{"id":"https://openalex.org/W2999929805","doi":"https://doi.org/10.1371/journal.pcbi.1007046","title":"A new method for inferring timetrees from temporally sampled molecular sequences","display_name":"A new method for inferring timetrees from temporally sampled molecular sequences","publication_year":2020,"publication_date":"2020-01-17","ids":{"openalex":"https://openalex.org/W2999929805","doi":"https://doi.org/10.1371/journal.pcbi.1007046","mag":"2999929805","pmid":"https://pubmed.ncbi.nlm.nih.gov/31951607"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007046&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.1007046&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062480014","display_name":"Sayaka Miura","orcid":"https://orcid.org/0000-0001-9881-2848"},"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":"Sayaka Miura","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9881-2848","affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007823743","display_name":"Koichiro Tamura","orcid":"https://orcid.org/0000-0001-7189-5399"},"institutions":[{"id":"https://openalex.org/I69740276","display_name":"Tokyo Metropolitan University","ror":"https://ror.org/00ws30h19","country_code":"JP","type":"education","lineage":["https://openalex.org/I69740276"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koichiro Tamura","raw_affiliation_strings":["Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan","Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan","institution_ids":["https://openalex.org/I69740276"]},{"raw_affiliation_string":"Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan","institution_ids":["https://openalex.org/I69740276"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016751952","display_name":"Qiqing Tao","orcid":"https://orcid.org/0000-0001-7360-409X"},"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":"Qiqing Tao","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7360-409X","affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005665859","display_name":"Louise A. Huuki-Myers","orcid":"https://orcid.org/0000-0001-5148-3602"},"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":"Louise A. Huuki","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011410563","display_name":"Sergei L. Kosakovsky Pond","orcid":"https://orcid.org/0000-0003-4817-4029"},"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":"Sergei L. Kosakovsky Pond","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073101412","display_name":"Jessica M. Priest","orcid":"https://orcid.org/0000-0001-7511-6284"},"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":"Jessica Priest","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7511-6284","affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086645000","display_name":"Jiamin Deng","orcid":"https://orcid.org/0000-0003-0566-4597"},"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":"Jiamin Deng","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-0566-4597","affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","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/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"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":["SA","US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia","Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9918-8212","affiliations":[{"raw_affiliation_string":"Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]},{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I185163786","https://openalex.org/I84392919"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.501,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.81872737,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"16","issue":"1","first_page":"e1007046","last_page":"e1007046"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9979000091552734,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9914000034332275,"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":0.6495327949523926},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.6148098707199097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5939614176750183},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.5690385103225708},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5437423586845398},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.5280200839042664},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