{"id":"https://openalex.org/W4385567503","doi":"https://doi.org/10.3389/fbinf.2023.1225807","title":"Molecular timetrees using relaxed clocks and uncertain phylogenies","display_name":"Molecular timetrees using relaxed clocks and uncertain phylogenies","publication_year":2023,"publication_date":"2023-08-03","ids":{"openalex":"https://openalex.org/W4385567503","doi":"https://doi.org/10.3389/fbinf.2023.1225807","pmid":"https://pubmed.ncbi.nlm.nih.gov/37600967"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1225807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1225807","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1225807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1225807/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000997109","display_name":"Jose Barba\u2010Montoya","orcid":"https://orcid.org/0000-0002-1337-8139"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Barba-Montoya","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020357256","display_name":"Sudip Sharma","orcid":"https://orcid.org/0000-0002-0469-1211"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudip Sharma","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.593,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69780066,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"3","issue":null,"first_page":"1225807","last_page":"1225807"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.998199999332428,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9955000281333923,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7590203285217285},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.68357914686203},{"id":"https://openalex.org/keywords/molecular-clock","display_name":"Molecular clock","score":0.6766455173492432},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6269823908805847},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5744481682777405},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5633739829063416},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.5605568885803223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4972224533557892},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.37765318155288696},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3613698184490204},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34586718678474426},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33373647928237915},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07588732242584229}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7590203285217285},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.68357914686203},{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.6766455173492432},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6269823908805847},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5744481682777405},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5633739829063416},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5605568885803223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4972224533557892},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.37765318155288696},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3613698184490204},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34586718678474426},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33373647928237915},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07588732242584229},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2023.1225807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1225807","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1225807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37600967","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37600967","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10435864","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10435864","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10435864/pdf/fbinf-03-1225807.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d7286e3895d44fd18f59524a77492083","is_oa":true,"landing_page_url":"https://doaj.org/article/d7286e3895d44fd18f59524a77492083","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1225807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1225807","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1225807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"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":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385567503.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W191821314","https://openalex.org/W1605984840","https://openalex.org/W1980047218","https://openalex.org/W1992566665","https://openalex.org/W2005633246","https://openalex.org/W2007593785","https://openalex.org/W2009596137","https://openalex.org/W2024612778","https://openalex.org/W2026551295","https://openalex.org/W2028707635","https://openalex.org/W2030966943","https://openalex.org/W2045517599","https://openalex.org/W2060425093","https://openalex.org/W2071717427","https://openalex.org/W2094939159","https://openalex.org/W2108034499","https://openalex.org/W2111647009","https://openalex.org/W2125359798","https://openalex.org/W2127779696","https://openalex.org/W2130362098","https://openalex.org/W2148698435","https://openalex.org/W2159597448","https://openalex.org/W2166029367","https://openalex.org/W2180090668","https://openalex.org/W2187450834","https://openalex.org/W2207288795","https://openalex.org/W2342704856","https://openalex.org/W2408731419","https://openalex.org/W2554017006","https://openalex.org/W2732250892","https://openalex.org/W2762173626","https://openalex.org/W2796242207","https://openalex.org/W2799524357","https://openalex.org/W2803397292","https://openalex.org/W2888190843","https://openalex.org/W2901927999","https://openalex.org/W2901954177","https://openalex.org/W2902515710","https://openalex.org/W2949127318","https://openalex.org/W2949972517","https://openalex.org/W2950355266","https://openalex.org/W2991998196","https://openalex.org/W2999168229","https://openalex.org/W3025857586","https://openalex.org/W3082270223","https://openalex.org/W3116854850","https://openalex.org/W3123240947","https://openalex.org/W3137036375","https://openalex.org/W3199805689","https://openalex.org/W3212910140","https://openalex.org/W4200339067"],"related_works":["https://openalex.org/W4230346575","https://openalex.org/W1580870255","https://openalex.org/W2505460932","https://openalex.org/W4236902373","https://openalex.org/W2958638543","https://openalex.org/W2997493526","https://openalex.org/W2052991522","https://openalex.org/W3110873485","https://openalex.org/W2094939159","https://openalex.org/W2407375987"],"abstract_inverted_index":{"A":[0],"common":[1],"practice":[2,27],"in":[3,66,93,109],"molecular":[4,56],"systematics":[5],"is":[6,44],"to":[7,14,45,51,81],"infer":[8,46],"phylogeny":[9,47,103,164],"and":[10,22,38,48,72,78,86,150,160],"then":[11],"scale":[12],"it":[13],"time":[15,36],"by":[16,175],"using":[17,70],"a":[18,180],"relaxed":[19],"clock":[20],"method":[21,168],"calibrations.":[23],"This":[24],"sequential":[25,77],"analysis":[26],"ignores":[28],"the":[29,60,102,111,143,170],"effect":[30],"of":[31,62,145],"phylogenetic":[32,53,87],"uncertainty":[33],"on":[34],"divergence":[35,84,158],"estimates":[37],"their":[39],"confidence/credibility":[40],"intervals.":[41],"An":[42],"alternative":[43,136],"times":[49,85],"jointly":[50],"incorporate":[52],"errors":[54],"into":[55],"dating.":[57],"We":[58,75,133],"compared":[59],"performance":[61],"these":[63],"two":[64],"alternatives":[65],"reconstructing":[67],"evolutionary":[68,156],"timetrees":[69],"computer-simulated":[71],"empirical":[73],"datasets.":[74],"found":[76],"joint":[79,97,112,118,139],"analyses":[80],"produce":[82],"similar":[83,181],"relationships,":[88,157],"except":[89],"for":[90,123,138,153],"some":[91],"nodes":[92],"particular":[94],"cases.":[95],"The":[96,166],"inference":[98,113,119,140],"performed":[99],"better":[100],"when":[101],"was":[104],"not":[105],"well":[106],"resolved,":[107],"situations":[108],"which":[110],"should":[114],"be":[115,121],"preferred.":[116],"However,":[117],"can":[120],"infeasible":[122],"large":[124],"datasets":[125],"because":[126],"available":[127],"Bayesian":[128,176],"methods":[129,177],"are":[130],"computationally":[131],"burdensome.":[132],"present":[134],"an":[135],"approach":[137],"that":[141],"combines":[142],"bag":[144],"little":[146],"bootstraps,":[147],"maximum":[148],"likelihood,":[149],"RelTime":[151],"approaches":[152],"simultaneously":[154],"inferring":[155],"times,":[159],"confidence":[161],"intervals,":[162],"incorporating":[163],"uncertainty.":[165],"new":[167],"alleviates":[169],"high":[171],"computational":[172],"burden":[173],"imposed":[174],"while":[178],"achieving":[179],"result.":[182]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
