{"id":"https://openalex.org/W1999955287","doi":"https://doi.org/10.1186/1471-2105-11-s6-s21","title":"A predictive model for secondary RNA structure using graph theory and a neural network","display_name":"A predictive model for secondary RNA structure using graph theory and a neural network","publication_year":2010,"publication_date":"2010-10-01","ids":{"openalex":"https://openalex.org/W1999955287","doi":"https://doi.org/10.1186/1471-2105-11-s6-s21","mag":"1999955287","pmid":"https://pubmed.ncbi.nlm.nih.gov/20946605"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s6-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s6-s21","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-S6-S21.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-S6-S21.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055612337","display_name":"Denise R. Koessler","orcid":null},"institutions":[{"id":"https://openalex.org/I119443389","display_name":"East Tennessee State University","ror":"https://ror.org/05rfqv493","country_code":"US","type":"education","lineage":["https://openalex.org/I119443389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Denise R Koessler","raw_affiliation_strings":["Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN 37614, USA","Department of Mathematics and Statistics, East Tennessee State University, Johnson City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, East Tennessee State University, Johnson City, USA","institution_ids":["https://openalex.org/I119443389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091878567","display_name":"Debra Knisley","orcid":"https://orcid.org/0000-0002-8826-8444"},"institutions":[{"id":"https://openalex.org/I119443389","display_name":"East Tennessee State University","ror":"https://ror.org/05rfqv493","country_code":"US","type":"education","lineage":["https://openalex.org/I119443389"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Debra J Knisley","raw_affiliation_strings":["Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","The Institute for Quantitative Biology, East Tennessee State University, Johnson City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"The Institute for Quantitative Biology, East Tennessee State University, Johnson City, USA","institution_ids":["https://openalex.org/I119443389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010477546","display_name":"Jeff Knisley","orcid":null},"institutions":[{"id":"https://openalex.org/I119443389","display_name":"East Tennessee State University","ror":"https://ror.org/05rfqv493","country_code":"US","type":"education","lineage":["https://openalex.org/I119443389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Knisley","raw_affiliation_strings":["Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","The Institute for Quantitative Biology, East Tennessee State University, Johnson City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"The Institute for Quantitative Biology, East Tennessee State University, Johnson City, USA","institution_ids":["https://openalex.org/I119443389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070458571","display_name":"Teresa W. Haynes","orcid":"https://orcid.org/0000-0002-0865-0871"},"institutions":[{"id":"https://openalex.org/I119443389","display_name":"East Tennessee State University","ror":"https://ror.org/05rfqv493","country_code":"US","type":"education","lineage":["https://openalex.org/I119443389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teresa Haynes","raw_affiliation_strings":["Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","East Tennessee State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"The Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, 37614, USA","institution_ids":["https://openalex.org/I119443389"]},{"raw_affiliation_string":"East Tennessee State University","institution_ids":["https://openalex.org/I119443389"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091878567"],"corresponding_institution_ids":["https://openalex.org/I119443389"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.6187,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.82112337,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"S6","first_page":"S21","last_page":"S21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.965499997138977,"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":0.965499997138977,"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/T11482","display_name":"RNA modifications and cancer","score":0.010400000028312206,"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/T11445","display_name":"Origins and Evolution of Life","score":0.006099999882280827,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.7428629398345947},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.7291839122772217},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.6846469044685364},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5876327753067017},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5658210515975952},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.47725436091423035},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4347221255302429},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43222394585609436},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.41946959495544434},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4186549186706543},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39336341619491577},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36298686265945435},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1586950421333313},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08762893080711365},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08306252956390381}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7428629398345947},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.7291839122772217},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.6846469044685364},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5876327753067017},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5658210515975952},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.47725436091423035},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4347221255302429},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43222394585609436},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.41946959495544434},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4186549186706543},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39336341619491577},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36298686265945435},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1586950421333313},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08762893080711365},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08306252956390381},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.0},{"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-11-s6-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s6-s21","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-S6-S21.