.5186271071434021},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.5062612295150757},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5060026049613953},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4717726707458496},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.437171995639801},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38813120126724243},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34408220648765564},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28042370080947876},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09942537546157837}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6495327949523926},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.6148098707199097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5939614176750183},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.5690385103225708},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5437423586845398},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.5280200839042664},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.5186271071434021},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5062612295150757},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5060026049613953},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4717726707458496},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.437171995639801},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38813120126724243},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34408220648765564},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28042370080947876},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09942537546157837},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":[{"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007046&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:31951607","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31951607","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:pcbi00:1007046","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007046","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:a64b8cc22e1849b9a77bcb066896e6a2","is_oa":true,"landing_page_url":"https://doaj.org/article/a64b8cc22e1849b9a77bcb066896e6a2","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":"PLoS Computational Biology, Vol 16, Iss 1, p e1007046 (2020)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5982164","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7018096","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/11639481","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_new_method_for_inferring_timetrees_from_temporally_sampled_molecular_sequences/11639481","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.1007046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007046&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":[],"awards":[{"id":"https://openalex.org/G1126534504","display_name":null,"funder_award_id":"R01GM126567","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1297753613","display_name":"ABI Development: Open-source, extensible, and cross-platform MEGA","funder_award_id":"1661218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1466802593","display_name":null,"funder_award_id":"ABI 1661218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1550371143","display_name":null,"funder_award_id":"TU-420721","funder_id":"https://openalex.org/F4320308109","funder_display_name":"Pennsylvania Department of Health"},{"id":"https://openalex.org/G2466576084","display_name":"SCIENCE GOALS: WHEN RECONSTRUCTING EVOLUTIONARY HISTORIES OF LIFE ON EARTH PRIMARY SOURCES OF INFORMATION ARE GEOLOGIC DATA  APPLICABLE MOSTLY TO PHANEROZOIC LIFE FORMS  AND MOLECULAR DATA FOR PRE-CAMBRIAN LIFE. TIMELINES INFERRED FROM THESE TWO SOURCES ARE GENERALLY IN AGREEMENT BUT MAJOR CHALLENGES FOR KEY EVOLUTIONARY STEPS REMAIN. THIS IS ESPECIALLY TRUE FOR TIMELINES OF EARLY MICROBIAL LIFE THAT  DUE TO THE ALMOST COMPLETE LACK OF GEOLOGIC RECORD  ARE HEAVILY DEPENDENT ON MOLECULAR-BASED APPROACHES THAT OFTEN PRODUCE CONTRASTING EVOLUTIONARY HISTORIES. TO IMPROVE THE CONFIDENCE IN THE ESTIMATED TIMELINES IT IS THEREFORE IMPERATIVE TO (I) RECONCILE CONTRASTING TIMELINES FROM MOLECULAR DATA WITH EACH OTHER AND ALSO WITH THE GEOLOGIC TIMELINE AND (II) DESIGN AN OBJECTIVE PROCEDURE TO IDENTIFY BIASES IN ESTIMATIONS EVEN IN CASES WHEN ALTERNATIVE INDEPENDENT EVIDENCE