{"id":"https://openalex.org/W4400128023","doi":"https://doi.org/10.1093/bioinformatics/btae229","title":"Median and small parsimony problems on RNA trees","display_name":"Median and small parsimony problems on RNA trees","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400128023","doi":"https://doi.org/10.1093/bioinformatics/btae229","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940169"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i237/58355040/btae229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i237/58355040/btae229.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014123931","display_name":"Bertrand Marchand","orcid":"https://orcid.org/0000-0001-8060-6640"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Bertrand Marchand","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028363985","display_name":"Yoann Anselmetti","orcid":"https://orcid.org/0000-0002-6689-1163"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yoann Anselmetti","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016796629","display_name":"Manuel Lafond","orcid":"https://orcid.org/0000-0002-5305-7372"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Manuel Lafond","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004463624","display_name":"A\u00efda Ouangraoua","orcid":"https://orcid.org/0000-0002-2040-4948"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"A\u00efda Ouangraoua","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-2040-4948","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4082,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61731101,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i237","last_page":"i246"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.7828999757766724,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.7828999757766724,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13580000400543213,"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/T12610","display_name":"RNA regulation and disease","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.845635712146759},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6441000699996948},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5834057331085205},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5761188268661499},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5678853392601013},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.532285749912262},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.48938554525375366},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.48354601860046387},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4776807427406311},{"id":"https://openalex.org/keywords/rna-editing","display_name":"RNA editing","score":0.46919485926628113},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.4327438175678253},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4245089292526245},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31689774990081787}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.845635712146759},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6441000699996948},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5834057331085205},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5761188268661499},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5678853392601013},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.532285749912262},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.48938554525375366},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.48354601860046387},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4776807427406311},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.46919485926628113},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4327438175678253},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4245089292526245},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31689774990081787},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":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":"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},{"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},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i237/58355040/btae229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38940169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940169","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:pubmedcentral.nih.gov:11256950","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11256950","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11256950/pdf/btae229.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i237/58355040/btae229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1399340445","display_name":null,"funder_award_id":"950-230577","funder_id":"https://openalex.org/F4320320994","funder_display_name":"Canada Research Chairs"},{"id":"https://openalex.org/G332225712","display_name":null,"funder_award_id":"RGPIN-2019-05817","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3654624825","display_name":null,"funder_award_id":"RGPIN-2023-05474","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4971694158","display_name":null,"funder_award_id":"18EURE0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G832689143","display_name":null,"funder_award_id":"RGPIN-2019","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320319860","display_name":"Institut Polytechnique de Paris","ror":null},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320994","display_name":"Canada Research Chairs","ror":"https://ror.org/0517h6h17"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400128023.