{"id":"https://openalex.org/W2080723129","doi":"https://doi.org/10.1371/journal.pcbi.1003457","title":"Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data","display_name":"Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data","publication_year":2014,"publication_date":"2014-01-23","ids":{"openalex":"https://openalex.org/W2080723129","doi":"https://doi.org/10.1371/journal.pcbi.1003457","mag":"2080723129","pmid":"https://pubmed.ncbi.nlm.nih.gov/24465202"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003457&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.1003457&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013810794","display_name":"Thibaut Jombart","orcid":"https://orcid.org/0000-0003-2226-8692"},"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":true,"raw_author_name":"Thibaut Jombart","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000395707","display_name":"Anne Cori","orcid":"https://orcid.org/0000-0002-8443-9162"},"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":"Anne Cori","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042745262","display_name":"Xavier Didelot","orcid":"https://orcid.org/0000-0003-1885-500X"},"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":"Xavier Didelot","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008514010","display_name":"Simon Cauchemez","orcid":"https://orcid.org/0000-0001-9186-4549"},"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":"Simon Cauchemez","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"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":true,"raw_author_name":"Christophe Fraser","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008407354","display_name":"Neil M. Ferguson","orcid":"https://orcid.org/0000-0002-1154-8093"},"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":"Neil Ferguson","raw_affiliation_strings":["MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5013810794","https://openalex.org/A5027792801"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":20.3703,"has_fulltext":true,"cited_by_count":266,"citation_normalized_percentile":{"value":0.99796936,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"1","first_page":"e1003457","last_page":"e1003457"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9972000122070312,"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"}},{"id":"https://openalex.org/T11684","display_name":"Vibrio bacteria research studies","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/outbreak","display_name":"Outbreak","score":0.7686845064163208},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4974706470966339},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.49051302671432495},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.43863606452941895},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4356541633605957},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.4215976595878601},{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.41264432668685913},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3815845549106598},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37522387504577637},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37175607681274414},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2664667069911957},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.18825167417526245},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.09941491484642029},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.09006550908088684}],"concepts":[{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.7686845064163208},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4974706470966339},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.49051302671432495},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.43863606452941895},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4356541633605957},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.4215976595878601},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.41264432668685913},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3815845549106598},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37522387504577637},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37175607681274414},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2664667069911957},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.18825167417526245},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.09941491484642029},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.09006550908088684},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"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/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","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":"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":"D003140","descriptor_name":"Communicable Disease Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003140","descriptor_name":"Communicable Disease Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003140","descriptor_name":"Communicable Disease Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003140","descriptor_name":"Communicable Disease Control","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":true},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012846","descriptor_name":"Singapore","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012846","descriptor_name":"Singapore","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012846","descriptor_name":"Singapore","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012846","descriptor_name":"Singapore","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D045169","descriptor_name":"Severe Acute Respiratory Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D045473","descriptor_name":"Severe acute respiratory syndrome-related coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045473","descriptor_name":"Severe acute respiratory syndrome-related coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045473","descriptor_name":"Severe acute respiratory syndrome-related coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045473","descriptor_name":"Severe acute respiratory syndrome-related coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","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":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003457&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:24465202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24465202","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:researchonline.lshtm.ac.uk:4651622","is_oa":false,"landing_page_url":"https://researchonline.lshtm.ac.uk/view/creators/eidetjom.html>;","pdf_url":null,"source":{"id":"https://openalex.org/S4306402527","display_name":"LSHTM