IS LACKING. OBJECTIVES: IN RESPONSE TO THESE NEEDS  HERE WE PROPOSE TO ESTABLISH AN OBJECTIVE AND COMPUTATIONALLY EASY PROCEDURE TO EVALUATE THE ACCURACY OF PUBLISHED AND FUTURE TIMETREES THAT WILL LEAD TO MORE ACCURATE AND CONCORDANT TIMELINES. OUR METHOD INVESTIGATES THE PARAMETERS ASSOCIATED WITH CALIBRATION POINTS AND EVOLUTIONARY RATE VARIATION AMONG LINEAGES  PARAMETERS THAT ARE KNOWN TO AFFECT THE ACCURACY OF RELAXED MOLECULAR CLOCKS. WE PROPOSE TO USE A RELATIVE FRAMEWORK ESTABLISHED FROM PRIOR-FREE MODELS (FOURTH GENERATION MOLECULAR CLOCKS) TO DETECT BIASES IN THESE PARAMETERS  WHICH CAN THEN BE REMOVED TO INCREASE ACCURACY OF INDIVIDUAL ESTIMATES. WE SHOW PRELIMINARY DATA FROM THE APPLICATION OF THE PROPOSED APPROACH IN SIMULATED SCENARIOS AND AN EMPIRICAL DATASET RELATED TO A HIGHLY CONTROVERSIAL EVOLUTIONARY EVENT  THE TIMELINE OF THE ORIGIN AND DIVERSIFICATION OF ANIMALS. THE RESULTS SUPPORT THE VALIDITY OF THE PROPOSED APPROACH THAT WE PLAN TO APPLY TO HUNDREDS OF PUBLISHED TIMETREES WITH KNOWN DISAGREEMENTS  IN AN EFFORT TO PRODUCE AN ACCURATE TIMELINE OF THE EVOLUTION OF LIFE. THE ESTABLISHED PROCEDURE WILL BE PARTICULARLY USEFUL IN INVESTIGATIONS OF EARLY MICROBIAL LIFE FOR WHICH MOLECULAR DATA IS VIRTUALLY THE ONLY RECORD OF THEIR EVOLUTIONARY HISTORY. METHODS: BASED ON THE OVERALL GOAL OF THIS PROPOSAL  WE HAVE IDENTIFIED TWO AIMS. IN AIM #1 WE WILL FOCUS ON THE EVALUATION OF CALIBRATION BOUNDARIES AND THEIR EFFECTS ON DIVERGENCE TIMES. THIS IS AN APPLIED AIM THAT WILL FIRST EVALUATE TIMETREES FROM THE LITERATURE TO IDENTIFY THE MOST COMMON WEAKNESSES AND RE-ESTIMATE NEW TIMETREES WITH IMPROVED PARAMETERS AND TAXONOMIC SAMPLING. THE OUTCOMES OF THIS AIM WILL BE THE FIRST LARGE-SCALE ASSESSMENT OF PUBLISHED TIMETREES AND THE ESTIMATION OF NEW  MORE ACCURATE  DIVERGENCE TIMES FOR A WIDE RANGE OF TAXONOMIC GROUPS FOCUSING ON EARLY MICROBIAL SPECIES. AIM #2 WILL PROVIDE THEORETICAL AND COMPUTATIONAL SUPPORT FOR THE APPLIED ANALYSIS OF THE PREVIOUS AIM BY INVESTIGATING DISTRIBUTIONS OF RATE VARIATION AMONG LINEAGES FOR DIFFERENT SIMULATED DATASETS. THESE DISTRIBUTIONS WILL SERVE AS REFERENCE TO DETERMINE PATTERNS OF RATE VARIATION IN EMPIRICAL DATA AND WILL PROVIDE INFORMATION TO OPTIMIZE OUR METHODOLOGY. THE NEW TESTING PROCEDURE DEVELOPED IN AIMS #1 AND #2 WILL THEN BE IMPLEMENTED IN A NEW SOFTWARE THAT WILL ALLOW EXPERTS AND NON-EXPERTS TO EVALUATE THE DEPENDENCY OF THEIR ESTIMATED DIVERGENCE TIMES ON THE CHOSEN PARAMETERS. SIGNIFICANCE: WE EXPECT THIS PROJECT TO BE HIGHLY SIGNIFICANT BECAUSE  BY IMPROVING MOLECULAR DATING METHODS  IT WILL PROVIDE THE MEANS TO ESTIMATE A TIMELINE OF THE EVOLUTION OF LIFE THAT WILL BRING INTO CLOSER AGREEMENT BIOLOGICAL  GEOLOGICAL  AND PALEONTOLOGICAL VIEWS OF THE CONDITIONS ON EARLY EARTH. RECONSTRUCTING A CHRONOLOGY OF LIFE ON EARTH HAS BEEN A LONGSTANDING GOAL IN ASTROBIOLOGY AS IT EMPOWERS RESEARCHERS TO DRAW INFERENCES ON THE CO-EVOLUTION OF LIFE AND HABITABLE CONDITIONS OF A PLANET.","funder_award_id":"NNX16AJ30G","funder_id":"https://openalex.org/F4320306101","funder_display_name":"National Aeronautics and Space Administration"},{"id":"https://openalex.org/G361630040","display_name":null,"funder_award_id":"DB105","funder_id":"https://openalex.org/F4320326286","funder_display_name":"Tokyo Metropolitan University"},{"id":"https://openalex.org/G6883517829","display_name":null,"funder_award_id":"R01 LM012487","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6997571547","display_name":null,"funder_award_id":"R01 GM126567","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G881473871","display_name":null,"funder_award_id":"R01GM126567-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8904003141","display_name":null,"funder_award_id":"T32 GM008720","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320308109","display_name":"Pennsylvania Department of Health","ror":"https://ror.org/00ra1fg11"},{"id":"https://openalex.org/F4320326286","display_name":"Tokyo Metropolitan University","ror":"https://ror.org/00ws30h19"},{"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"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2999929805.pdf","grobid_xml":"https://content.openalex.org/works/W2999929805.