{"id":"https://openalex.org/W2775128358","doi":"https://doi.org/10.1137/17m1114946","title":"Tajima's D and Site-Specific Nucleotide Frequency in a Population during an Infectious Disease Outbreak","display_name":"Tajima's D and Site-Specific Nucleotide Frequency in a Population during an Infectious Disease Outbreak","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2775128358","doi":"https://doi.org/10.1137/17m1114946","mag":"2775128358"},"language":"en","primary_location":{"id":"doi:10.1137/17m1114946","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1114946","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1114946","source":{"id":"https://openalex.org/S77200987","display_name":"SIAM Journal on Applied Mathematics","issn_l":"0036-1399","issn":["0036-1399","1095-712X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Mathematics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1114946","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003852286","display_name":"Ryosuke Omori","orcid":"https://orcid.org/0000-0002-9635-1459"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ryosuke Omori","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9635-1459","affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Jianhong Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jianhong Wu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4372,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.73478041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"77","issue":"6","first_page":"2156","last_page":"2171"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998999834060669,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9966999888420105,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9941999912261963,"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/biology","display_name":"Biology","score":0.5856872200965881},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5838497281074524},{"id":"https://openalex.org/keywords/mutation-rate","display_name":"Mutation rate","score":0.4568082392215729},{"id":"https://openalex.org/keywords/epidemic-model","display_name":"Epidemic model","score":0.45525938272476196},{"id":"https://openalex.org/keywords/genetic-diversity","display_name":"Genetic diversity","score":0.43988269567489624},{"id":"https://openalex.org/keywords/outbreak","display_name":"Outbreak","score":0.43595147132873535},{"id":"https://openalex.org/keywords/nucleotide-diversity","display_name":"Nucleotide diversity","score":0.41203680634498596},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.40642479062080383},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.404777854681015},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.36417824029922485},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31708359718322754},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.23579096794128418},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2054317593574524},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1732395589351654},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.10554483532905579},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.10363775491714478},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.09187686443328857}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5856872200965881},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5838497281074524},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.4568082392215729},{"id":"https://openalex.org/C1627819","wikidata":"https://www.wikidata.org/wiki/Q2572354","display_name":"Epidemic model","level":3,"score":0.45525938272476196},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.43988269567489624},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.43595147132873535},{"id":"https://openalex.org/C26589402","wikidata":"https://www.wikidata.org/wiki/Q7068267","display_name":"Nucleotide diversity","level":5,"score":0.41203680634498596},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.40642479062080383},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.404777854681015},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.36417824029922485},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31708359718322754},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.23579096794128418},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2054317593574524},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1732395589351654},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.10554483532905579},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.10363775491714478},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.09187686443328857},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1137/17m1114946","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1114946","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1114946","source":{"id":"https://openalex.org/S77200987","display_name":"SIAM Journal on Applied Mathematics","issn_l":"0036-1399","issn":["0036-1399","1095-712X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Mathematics","raw_type":"journal-article"},{"id":"pmh:oai:eprints.lib.hokudai.ac.jp:2115/70807","is_oa":true,"landing_page_url":"http://hdl.handle.net/2115/70807","pdf_url":null,"source":{"id":"https://openalex.org/S4306400549","display_name":"Hokkaido University Collection of Scholarly and Academic Papers (Hokkaido University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205349734","host_organization_name":"Hokkaido University","host_organization_lineage":["https://openalex.org/I205349734"],"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":"article"},{"id":"pmh:oai:irdb.nii.ac.jp:01364:0007184609","is_oa":true,"landing_page_url":"https://hdl.handle.net/2115/70807","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"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":"SIAM journal on applied mathematics","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1137/17m1114946","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1114946","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1114946","source":{"id":"https://openalex.org/S77200987","display_name":"SIAM Journal on Applied Mathematics","issn_l":"0036-1399","issn":["0036-1399","1095-712X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Mathematics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3712386483","display_name":null,"funder_award_id":"105588-2011","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5532268160","display_name":null,"funder_award_id":"230720","funder_id":"https://openalex.org/F4320320994","funder_display_name":"Canada Research Chairs"}],"funders":[{"id":"https://openalex.org/F4320320994","display_name":"Canada Research Chairs","ror":"https://ror.org/0517h6h17"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338111","display_name":"Precursory Research for Embryonic Science and Technology","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2775128358.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W184081997","https://openalex.org/W1525734744","https://openalex.org/W1956721446","https://openalex.org/W1980518783","https://openalex.org/W1987957425","https://openalex.org/W1989932652","https://openalex.org/W1993210385","https://openalex.org/W1996887960","https://openalex.org/W2001488223","https://openalex.org/W2065461553","https://openalex.org/W2072895797","https://openalex.org/W2115837217","https://openalex.org/W2116668053","https://openalex.org/W2124892806","https://openalex.org/W2134213231","https://openalex.org/W2140784970","https://openalex.org/W2144410236","https://openalex.org/W2155081753","https://openalex.org/W2160253520","https://openalex.org/W2163357043","https://openalex.org/W2237374776"],"related_works":["https://openalex.org/W2359113872","https://openalex.org/W1865092839","https://openalex.org/W2166851110","https://openalex.org/W2062147302","https://openalex.org/W2378468741","https://openalex.org/W2156234555","https://openalex.org/W3160551698","https://openalex.org/W4282920139","https://openalex.org/W2464771708","https://openalex.org/W2322865176"],"abstract_inverted_index":{"Tajima's":[0,23,75,111],"D":[1,24,76,112],"measures":[2],"the":[3,35,59,63,67,72,80,86,95,99,114,124,134],"difference":[4],"between":[5],"two":[6],"estimates":[7],"of":[8,15,66,74,79,94,110,123,126,140],"genetic":[9,138],"diversity":[10,139],"in":[11,98],"a":[12,40,121,141],"given":[13],"set":[14],"nucleic":[16],"acid":[17],"sequences.":[18],"Here":[19],"we":[20,105],"show":[21,51,107],"how":[22],"can":[25],"be":[26],"calculated/estimated":[27],"by":[28,58],"developing":[29],"an":[30,92],"inductive":[31],"algorithm":[32],"for":[33,133],"calculating":[34],"site-specific":[36],"nucleotide":[37],"frequencies":[38,54],"from":[39],"standard":[41],"multistrain":[42],"susceptible-infective-removed":[43],"(SIR)":[44],"model":[45],"(both":[46],"deterministic":[47,100],"and":[48,62,84,117],"stochastic).":[49],"We":[50,69],"that":[52,71,85,108],"these":[53],"are":[55],"fully":[56],"determined":[57],"mutation":[60],"rate":[61],"initial":[64],"condition":[65],"frequencies.":[68],"prove":[70],"sign":[73,88],"is":[77,120,131],"independent":[78],"disease":[81,115],"population":[82,97],"dynamics":[83,119],"negative":[87],"does":[89],"not":[90],"imply":[91],"expansion":[93],"infected":[96],"model.":[101],"Using":[102],"individual-based":[103],"simulations,":[104],"also":[106],"dependence":[109,135],"on":[113],"transmission":[116],"evolution":[118],"result":[122],"stochasticity":[125],"those":[127],"dynamics.":[128],"The":[129],"same":[130],"true":[132],"related":[136],"to":[137],"pathogen.":[142]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
