{"id":"https://openalex.org/W2047755723","doi":"https://doi.org/10.1371/journal.pcbi.1000483","title":"Evolutionary Triplet Models of Structured RNA","display_name":"Evolutionary Triplet Models of Structured RNA","publication_year":2009,"publication_date":"2009-08-28","ids":{"openalex":"https://openalex.org/W2047755723","doi":"https://doi.org/10.1371/journal.pcbi.1000483","mag":"2047755723","pmid":"https://pubmed.ncbi.nlm.nih.gov/19714212"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000483","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000483","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000483&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.1000483&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032741707","display_name":"Robert K. Bradley","orcid":"https://orcid.org/0000-0002-8046-1063"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert K. Bradley","raw_affiliation_strings":["Biophysics Graduate Group, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biophysics Graduate Group, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ian Holmes","raw_affiliation_strings":["Biophysics Graduate Group, University of California, Berkeley, California, United States of America","Department of Bioengineering, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biophysics Graduate Group, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054625887"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.7559,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.69622668,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":"8","first_page":"e1000483","last_page":"e1000483"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6096004247665405},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5668579339981079},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5402533411979675},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4969644844532013},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4719592332839966},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.467503160238266},{"id":"https://openalex.org/keywords/posterior-probability","display_name":"Posterior probability","score":0.4475807845592499},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.43521106243133545},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.42664793133735657},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41652244329452515},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.39680591225624084},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.34099140763282776},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29809093475341797},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18500664830207825},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16646477580070496}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6096004247665405},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5668579339981079},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5402533411979675},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4969644844532013},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4719592332839966},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.467503160238266},{"id":"https://openalex.org/C57830394","wikidata":"https://www.wikidata.org/wiki/Q278079","display_name":"Posterior probability","level":3,"score":0.4475807845592499},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.43521106243133545},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.42664793133735657},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41652244329452515},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.39680591225624084},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.34099140763282776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29809093475341797},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18500664830207825},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16646477580070496},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1000483","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000483","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000483&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:19714212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19714212","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:CiteSeerX.psu:10.1.1.355.7687","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.355.7687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/05/ce/PLoS_Comput_Biol_2009_Aug_28_5(8)_e1000483.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000483","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000483","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:58aedd44c48648c68cd526b8a67b26b8","is_oa":true,"landing_page_url":"https://doaj.org/article/58aedd44c48648c68cd526b8a67b26b8","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 5, Iss 8, p e1000483 (2009)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/146633","is_oa":true,"landing_page_url":"https://figshare.com/articles/Evolutionary_Triplet_Models_of_Structured_RNA/146633","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2725318","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2725318","pdf_url":null,"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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000483","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000483","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000483&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":[{"id":"https://metadata.un.org/sdg/4","score":0.7200000286102295,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4670916211","display_name":null,"funder_award_id":"R01-GM076705","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5946076000","display_name":null,"funder_award_id":"GM076705","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2047755723.pdf","grobid_xml":"https://content.openalex.org/works/W2047755723.grobid-xml"},"referenced_works_count":115,"referenced_works":["https://openalex.org/W10219220","https://openalex.org/W638482479","https://openalex.org/W1522740115","https://openalex.org/W1542426682","https://openalex.org/W1593799327","https://openalex.org/W1822105579","https://openalex.org/W1861164398","https://openalex.org/W1866859902","https://openalex.org/W1909512798","https://openalex.org/W1950410402","https://openalex.org/W1963587568","https://openalex.org/W1966327236","https://openalex.org/W1967538502","https://openalex.org/W1968256798","https://openalex.org/W1968700991","https://openalex.org/W1979257831","https://openalex.org/W1986736188","https://openalex.org/W1987502048","https://openalex.org/W1990853496","https://openalex.org/W1991311566","https://openalex.org/W1995143868","https://openalex.org/W1998447705","https://openalex.org/W1998695976","https://openalex.org/W1999707793","https://openalex.org/W2005743153","https://openalex.org/W2009570821","https://openalex.org/W2011368877","https://openalex.org/W2019185429","https://openalex.org/W2023206235","https://openalex.org/W2025595745","https://openalex.org/W2026551295","https://openalex.org/W2031893353","https://openalex.org/W2034179641","https://openalex.org/W2036953061","https://openalex.org/W2037592262","https://openalex.org/W2042217359","https://openalex.org/W2045864964","https://openalex.org/W2046932483","https://openalex.org/W2048541401","https://openalex.org/W2058044724","https://openalex.org/W2060555982","https://openalex.org/W2061149284","https://openalex.org/W2062018285","https://openalex.org/W2062275397","https://openalex.org/W2065400176","https://openalex.org/W2066502527","https://openalex.org/W2067579500","https://openalex.org/W2069182996","https://openalex.org/W2069787595","https://openalex.org/W2071461674","https://openalex.org/W2073234837","https://openalex.org/W2073265639","https://openalex.org/W2076505328","https://openalex.org/W2085950579","https://openalex.org/W2086722931","https://openalex.org/W2091777602","https://openalex.org/W2092979861","https://openalex.org/W2095145214","https://openalex.org/W2100783529","https://openalex.org/W2102424972","https://openalex.org/W2107689725","https://openalex.org/W2110094317","https://openalex.org/W2114001343","https://openalex.org/W2114122189","https://openalex.org/W2114759809","https://openalex.org/W2116584794","https://openalex.org/W2118829610","https://openalex.org/W2122035121","https://openalex.org/W2123241418","https://openalex.org/W2128482297","https://openalex.org/W2130640131","https://openalex.org/W2132430052","https://openalex.org/W2133279153","https://openalex.org/W2133326994","https://openalex.org/W2137640371","https://openalex.org/W2137923318","https://openalex.org/W2138664009","https://openalex.org/W2141411672","https://openalex.org/W2142113273","https://openalex.org/W2143253866","https://openalex.org/W2143676827","https://openalex.org/W2145396697","https://openalex.org/W2145780430","https://openalex.org/W2146974293","https://openalex.org/W2147847662","https://openalex.org/W2151120398","https://openalex.org/W2154649313","https://openalex.org/W2156094048","https://openalex.org/W2157451851","https://openalex.org/W2158381555","https://openalex.org/W2158826174","https://openalex.org/W2163798335","https://openalex.org/W2164618384","https://openalex.org/W2167055123","https://openalex.org/W2167673850","https://openalex.org/W2170748882","https://openalex.org/W2174270339","https://openalex.org/W2220739918","https://openalex.org/W2259225862","https://openalex.org/W2322480514","https://openalex.org/W2492276076","https://openalex.org/W2610493105","https://openalex.org/W2744744159","https://openalex.org/W4212892542","https://openalex.org/W4231060015","https://openalex.org/W4233815609","https://openalex.org/W4234879553","https://openalex.org/W4234887284","https://openalex.org/W4240153261","https://openalex.org/W4245668478","https://openalex.org/W4320287894","https://openalex.org/W6635485671","https://openalex.org/W6639182465","https://openalex.org/W6688590577","https://openalex.org/W7066511990"],"related_works":["https://openalex.org/W2194132979","https://openalex.org/W2018356890","https://openalex.org/W1482324242","https://openalex.org/W2051969447","https://openalex.org/W2129361631","https://openalex.org/W2079145549","https://openalex.org/W4389053053","https://openalex.org/W2903170547","https://openalex.org/W1608334680","https://openalex.org/W2119732072"],"abstract_inverted_index":{"The":[0,77],"reconstruction":[1],"and":[2,30,100,126,166,170,205,239],"synthesis":[3],"of":[4,27,44,50,64,74,79,112,116,128,132,135,147,161,172,185,201,213,221,235,242,263,280],"ancestral":[5,130,175],"RNAs":[6],"is":[7,83],"a":[8,20,35,55,84,133,144,167,183,207],"feasible":[9],"goal":[10],"for":[11,24,39,103,143,156,194,211,229,283],"paleogenetics.":[12],"This":[13,58],"will":[14],"require":[15],"new":[16],"bioinformatics":[17],"methods,":[18],"including":[19,190,290],"robust":[21,96],"statistical":[22],"framework":[23],"reconstructing":[25],"histories":[26],"substitutions,":[28],"indels":[29],"structural":[31,46,110,117,150],"changes.":[32],"We":[33,89,138,177],"describe":[34,90],"\"transducer":[36],"composition\"":[37],"algorithm":[38,59,73,82,181,210],"extending":[40],"pairwise":[41,148],"probabilistic":[42,274],"models":[43,49,63,196],"RNA":[45,149,164],"evolution":[47],"to":[48,97,123,182,293],"multiple":[51],"sequences":[52],"related":[53],"by":[54],"phylogenetic":[56,256],"tree.":[57],"draws":[60],"on":[61,288],"formal":[62],"computational":[65],"linguistics":[66],"as":[67,69],"well":[68],"the":[70,80,129,140,154,173,202,214,225,243,261,278,295],"1985":[71],"protosequence":[72],"David":[75],"Sankoff.":[76],"output":[78],"composition":[81,282],"multiple-sequence":[85],"stochastic":[86],"context-free":[87],"grammar.":[88,106],"dynamic":[91],"programming":[92],"algorithms,":[93],"which":[94],"are":[95],"null":[98],"cycles":[99],"empty":[101],"bifurcations,":[102],"parsing":[104],"this":[105,179,259],"Example":[107],"applications":[108],"include":[109],"alignment":[111,160,192,209,231],"non-coding":[113],"RNAs,":[114],"propagation":[115],"information":[118],"from":[119],"an":[120],"experimentally-characterized":[121],"sequence":[122],"its":[124],"homologs,":[125],"inference":[127,171,287],"structure":[131,223],"set":[134],"diverged":[136],"RNAs.":[137],"implemented":[139],"above":[141],"algorithms":[142,155,193],"simple":[145],"model":[146,204,244],"evolution;":[151],"in":[152],"particular,":[153],"maximum":[157],"likelihood":[158],"(ML)":[159],"three":[162],"known":[163,168],"structures":[165],"phylogeny":[169],"common":[174],"structure.":[176],"compared":[178],"ML":[180,191,284],"variety":[184],"related,":[186],"but":[187],"simpler,":[188],"techniques,":[189],"simpler":[195,215],"that":[197],"omitted":[198],"various":[199],"aspects":[200],"full":[203],"also":[206],"posterior-decoding":[208,236],"one":[212],"models.":[216],"In":[217],"our":[218],"tests,":[219],"incorporation":[220],"basepair":[222],"was":[224,237],"most":[226],"important":[227],"factor":[228],"accurate":[230],"inference;":[232],"appropriate":[233],"use":[234,262,279],"next;":[238],"fine":[240],"details":[241],"were":[245],"least":[246],"important.":[247],"Posterior-decoding":[248],"heuristics":[249,265],"can":[250],"be":[251],"substantially":[252],"faster":[253],"than":[254],"exact":[255,273],"inference,":[257,275],"so":[258],"motivates":[260],"sum-over-pairs":[264],"where":[266],"possible":[267,291],"(and":[268],"approximate":[269],"sum-over-pairs).":[270],"For":[271],"more":[272],"we":[276],"discuss":[277],"transducer":[281],"(or":[285],"MCMC)":[286],"phylogenies,":[289],"ways":[292],"make":[294],"core":[296],"operations":[297],"tractable.":[298]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}