{"id":"https://openalex.org/W2148439324","doi":"https://doi.org/10.1093/bioinformatics/btt153","title":"Fast simulation of reconstructed phylogenies under global time-dependent birth\u2013death processes","display_name":"Fast simulation of reconstructed phylogenies under global time-dependent birth\u2013death processes","publication_year":2013,"publication_date":"2013-03-29","ids":{"openalex":"https://openalex.org/W2148439324","doi":"https://doi.org/10.1093/bioinformatics/btt153","mag":"2148439324","pmid":"https://pubmed.ncbi.nlm.nih.gov/23543414"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt153","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1367/17099319/btt153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1367/17099319/btt153.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110768391","display_name":"Sebastian H\u00f6hna","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Sebastian H\u00f6hna","raw_affiliation_strings":["Department of Mathematics, Stockholm University, Kr\u00e4ftriket Hus 6, S-10691 Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Stockholm University, Kr\u00e4ftriket Hus 6, S-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5110768391"],"corresponding_institution_ids":["https://openalex.org/I161593684"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":16.3757,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.9912858,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"29","issue":"11","first_page":"1367","last_page":"1374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.957099974155426,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.957099974155426,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10955","display_name":"Paleontology and Evolutionary Biology","score":0.012199999764561653,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.008100000210106373,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7288781404495239},{"id":"https://openalex.org/keywords/diversification","display_name":"Diversification (marketing strategy)","score":0.6094435453414917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5370696187019348},{"id":"https://openalex.org/keywords/independent-and-identically-distributed-random-variables","display_name":"Independent and identically distributed random variables","score":0.5191832780838013},{"id":"https://openalex.org/keywords/birth\u2013death-process","display_name":"Birth\u2013death process","score":0.5048907399177551},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.49060001969337463},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.4677227735519409},{"id":"https://openalex.org/keywords/replicate","display_name":"Replicate","score":0.45774075388908386},{"id":"https://openalex.org/keywords/phylogenetic-comparative-methods","display_name":"Phylogenetic comparative methods","score":0.45496708154678345},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.43557465076446533},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.43448615074157715},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3966653048992157},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3452123999595642},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.321880966424942},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17567762732505798},{"id":"https://openalex.org/keywords/random-variable","display_name":"Random variable","score":0.13988035917282104},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.10916391015052795}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7288781404495239},{"id":"https://openalex.org/C180916674","wikidata":"https://www.wikidata.org/wiki/Q3711935","display_name":"Diversification (marketing strategy)","level":2,"score":0.6094435453414917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5370696187019348},{"id":"https://openalex.org/C141513077","wikidata":"https://www.wikidata.org/wiki/Q378542","display_name":"Independent and identically distributed random variables","level":3,"score":0.5191832780838013},{"id":"https://openalex.org/C65990518","wikidata":"https://www.wikidata.org/wiki/Q1456275","display_name":"Birth\u2013death process","level":3,"score":0.5048907399177551},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.49060001969337463},{"id":"https://openalex.org/C2776838516","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.4677227735519409},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.45774075388908386},{"id":"https://openalex.org/C176771619","wikidata":"https://www.wikidata.org/wiki/Q7189434","display_name":"Phylogenetic comparative methods","level":4,"score":0.45496708154678345},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.43557465076446533},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43448615074157715},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3966653048992157},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3452123999595642},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.321880966424942},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17567762732505798},{"id":"https://openalex.org/C122123141","wikidata":"https://www.wikidata.org/wiki/Q176623","display_name":"Random variable","level":2,"score":0.13988035917282104},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.10916391015052795},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt153","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1367/17099319/btt153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23543414","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23543414","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt153","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1367/17099319/btt153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2148439324.pdf","grobid_xml":"https://content.openalex.org/works/W2148439324.