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W129436484","https://openalex.org/W207390916","https://openalex.org/W1608071358","https://openalex.org/W1834982196","https://openalex.org/W1967762061","https://openalex.org/W1968248848","https://openalex.org/W1970977492","https://openalex.org/W1972390207","https://openalex.org/W1976373002","https://openalex.org/W1992599313","https://openalex.org/W1994042976","https://openalex.org/W1995827784","https://openalex.org/W2000034617","https://openalex.org/W2002124496","https://openalex.org/W2004130948","https://openalex.org/W2008288996","https://openalex.org/W2018414460","https://openalex.org/W2030794106","https://openalex.org/W2047755723","https://openalex.org/W2060425093","https://openalex.org/W2065973977","https://openalex.org/W2086561953","https://openalex.org/W2088528526","https://openalex.org/W2092979861","https://openalex.org/W2113317197","https://openalex.org/W2126577900","https://openalex.org/W2128873679","https://openalex.org/W2134861301","https://openalex.org/W2153140501","https://openalex.org/W2154649313","https://openalex.org/W2159117141","https://openalex.org/W2554271273","https://openalex.org/W3100348855","https://openalex.org/W4226045769","https://openalex.org/W4233371305","https://openalex.org/W4245682324","https://openalex.org/W4254717640","https://openalex.org/W4388212639","https://openalex.org/W4401058734","https://openalex.org/W6672261310"],"related_works":["https://openalex.org/W4318218930","https://openalex.org/W2057388609","https://openalex.org/W2159621058","https://openalex.org/W2412575231","https://openalex.org/W2063831899","https://openalex.org/W2105070391","https://openalex.org/W4386776060","https://openalex.org/W2097168352","https://openalex.org/W4388307933","https://openalex.org/W1557536303"],"abstract_inverted_index":{"MOTIVATION:":[0],"Noncoding":[1],"RNAs":[2,180],"(ncRNAs)":[3],"express":[4],"their":[5,263],"functions":[6],"by":[7],"adopting":[8],"molecular":[9,30],"structures.":[10],"Specifically,":[11],"RNA":[12,35,49,54,67,70,90,130,156],"secondary":[13,38,108],"structures":[14,39,68,109],"serve":[15],"as":[16,112],"a":[17,26,125,133,195],"relatively":[18],"stable":[19],"intermediate":[20],"step":[21],"before":[22],"tertiary":[23],"structures,":[24],"offering":[25],"reliable":[27],"signature":[28],"of":[29,66,148,154,164,166,179,205,218,248],"function.":[31],"Consequently,":[32],"within":[33,52,69],"an":[34,53],"functional":[36,80],"family,":[37],"are":[40,110,209,253],"generally":[41],"more":[42,187,196],"evolutionarily":[43],"conserved":[44],"than":[45,181],"sequences.":[46],"Conversely,":[47],"homologous":[48],"families":[50,71,257],"grouped":[51],"clan":[55],"share":[56],"ancestors":[57],"but":[58],"typically":[59],"exhibit":[60],"structural":[61,177],"differences.":[62],"Inferring":[63],"the":[64,88,96,100,117,137,142,158,162,182,203,215,219,223,228,249,259],"evolution":[65],"and":[72,84,99,132,222,232,237],"clans":[73],"is":[74,171,186],"crucial":[75],"for":[76,104,244],"gaining":[77],"insights":[78],"into":[79],"adaptations":[81],"over":[82],"time":[83],"providing":[85],"clues":[86],"about":[87],"Ancient":[89],"World":[91],"Hypothesis.":[92],"RESULTS:":[93],"We":[94,115,192,213],"introduce":[95],"median":[97,220],"problem":[98,103,221,226],"small":[101,224],"parsimony":[102,225,242],"ncRNA":[105,256],"families,":[106],"where":[107],"represented":[111],"leaf-labeled":[113],"trees.":[114],"utilize":[116],"Robinson-Foulds":[118],"(RF)":[119],"tree":[120,144,198],"distance,":[121,184],"which":[122,185],"corresponds":[123],"to":[124,255],"specific":[126],"edit":[127,199],"distance":[128,145,160,200,230],"between":[129],"trees,":[131,157],"new":[134],"metric":[135],"called":[136],"Internal-Leafset":[138],"(IL)":[139],"distance.":[140],"While":[141],"RF":[143,183],"compares":[146,161],"sets":[147],"leaves":[149],"descending":[150],"from":[151,258],"internal":[152,167],"nodes":[153],"two":[155],"IL":[159],"collection":[163],"leaf-children":[165],"nodes.":[168],"The":[169],"latter":[170],"better":[172],"at":[173],"capturing":[174],"differences":[175],"in":[176],"elements":[178],"focused":[188],"on":[189],"base":[190,206],"pairs.":[191],"also":[193],"consider":[194],"general":[197],"that":[201,208],"allows":[202],"mapping":[204],"pairs":[207],"not":[210],"perfectly":[211],"aligned.":[212],"study":[214],"theoretical":[216],"complexity":[217],"under":[227],"three":[229],"metrics":[231],"various":[233],"biologically":[234],"relevant":[235],"constraints,":[236],"we":[238],"present":[239],"polynomial-time":[240],"maximum":[241],"algorithms":[243,252],"solving":[245],"some":[246],"versions":[247],"problems.":[250],"Our":[251],"applied":[254],"RFAM":[260],"database,":[261],"illustrating":[262],"practical":[264],"utility.":[265],"AVAILABILITY":[266],"AND":[267],"IMPLEMENTATION:":[268],"https://github.com/bmarchand/rna\\_small\\_parsimony.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
