{"id":"https://openalex.org/W2103116723","doi":"https://doi.org/10.1093/bioinformatics/bts580","title":"A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection","display_name":"A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection","publication_year":2012,"publication_date":"2012-10-12","ids":{"openalex":"https://openalex.org/W2103116723","doi":"https://doi.org/10.1093/bioinformatics/bts580","mag":"2103116723","pmid":"https://pubmed.ncbi.nlm.nih.gov/23064000"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts580","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts580","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3579240","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039280845","display_name":"Philippe Lemey","orcid":"https://orcid.org/0000-0003-2826-5353"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE","US"],"is_corresponding":true,"raw_author_name":"Philippe Lemey","raw_affiliation_strings":["1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I99464096","https://openalex.org/I161318765","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089671301","display_name":"Vladimir N. Minin","orcid":"https://orcid.org/0000-0002-1917-9288"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE","US"],"is_corresponding":false,"raw_author_name":"Vladimir N. Minin","raw_affiliation_strings":["1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I99464096","https://openalex.org/I161318765","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075073766","display_name":"Filip Bielejec","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE","US"],"is_corresponding":false,"raw_author_name":"Filip Bielejec","raw_affiliation_strings":["1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I99464096","https://openalex.org/I161318765","https://openalex.org/I201448701"]}]},{"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/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["BE","US"],"is_corresponding":false,"raw_author_name":"Sergei L. Kosakovsky Pond","raw_affiliation_strings":["1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I99464096","https://openalex.org/I161318765","https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039905606","display_name":"Marc A. Suchard","orcid":"https://orcid.org/0000-0001-9818-479X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["BE","US"],"is_corresponding":false,"raw_author_name":"Marc A. Suchard","raw_affiliation_strings":["1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium, 2Department of Statistics, University of Washington, Seattle, WA 98195, 3Department of Medicine, University of California, San Diego, CA 92103, 4Department of Biomathematics, 5Department of Human Genetics, David Geffen School of Medicine and 6Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I99464096","https://openalex.org/I161318765","https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5039280845"],"corresponding_institution_ids":["https://openalex.org/I161318765","https://openalex.org/I201448701","https://openalex.org/I36258959","https://openalex.org/I99464096"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6892,"has_fulltext":false,"cited_by_count":97,"citation_normalized_percentile":{"value":0.90604858,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"28","issue":"24","first_page":"3248","last_page":"3256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9955000281333923,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9937999844551086,"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/bayes-theorem","display_name":"Bayes' theorem","score":0.7913156747817993},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5714319348335266},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5572759509086609},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5357481837272644},{"id":"https://openalex.org/keywords/bayes-factor","display_name":"Bayes factor","score":0.4506256878376007},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.44574981927871704},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.41729745268821716},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3764675259590149},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35989564657211304},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33370041847229004}],"concepts":[{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.7913156747817993},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5714319348335266},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5572759509086609},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5357481837272644},{"id":"https://openalex.org/C142291917","wikidata":"https://www.wikidata.org/wiki/Q4165283","display_name":"Bayes