{"id":"https://openalex.org/W4293193292","doi":"https://doi.org/10.1371/journal.pcbi.1010409","title":"VGsim: Scalable viral genealogy simulator for global pandemic","display_name":"VGsim: Scalable viral genealogy simulator for global pandemic","publication_year":2022,"publication_date":"2022-08-24","ids":{"openalex":"https://openalex.org/W4293193292","doi":"https://doi.org/10.1371/journal.pcbi.1010409","pmid":"https://pubmed.ncbi.nlm.nih.gov/36001646"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010409","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010409","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010409&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.1010409&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086098490","display_name":"Vladimir Shchur","orcid":"https://orcid.org/0000-0002-1431-5260"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Vladimir Shchur","raw_affiliation_strings":["International laboratory of statistical and computational genomics, HSE University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"International laboratory of statistical and computational genomics, HSE University, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055583699","display_name":"Vadim Spirin","orcid":"https://orcid.org/0000-0002-0331-8060"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vadim Spirin","raw_affiliation_strings":["International laboratory of statistical and computational genomics, HSE University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"International laboratory of statistical and computational genomics, HSE University, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091074596","display_name":"Dmitry Sirotkin","orcid":"https://orcid.org/0000-0002-2682-9867"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitry Sirotkin","raw_affiliation_strings":["International laboratory of statistical and computational genomics, HSE University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"International laboratory of statistical and computational genomics, HSE University, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030454460","display_name":"Evgeni Burovski","orcid":"https://orcid.org/0000-0001-8149-0483"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Evgeni Burovski","raw_affiliation_strings":["HSE University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"HSE University, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030621715","display_name":"Nicola De Maio","orcid":"https://orcid.org/0000-0002-1776-8564"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicola De Maio","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076593250","display_name":"Russell Corbett\u2010Detig","orcid":"https://orcid.org/0000-0001-6535-2478"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell Corbett-Detig","raw_affiliation_strings":["Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California, United States of America","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5086098490"],"corresponding_institution_ids":["https://openalex.org/I118501908"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1283,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.76682985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"8","first_page":"e1010409","last_page":"e1010409"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}},{"id":"https://openalex.org/T10494","display_name":"Plant Virus Research Studies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant 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"}}],"keywords":[{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.6598964929580688},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.6236680746078491},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5407495498657227},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5374650955200195},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5243088006973267},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.5060269236564636},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3479682207107544},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34040531516075134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21868765354156494},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.19989165663719177},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19806447625160217},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.16386154294013977}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.6598964929580688},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.6236680746078491},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5407495498657227},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5374650955200195},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5243088006973267},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.5060269236564636},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3479682207107544},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34040531516075134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21868765354156494},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.19989165663719177},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19806447625160217},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.16386154294013977},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"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":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010409","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010409","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010409&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:36001646","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36001646","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:RePEc:plo:pcbi00:1010409","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010409","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:d2e2aba4038b49308cabeffce68ef010","is_oa":true,"landing_page_url":"https://doaj.org/article/d2e2aba4038b49308cabeffce68ef010","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 8, p e1010409 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9447924","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9447924","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1010409","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010409","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010409&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":[{"score":0.8299999833106995,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3969577304","display_name":null,"funder_award_id":"20-04-","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G473593538","display_name":null,"funder_award_id":"Molecular","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5197367088","display_name":null,"funder_award_id":"20-04-60556","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"},{"id":"https://openalex.org/G5921679036","display_name":null,"funder_award_id":"Project