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20946605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20946605","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3026369","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3026369","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:dc.etsu.edu:etd-3039","is_oa":false,"landing_page_url":"https://dc.etsu.edu/etd/1684","pdf_url":null,"source":{"id":"https://openalex.org/S4377196424","display_name":"Digital Commons - East Tennessee State University (East Tennessee State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I119443389","host_organization_name":"East Tennessee State University","host_organization_lineage":["https://openalex.org/I119443389"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Electronic Theses and Dissertations","raw_type":"text"},{"id":"pmh:oai:dc.etsu.edu:etsu-works-17909","is_oa":true,"landing_page_url":"https://dc.etsu.edu/etsu-works/16643","pdf_url":null,"source":{"id":"https://openalex.org/S4377196424","display_name":"Digital Commons - East Tennessee State University (East Tennessee State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I119443389","host_organization_name":"East Tennessee State University","host_organization_lineage":["https://openalex.org/I119443389"],"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":"ETSU Faculty Works","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:fc96a2bb161141ae91f763ea90b541c3","is_oa":false,"landing_page_url":"https://doaj.org/article/fc96a2bb161141ae91f763ea90b541c3","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss Suppl 6, p S21 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s6-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s6-s21","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-S6-S21.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.699999988079071,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G833762810","display_name":"Science First!","funder_award_id":"0742364","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337368","display_name":"Division of Graduate Education","ror":"https://ror.org/00whkrf32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1999955287.pdf","grobid_xml":"https://content.openalex.org/works/W1999955287.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W132152465","https://openalex.org/W1493071618","https://openalex.org/W1498954346","https://openalex.org/W1589712216","https://openalex.org/W1600463518","https://openalex.org/W1625699506","https://openalex.org/W1964400019","https://openalex.org/W1984987205","https://openalex.org/W1990529500","https://openalex.org/W2000483727","https://openalex.org/W2006927892","https://openalex.org/W2014989101","https://openalex.org/W2018414460","https://openalex.org/W2029426756","https://openalex.org/W2033872649","https://openalex.org/W2056151289","https://openalex.org/W2075167911","https://openalex.org/W2096327663","https://openalex.org/W2121289117","https://openalex.org/W2140302584","https://openalex.org/W2163557777","https://openalex.org/W2170181617","https://openalex.org/W2407701934","https://openalex.org/W2796976177"],"related_works":["https://openalex.org/W1975806245","https://openalex.org/W2558432341","https://openalex.org/W3047450301","https://openalex.org/W1472344963","https://openalex.org/W2345156963","https://openalex.org/W2159621058","https://openalex.org/W2581348958","https://openalex.org/W1998495298","https://openalex.org/W2412575231","https://openalex.org/W4385457841"],"abstract_inverted_index":{"BACKGROUND:":[0],"Determining":[1],"the":[2,8,25,29,70,138,150,157,195,200,203,225,229,264,278,318,338,347],"secondary":[3,26,56,65,75,81,212,226,243,267,281,321],"structure":[4,10,27,58,82,106,214,227],"of":[5,18,44,64,72,159,172,184,202,211,257,266,280,306,320,336,346],"RNA":[6,57,66,74,213,244,268,282,322],"from":[7,28,115],"primary":[9,30],"is":[11,33,37,120,269,272,311],"a":[12,52,60,79,84,123,133,142,160,169,181,209,239,252,258,304,309,334],"challenging":[13],"computational":[14],"problem.":[15],"A":[16],"number":[17,210],"algorithms":[19,216,324],"have":[20],"been":[21],"developed":[22],"to":[23,77,140,174,186,198,261,277,289],"predict":[24,199],"structure.":[31,67],"It":[32],"agreed":[34],"that":[35,102,109,308,317],"there":[36],"still":[38],"room":[39],"for":[40,55,132,242,251,295],"improvement":[41],"in":[42,105],"each":[43,116],"these":[45,127],"approaches.":[46],"In":[47,234,299],"this":[48,235],"work":[49],"we":[50,87,237],"build":[51],"predictive":[53,240],"model":[54,69],"using":[59,95,246],"graph-theoretic":[61,247],"tree":[62,98,117,143,161,310],"representation":[63],"We":[68,90,125,192],"bonding":[71,265],"two":[73],"structures":[76,245,343],"form":[78],"larger":[80],"with":[83,228],"graph":[85,259],"operation":[86,119,260],"call":[88],"merge.":[89],"consider":[91],"all":[92,96,296,345],"combinatorial":[93],"possibilities":[94],"possible":[97,329,348],"inputs,":[99],"both":[100],"those":[101,108,187],"are":[103,110,208,221],"RNA-like":[104,145,179,291,294,312],"and":[107,136,180,271],"not.":[111],"The":[112,154,165,255],"resulting":[113],"data":[114,152],"merge":[118,151],"represented":[121],"by":[122],"vector.":[124,153],"use":[126,256],"vectors":[128],"as":[129,144,178,189,249],"input":[130,250],"values":[131,248],"neural":[134,196,253],"network":[135,139,155,166,197],"train":[137],"recognize":[141],"or":[146,292,313,340],"not,":[147],"based":[148,222],"on":[149,223],"estimates":[156],"probability":[158,171,183],"being":[162],"RNA-like.":[163,191,315],"RESULTS:":[164],"correctly":[167,286],"assigned":[168],"high":[170],"RNA-likeness":[173,185,201],"trees":[175,288],"previously":[176],"identified":[177],"low":[182],"classified":[188],"not":[190,293,314],"then":[193],"used":[194],"unclassified":[204],"trees.":[205],"CONCLUSIONS:":[206],"There":[207],"prediction":[215,279],"available":[217],"online.":[218],"These":[219],"programs":[220],"finding":[224],"lowest":[230],"total":[231],"free":[232],"energy.":[233],"work,":[236],"create":[238],"tool":[241],"network.":[254],"theoretically":[262],"describe":[263],"novel":[270],"an":[273],"entirely":[274],"different":[275],"approach":[276],"structures.":[283],"Our":[284],"method":[285,332],"predicted":[287],"be":[290],"known":[297],"cases.":[298],"addition,":[300],"our":[301,331],"results":[302],"convey":[303],"measure":[305],"likelihood":[307],"Given":[316],"majority":[319],"folding":[323],"return":[325],"more":[326],"than":[327],"one":[328],"outcome,":[330],"provides":[333],"means":[335],"determining":[337],"best":[339],"most":[341],"likely":[342],"among":[344],"outcomes.":[349]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}