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1923320973","https://openalex.org/W1965142145","https://openalex.org/W1981560968","https://openalex.org/W1988757126","https://openalex.org/W1988764860","https://openalex.org/W1992566665","https://openalex.org/W1993210385","https://openalex.org/W2001259823","https://openalex.org/W2009111710","https://openalex.org/W2009596137","https://openalex.org/W2018417559","https://openalex.org/W2023013281","https://openalex.org/W2045517599","https://openalex.org/W2056353776","https://openalex.org/W2081539383","https://openalex.org/W2094939159","https://openalex.org/W2108364055","https://openalex.org/W2109439815","https://openalex.org/W2110335151","https://openalex.org/W2110835349","https://openalex.org/W2111211467","https://openalex.org/W2114058417","https://openalex.org/W2114419043","https://openalex.org/W2116474217","https://openalex.org/W2117681388","https://openalex.org/W2118048521","https://openalex.org/W2125359798","https://openalex.org/W2144975624","https://openalex.org/W2147861350","https://openalex.org/W2150672104","https://openalex.org/W2154331465","https://openalex.org/W2159368494","https://openalex.org/W2171142493","https://openalex.org/W2274601509","https://openalex.org/W2322358787","https://openalex.org/W2463019824","https://openalex.org/W2542611942","https://openalex.org/W2554017006","https://openalex.org/W2752084418","https://openalex.org/W2797734999","https://openalex.org/W2799524357","https://openalex.org/W2915370094","https://openalex.org/W2949972517","https://openalex.org/W2951878836","https://openalex.org/W2953127619","https://openalex.org/W2981560014","https://openalex.org/W3187962553","https://openalex.org/W6743818678"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2343819364","https://openalex.org/W2133205540","https://openalex.org/W2164129707","https://openalex.org/W4292122269","https://openalex.org/W2949366006"],"abstract_inverted_index":{"Pathogen":[0],"timetrees":[1,28,68],"are":[2,29],"phylogenies":[3],"scaled":[4],"to":[5,65,135,149,186],"time.":[6],"They":[7],"reveal":[8],"the":[9,17,22,48,76,97,120,127,153,173,188,211],"temporal":[10],"history":[11,24],"of":[12,25,35,50,96,111,115,122,130,140,214],"a":[13,57,71,181,202],"pathogen":[14,67],"spread":[15],"through":[16],"populations":[18],"as":[19],"captured":[20],"in":[21,82,152,175,192,207,210],"evolutionary":[23],"strains.":[26],"These":[27],"inferred":[30],"by":[31,100],"using":[32],"molecular":[33],"sequences":[34,46],"pathogenic":[36],"strains":[37],"sampled":[38,45],"at":[39],"different":[40],"times.":[41,53],"That":[42],"is,":[43],"temporally":[44],"enable":[47],"inference":[49],"sequence":[51],"divergence":[52],"Here,":[54],"we":[55,118,167,179],"present":[56],"new":[58],"approach":[59,78],"(RelTime":[60],"with":[61,158],"Dated":[62],"Tips":[63],"[RTDT])":[64],"estimating":[66],"based":[69],"on":[70],"relative":[72],"rate":[73],"framework":[74],"underlying":[75],"RelTime":[77],"that":[79,146,169],"is":[80,197],"algebraic":[81],"nature":[83],"and":[84,103,126,160,165,206],"distinct":[85],"from":[86,221],"all":[87],"other":[88],"current":[89],"methods.":[90],"RTDT":[91,123,143,196],"does":[92],"not":[93],"require":[94],"many":[95],"priors":[98],"demanded":[99],"Bayesian":[101,159],"approaches,":[102],"it":[104],"has":[105],"light":[106],"computing":[107],"requirements.":[108],"In":[109,138,155],"analyses":[110,139],"an":[112],"extensive":[113],"collection":[114],"computer-simulated":[116],"datasets,":[117,142],"found":[119,168],"accuracy":[121],"time":[124],"estimates":[125],"coverage":[128],"probabilities":[129],"their":[131],"confidence":[132],"intervals":[133],"(CIs)":[134],"be":[136],"excellent.":[137],"empirical":[141,193],"produced":[144],"dates":[145],"were":[147],"similar":[148],"those":[150],"reported":[151],"literature.":[154],"comparative":[156],"benchmarking":[157],"non-Bayesian":[161],"methods":[162],"(LSD,":[163],"TreeTime,":[164],"treedater),":[166],"no":[170],"method":[171,191],"performed":[172],"best":[174],"every":[176],"scenario.":[177],"So,":[178],"provide":[180],"brief":[182],"guideline":[183],"for":[184,199],"users":[185],"select":[187],"most":[189],"appropriate":[190],"data":[194],"analysis.":[195],"implemented":[198],"use":[200],"via":[201],"graphical":[203],"user":[204],"interface":[205],"high-throughput":[208],"settings":[209],"newest":[212],"release":[213],"cross-platform":[215],"MEGA":[216],"X":[217],"software,":[218],"freely":[219],"available":[220],"http://www.megasoftware.net.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