Teams framework of MIEM HSE","funder_id":"https://openalex.org/F4320324261","funder_display_name":"National Research University Higher School of Economics"},{"id":"https://openalex.org/G5997868131","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"},{"id":"https://openalex.org/G6426371021","display_name":null,"funder_award_id":"Basic Research Program","funder_id":"https://openalex.org/F4320324261","funder_display_name":"National Research University Higher School of Economics"},{"id":"https://openalex.org/G7343549071","display_name":null,"funder_award_id":"R35GM128932","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G8274360035","display_name":null,"funder_award_id":"R35GM128932","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G843969383","display_name":null,"funder_award_id":"R35GM128932","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G898110086","display_name":null,"funder_award_id":"R35GM12893","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320324261","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4293193292.pdf","grobid_xml":"https://content.openalex.org/works/W4293193292.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W30489333","https://openalex.org/W1962960380","https://openalex.org/W1964525108","https://openalex.org/W2009505947","https://openalex.org/W2027506430","https://openalex.org/W2044859335","https://openalex.org/W2084840427","https://openalex.org/W2087884804","https://openalex.org/W2098062910","https://openalex.org/W2104266030","https://openalex.org/W2108670087","https://openalex.org/W2114058116","https://openalex.org/W2139871526","https://openalex.org/W2144658220","https://openalex.org/W2147477044","https://openalex.org/W2153432740","https://openalex.org/W2167154952","https://openalex.org/W2171463101","https://openalex.org/W2508517928","https://openalex.org/W2794619758","https://openalex.org/W2912052416","https://openalex.org/W2949210352","https://openalex.org/W2951641704","https://openalex.org/W2952663165","https://openalex.org/W2953324318","https://openalex.org/W2971662497","https://openalex.org/W3029878358","https://openalex.org/W3031121540","https://openalex.org/W3035965352","https://openalex.org/W3082463691","https://openalex.org/W3099665160","https://openalex.org/W3099878876","https://openalex.org/W3105980255","https://openalex.org/W3121606938","https://openalex.org/W3122209030","https://openalex.org/W3125499510","https://openalex.org/W3128186941","https://openalex.org/W3128213721","https://openalex.org/W3133464627","https://openalex.org/W3135191472","https://openalex.org/W3135749358","https://openalex.org/W3137157131","https://openalex.org/W3137469790","https://openalex.org/W3142627215","https://openalex.org/W3160568774","https://openalex.org/W3168349393","https://openalex.org/W3179423943","https://openalex.org/W3187962553","https://openalex.org/W3192740658","https://openalex.org/W3196426464","https://openalex.org/W4210633230","https://openalex.org/W4225249066","https://openalex.org/W4247464444","https://openalex.org/W4291016578","https://openalex.org/W6749321808","https://openalex.org/W6789105000","https://openalex.org/W6799421997"],"related_works":["https://openalex.org/W2952954362","https://openalex.org/W3093602888","https://openalex.org/W2762052495","https://openalex.org/W3156045358","https://openalex.org/W2921578049","https://openalex.org/W2581424563","https://openalex.org/W2020599444","https://openalex.org/W2089205969","https://openalex.org/W4300801083","https://openalex.org/W1495737144"],"abstract_inverted_index":{"Accurate":[0],"simulation":[1,152,158],"of":[2,10,30,52,72,86,100,135,137,151,174,180,187,202],"complex":[3,219],"biological":[4],"processes":[5,91],"is":[6,113,117,160],"an":[7,20,184],"essential":[8],"component":[9],"developing":[11],"and":[12,16,77,105,120,131,223],"validating":[13],"new":[14,101,143],"technologies":[15],"inference":[17],"approaches.":[18],"As":[19],"effort":[21],"to":[22,123,127],"help":[23],"contain":[24],"the":[25,40,70,73,98,125,149,166,169,178,181,188,192,206,212],"COVID-19":[26],"pandemic,":[27],"large":[28],"numbers":[29],"SARS-CoV-2":[31],"genomes":[32],"have":[33],"been":[34],"sequenced":[35],"from":[36,60],"most":[37],"regions":[38],"in":[39],"world.":[41],"More":[42],"than":[43],"5.5":[44],"million":[45],"viral":[46,58,133],"sequences":[47],"are":[48,82],"publicly":[49],"available":[50],"as":[51,63],"November":[53],"2021.":[54],"Many":[55],"studies":[56],"estimate":[57],"genealogies":[59,134,153],"these":[61,64],"sequences,":[62],"can":[65,217],"provide":[66],"valuable":[67],"information":[68,87],"about":[69,88],"spread":[71],"pandemic":[74,126,182],"across":[75],"time":[76],"space.":[78],"Additionally":[79],"such":[80],"data":[81],"a":[83,142,172,195,199],"rich":[84],"source":[85],"molecular":[89],"evolutionary":[90],"including":[92],"natural":[93],"selection,":[94],"for":[95],"example":[96],"allowing":[97],"identification":[99],"variants":[102],"with":[103],"transmissibility":[104],"immunity":[106,224],"evasion":[107],"advantages.":[108],"To":[109],"our":[110],"knowledge,":[111],"there":[112],"no":[114],"framework":[115],"that":[116],"both":[118],"efficient":[119],"flexible":[121],"enough":[122],"simulate":[124],"approximate":[128],"world-scale":[129],"scenarios":[130],"generate":[132],"millions":[136],"samples.":[138],"Here,":[139],"we":[140],"introduce":[141],"fast":[144],"simulator":[145],"VGsim":[146],"which":[147],"addresses":[148],"problem":[150],"under":[154],"epidemiological":[155],"models.":[156],"The":[157],"process":[159],"split":[161],"into":[162],"two":[163],"phases.":[164],"During":[165,191],"forward":[167,213],"run":[168,194],"algorithm":[170],"generates":[171,198],"chain":[173,209],"population-level":[175,207],"events":[176,208],"reflecting":[177],"dynamics":[179],"using":[183],"hierarchical":[185],"version":[186],"Gillespie":[189],"algorithm.":[190],"backward":[193],"coalescent-like":[196],"approach":[197],"tree":[200],"genealogy":[201],"samples":[203],"conditioning":[204],"on":[205],"generated":[210],"during":[211],"run.":[214],"Our":[215],"software":[216],"model":[218],"population":[220],"structure,":[221],"epistasis":[222],"escape.":[225]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}