factor","level":4,"score":0.4506256878376007},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.44574981927871704},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.41729745268821716},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3764675259590149},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35989564657211304},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33370041847229004}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"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":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bts580","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts580","pdf_url":null,"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:23064000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23064000","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},{"id":"pmh:oai:europepmc.org:2828029","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3579240","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:lirias2repo.kuleuven.be:123456789/372678","is_oa":false,"landing_page_url":"https://lirias.kuleuven.be/bitstream/123456789/372678/1/Lemey-bioinformatics_2012_bts580.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol. 28 (24), (3248-3256)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:3579240","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3579240","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:3579240","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3579240","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"score":0.6200000047683716,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1590636096","https://openalex.org/W1829137581","https://openalex.org/W1881807356","https://openalex.org/W1920973730","https://openalex.org/W1964475452","https://openalex.org/W1968043909","https://openalex.org/W1974185791","https://openalex.org/W1975963750","https://openalex.org/W1977862457","https://openalex.org/W1980537979","https://openalex.org/W1993210385","https://openalex.org/W1994132342","https://openalex.org/W2001363675","https://openalex.org/W2006556166","https://openalex.org/W2009596137","https://openalex.org/W2011279174","https://openalex.org/W2020657010","https://openalex.org/W2028331262","https://openalex.org/W2029353325","https://openalex.org/W2045641296","https://openalex.org/W2046134251","https://openalex.org/W2056384440","https://openalex.org/W2061140759","https://openalex.org/W2070112803","https://openalex.org/W2082414801","https://openalex.org/W2084513007","https://openalex.org/W2088267428","https://openalex.org/W2092075920","https://openalex.org/W2095524756","https://openalex.org/W2105585336","https://openalex.org/W2107377540","https://openalex.org/W2119632499","https://openalex.org/W2127320825","https://openalex.org/W2130362098","https://openalex.org/W2133585817","https://openalex.org/W2134912004","https://openalex.org/W2135124387","https://openalex.org/W2136485386","https://openalex.org/W2136847298","https://openalex.org/W2137698258","https://openalex.org/W2138178197","https://openalex.org/W2139166200","https://openalex.org/W2142773663","https://openalex.org/W2144368480","https://openalex.org/W2145818984","https://openalex.org/W2152938409","https://openalex.org/W2164555431","https://openalex.org/W2168934042","https://openalex.org/W2169981472","https://openalex.org/W2170038561","https://openalex.org/W2170565120","https://openalex.org/W2796425399","https://openalex.org/W2912635573","https://openalex.org/W3100338287","https://openalex.org/W3101924122","https://openalex.org/W6622657718","https://openalex.org/W6635437809","https://openalex.org/W6638643671","https://openalex.org/W6639376086","https://openalex.org/W6640287769","https://openalex.org/W6684547848"],"related_works":["https://openalex.org/W3034774545","https://openalex.org/W4390542592","https://openalex.org/W2083677154","https://openalex.org/W4287269571","https://openalex.org/W2188650561","https://openalex.org/W3137735170","https://openalex.org/W2825391699","https://openalex.org/W3104584085","https://openalex.org/W2089519699","https://openalex.org/W4237728685"],"abstract_inverted_index":{"We":[0,82],"propose":[1],"a":[2,23,44],"hybrid":[3,40],"solution":[4],"that":[5,66],"borrows":[6],"the":[7,49,84],"computational":[8],"strength":[9],"of":[10,30,52,86],"counting":[11],"methods,":[12],"but":[13],"augments":[14],"these":[15],"methods":[16],"with":[17,71],"empirical":[18],"Bayes":[19],"modeling":[20],"to":[21,57],"produce":[22],"relatively":[24],"fast":[25],"and":[26,54,95],"reliable":[27],"method":[28,68,88],"capable":[29],"estimating":[31],"site-specific":[32,61],"dN/dS":[33,62],"values":[34],"in":[35,43,76],"large":[36],"datasets.":[37],"Importantly,":[38],"our":[39,87],"approach,":[41],"set":[42],"Bayesian":[45],"framework,":[46],"integrates":[47],"over":[48],"posterior":[50],"distribution":[51],"phylogenies":[53],"ancestral":[55],"reconstructions":[56],"quantify":[58],"uncertainty":[59],"about":[60],"estimates.":[63],"Simulations":[64],"demonstrate":[65],"this":[67],"competes":[69],"well":[70],"more-principled":[72],"statistical":[73],"procedures":[74],"and,":[75],"some":[77],"cases,":[78],"even":[79],"outperforms":[80],"them.":[81],"illustrate":[83],"utility":[85],"using":[89],"human":[90],"immunodeficiency":[91],"virus,":[92],"feline":[93],"panleukopenia":[94],"canine":[96],"parvovirus":[97],"evolution":[98],"examples.":[99]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