Research Online (London School of Hygiene and Tropical Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210089966","host_organization_name":"London School of Hygiene & Tropical Medicine","host_organization_lineage":["https://openalex.org/I4210089966"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"NonPeerReviewed"},{"id":"pmh:oai:datacompass.lshtm.ac.uk:1072","is_oa":false,"landing_page_url":"https://datacompass.lshtm.ac.uk/id/eprint/1072/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400091","display_name":"London School of Hygiene & Tropical Medicine","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210089966","host_organization_name":"London School of Hygiene & Tropical Medicine","host_organization_lineage":["https://openalex.org/I4210089966"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Data Collection"},{"id":"pmh:oai:doaj.org/article:968306cf50cf465fa3742e43e9b4dd84","is_oa":true,"landing_page_url":"https://doaj.org/article/968306cf50cf465fa3742e43e9b4dd84","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 10, Iss 1, p e1003457 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2885772","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3900386","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:figshare.com:article/910374","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Bayesian_Reconstruction_of_Disease_Outbreaks_by_Combining_Epidemiologic_and_Genomic_Data_/910374","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003457&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":0.8500000238418579}],"awards":[{"id":"https://openalex.org/G1128133788","display_name":null,"funder_award_id":"Gates","funder_id":"https://openalex.org/F4320306137","funder_display_name":"Bill and Melinda Gates Foundation"},{"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/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"},{"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/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2080723129.pdf","grobid_xml":"https://content.openalex.org/works/W2080723129.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1792758720","https://openalex.org/W1923274812","https://openalex.org/W1963568208","https://openalex.org/W1967498970","https://openalex.org/W1967669339","https://openalex.org/W1970771372","https://openalex.org/W1975205625","https://openalex.org/W1980030331","https://openalex.org/W1980099211","https://openalex.org/W1993210385","https://openalex.org/W1995606284","https://openalex.org/W2009678335","https://openalex.org/W2020570040","https://openalex.org/W2032866129","https://openalex.org/W2051903478","https://openalex.org/W2052558548","https://openalex.org/W2057434754","https://openalex.org/W2059041686","https://openalex.org/W2060919531","https://openalex.org/W2081775418","https://openalex.org/W2088701712","https://openalex.org/W2096565388","https://openalex.org/W2097446414","https://openalex.org/W2101372412","https://openalex.org/W2102187991","https://openalex.org/W2117002055","https://openalex.org/W2122396923","https://openalex.org/W2122919191","https://openalex.org/W2132926880","https://openalex.org/W2140050267","https://openalex.org/W2140885215","https://openalex.org/W2147166346","https://openalex.org/W2149408677","https://openalex.org/W2152974798","https://openalex.org/W2157725602","https://openalex.org/W2159937322","https://openalex.org/W2164852757","https://openalex.org/W2168358002","https://openalex.org/W2582743722","https://openalex.org/W6640330755"],"related_works":["https://openalex.org/W2045049461","https://openalex.org/W4381094582","https://openalex.org/W1978893398","https://openalex.org/W1977906818","https://openalex.org/W2369625323","https://openalex.org/W2364579609","https://openalex.org/W1522139108","https://openalex.org/W2353528968","https://openalex.org/W2032776242","https://openalex.org/W2127290136"],"abstract_inverted_index":{"Recent":[0],"years":[1],"have":[2],"seen":[3],"progress":[4],"in":[5,31],"the":[6,63,86,112,115,118,121,135,144,159,188,205],"development":[7],"of":[8,27,41,65,78,85,95,117,120,125,138,187,191,202,207],"statistically":[9],"rigorous":[10,216],"frameworks":[11],"to":[12,47,61,166],"infer":[13],"outbreak":[14,124,149],"transmission":[15,73],"trees":[16],"(\"who":[17],"infected":[18],"whom\")":[19],"from":[20,151],"epidemiological":[21],"and":[22,58,75,82,98,102,171,178,212],"genetic":[23,152],"data.":[24],"Making":[25],"use":[26],"pathogen":[28,56],"genome":[29],"sequences":[30,57],"such":[32],"analyses":[33],"remains":[34],"a":[35,39,51,200,215],"challenge,":[36],"however,":[37],"with":[38,114],"variety":[40],"heuristic":[42],"approaches":[43,174],"having":[44],"been":[45],"explored":[46],"date.":[48],"We":[49],"introduce":[50],"statistical":[52],"method":[53,113,197],"exploiting":[54],"both":[55],"collection":[59],"dates":[60,77],"unravel":[62],"dynamics":[64],"densely":[66,168,208],"sampled":[67,169,209],"outbreaks.":[68],"Our":[69,141],"approach":[70,107,142],"identifies":[71],"likely":[72],"events":[74],"infers":[76],"infections,":[79],"unobserved":[80,177],"cases":[81],"separate":[83],"introductions":[84,186],"disease.":[87],"It":[88,163],"also":[89],"proves":[90],"useful":[91],"for":[92,147,204,218],"inferring":[93],"numbers":[94],"secondary":[96],"infections":[97],"identifying":[99],"heterogeneous":[100],"infectivity":[101],"super-spreaders.":[103],"After":[104],"testing":[105],"our":[106],"using":[108],"simulations,":[109],"we":[110,194],"illustrate":[111],"analysis":[116,206],"beginning":[119],"2003":[122],"Singaporean":[123],"Severe":[126],"Acute":[127],"Respiratory":[128],"Syndrome":[129],"(SARS),":[130],"providing":[131],"new":[132],"insights":[133],"into":[134],"early":[136],"stage":[137],"this":[139,196],"epidemic.":[140],"is":[143,164],"first":[145],"tool":[146,201],"disease":[148,210],"reconstruction":[150],"data":[153],"widely":[154],"available":[155],"as":[156,181,183],"free":[157],"software,":[158],"R":[160],"package":[161],"outbreaker.":[162],"applicable":[165],"various":[167],"epidemics,":[170],"improves":[172],"previous":[173],"by":[175],"detecting":[176],"imported":[179],"cases,":[180],"well":[182],"allowing":[184],"multiple":[185],"pathogen.":[189],"Because":[190],"its":[192],"generality,":[193],"believe":[195],"will":[198,213],"become":[199],"choice":[203],"outbreaks,":[211],"form":[214],"framework":[217],"subsequent":[219],"methodological":[220],"developments.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":36},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":20},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":27},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}