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1628017834","https://openalex.org/W1979257831","https://openalex.org/W1983002447","https://openalex.org/W2018956877","https://openalex.org/W2029973096","https://openalex.org/W2039091939","https://openalex.org/W2045287093","https://openalex.org/W2045656233","https://openalex.org/W2056760934","https://openalex.org/W2065212460","https://openalex.org/W2073524434","https://openalex.org/W2097726506","https://openalex.org/W2100365145","https://openalex.org/W2116416291","https://openalex.org/W2117368100","https://openalex.org/W2118610143","https://openalex.org/W2126833785","https://openalex.org/W2129505888","https://openalex.org/W2129928578","https://openalex.org/W2131013059","https://openalex.org/W2133436664","https://openalex.org/W2135557692","https://openalex.org/W2136829296","https://openalex.org/W2137565061","https://openalex.org/W2138309709","https://openalex.org/W2140087131","https://openalex.org/W2146620998","https://openalex.org/W2147171518","https://openalex.org/W2148823819","https://openalex.org/W2149462580","https://openalex.org/W2150533820","https://openalex.org/W2151062029","https://openalex.org/W2151409320","https://openalex.org/W2151413057","https://openalex.org/W2154552181","https://openalex.org/W2163313260","https://openalex.org/W2163748076","https://openalex.org/W2171059556","https://openalex.org/W2180090668","https://openalex.org/W2229908198","https://openalex.org/W2259225862","https://openalex.org/W2582743722","https://openalex.org/W3122858766","https://openalex.org/W4231907244","https://openalex.org/W4232383088","https://openalex.org/W6679052492","https://openalex.org/W6682130099"],"related_works":["https://openalex.org/W4254851101","https://openalex.org/W3171007296","https://openalex.org/W22115721","https://openalex.org/W2211931904","https://openalex.org/W2065444835","https://openalex.org/W2321234655","https://openalex.org/W2470062578","https://openalex.org/W2952773340","https://openalex.org/W1976848834","https://openalex.org/W3141757862"],"abstract_inverted_index":{"MOTIVATION:":[0],"Diversification":[1],"rates":[2,94,96,173],"and":[3,14,31,42,59,117,125],"patterns":[4,24],"may":[5,97],"be":[6,131],"inferred":[7],"from":[8,112,197],"reconstructed":[9,114,136],"phylogenies.":[10],"Both":[11],"the":[12,15,21,36,68,75,81,92,106,109,142,146,149,155,158,162,192,198],"time-dependent":[13,85],"diversity-dependent":[16],"birth-death":[17,86,168],"process":[18,38,87,150,169],"can":[19,130],"produce":[20],"same":[22,93],"observed":[23],"of":[25,39,70,108,144,148,157,166],"diversity":[26],"over":[27,99],"time.":[28,100],"To":[29],"develop":[30],"test":[32],"new":[33],"models":[34,49,61],"describing":[35],"macro-evolutionary":[37],"diversification,":[40],"generic":[41],"fast":[43],"algorithms":[44],"to":[45,133],"simulate":[46,134],"under":[47],"these":[48],"are":[50,53,189,206],"necessary.":[51],"Simulations":[52],"not":[54],"only":[55],"important":[56],"for":[57],"testing":[58],"developing":[60],"but":[62,95],"play":[63],"an":[64],"influential":[65],"role":[66],"in":[67,186,191],"assessment":[69],"model":[71,82],"fit.":[72],"RESULTS:":[73],"In":[74],"present":[76],"article,":[77],"I":[78,104,153],"consider":[79],"as":[80],"a":[83,113,167,176],"global":[84],"where":[88],"each":[89,120],"species":[90],"has":[91],"vary":[98],"For":[101],"this":[102,187],"model,":[103],"derive":[105],"likelihood":[107],"speciation":[110,121],"times":[111],"phylogenetic":[115,137],"tree":[116],"show":[118,154],"that":[119],"event":[122],"is":[123],"independent":[124],"identically":[126],"distributed.":[127],"This":[128],"fact":[129],"used":[132],"efficiently":[135],"trees":[138],"when":[139],"conditioning":[140],"on":[141,175],"number":[143],"species,":[145],"time":[147],"or":[151],"both.":[152],"usability":[156],"simulation":[159],"by":[160],"approximating":[161],"posterior":[163],"predictive":[164],"distribution":[165],"with":[170],"decreasing":[171],"diversification":[172],"applied":[174],"published":[177],"bird":[178],"phylogeny":[179],"(family":[180],"Cettiidae).":[181],"AVAILABILITY:":[182],"The":[183],"methods":[184],"described":[185],"manuscript":[188],"implemented":[190],"R":[193],"package":[194],"TESS,":[195],"available":[196,207],"repository":[199],"CRAN":[200],"(http://cran.r-project.org/web/packages/TESS/).":[201],"SUPPLEMENTARY":[202],"INFORMATION:":[203],"Supplementary":[204],"data":[205],"at":[208],"Bioinformatics":[209],"online.":[210]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
