","https://openalex.org/W2130164103","https://openalex.org/W2140885215","https://openalex.org/W2142773663","https://openalex.org/W2164418313","https://openalex.org/W2169702034","https://openalex.org/W2171571703","https://openalex.org/W2487331830"],"related_works":["https://openalex.org/W2372267530","https://openalex.org/W2969189870","https://openalex.org/W2965643117","https://openalex.org/W4303857162","https://openalex.org/W2407375987","https://openalex.org/W3049691116","https://openalex.org/W2505726097","https://openalex.org/W2010643158","https://openalex.org/W2106867672","https://openalex.org/W3081214562"],"abstract_inverted_index":{"The":[0,244],"accurate":[1],"identification":[2],"of":[3,6,31,48,60,95,150,161,177,188,216,230,246,258,264,278],"the":[4,44,92,144,155,162,167,175,182,185,189,210,228,256,262,276],"route":[5],"transmission":[7,32,62,101,130,224],"taken":[8],"by":[9,74],"an":[10,35,39],"infectious":[11],"agent":[12],"through":[13],"a":[14,57,111,115,159,178,214,235,268],"host":[15],"population":[16],"is":[17,37,249,280],"critical":[18],"to":[19,88,104,114,126,146,173,202],"understanding":[20],"its":[21,27],"epidemiology":[22],"and":[23,46,54,80,122,132,158,198,226,282,295],"informing":[24],"measures":[25],"for":[26,238],"control.":[28],"However,":[29,83],"reconstruction":[30],"routes":[33],"during":[34,213],"epidemic":[36,212],"often":[38],"underdetermined":[40],"problem:":[41],"data":[42,98,207,248,266,297],"about":[43],"location":[45],"timings":[47],"infections":[49],"can":[50,71,286],"be":[51,72,89,105,287],"incomplete,":[52],"inaccurate,":[53],"compatible":[55],"with":[56,139,283],"large":[58,163],"number":[59],"different":[61,97],"scenarios.":[63],"For":[64],"fast-evolving":[65],"pathogens":[66],"like":[67],"RNA":[68],"viruses,":[69],"inference":[70,117,220],"strengthened":[73],"using":[75],"genetic":[76,121,247,296],"data,":[77,124,141],"nowadays":[78],"easily":[79],"affordably":[81],"generated.":[82],"significant":[84],"statistical":[85],"challenges":[86],"remain":[87,200],"overcome":[90],"in":[91,196,241,252,275,289],"full":[93],"integration":[94],"these":[96,265],"types":[99],"if":[100],"trees":[102],"are":[103,171,298],"reliably":[106],"estimated.":[107],"We":[108],"present":[109],"here":[110,274],"framework":[112],"leading":[113],"bayesian":[116],"scheme":[118,221],"that":[119],"combines":[120],"epidemiological":[123,239,253],"able":[125,172],"reconstruct":[127],"most":[128],"likely":[129],"patterns":[131],"infection":[133],"dates.":[134],"After":[135],"testing":[136],"our":[137,219],"approach":[138],"simulated":[140],"we":[142,170,205],"apply":[143],"method":[145],"two":[147,186],"UK":[148],"epidemics":[149],"Foot-and-Mouth":[151],"Disease":[152],"Virus":[153],"(FMDV):":[154],"2007":[156],"outbreak,":[157],"subset":[160],"2001":[164,211],"epidemic.":[165],"In":[166],"first":[168],"case,":[169],"confirm":[174],"role":[176],"specific":[179],"premise":[180],"as":[181],"link":[183],"between":[184],"phases":[187],"epidemics,":[190],"while":[191,272],"transmissions":[192],"more":[193],"densely":[194],"clustered":[195],"space":[197],"time":[199,215],"harder":[201],"resolve.":[203],"When":[204],"consider":[206],"collected":[208],"from":[209],"national":[217],"emergency,":[218],"robustly":[222],"infers":[223],"chains,":[225],"uncovers":[227],"presence":[229],"undetected":[231],"premises,":[232],"thus":[233],"providing":[234],"useful":[236],"tool":[237],"studies":[240],"real":[242],"time.":[243],"generation":[245],"becoming":[250],"routine":[251],"investigations,":[254],"but":[255],"development":[257],"analytical":[259],"tools":[260],"maximizing":[261],"value":[263],"remains":[267],"priority.":[269],"Our":[270],"method,":[271],"applied":[273],"context":[277],"FMDV,":[279],"general":[281],"slight":[284],"modification":[285],"used":[288],"any":[290],"situation":[291],"where":[292],"both":[293],"spatiotemporal":[294],"available.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}