{"id":"https://openalex.org/W2092777420","doi":"https://doi.org/10.1186/1471-2105-13-s5-s1","title":"Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds","display_name":"Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds","publication_year":2012,"publication_date":"2012-04-12","ids":{"openalex":"https://openalex.org/W2092777420","doi":"https://doi.org/10.1186/1471-2105-13-s5-s1","mag":"2092777420","pmid":"https://pubmed.ncbi.nlm.nih.gov/22537005"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s5-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s5-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S5-S1","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S5-S1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005662495","display_name":"Yingfeng Wang","orcid":"https://orcid.org/0000-0002-3715-5124"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yingfeng Wang","raw_affiliation_strings":["Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA. ywang802@uga.edu","Dept. of Computer Science, Univ. of Georgia, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA. ywang802@uga.edu","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Dept. of Computer Science, Univ. of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090753279","display_name":"Amir Manzour","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amir Manzour","raw_affiliation_strings":["Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","[Institute of Bioinformatics, University of Georgia, Athens, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"[Institute of Bioinformatics, University of Georgia, Athens, USA]","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068734237","display_name":"Pooya Shareghi","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pooya Shareghi","raw_affiliation_strings":["Department of Computer Science, University of Georgia, Athens, Georgia, 30602, USA","Dept. of Computer Science, Univ. of Georgia, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Dept. of Computer Science, Univ. of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029857449","display_name":"Timothy I. Shaw","orcid":"https://orcid.org/0000-0002-9316-1924"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy I Shaw","raw_affiliation_strings":["Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","[Institute of Bioinformatics, University of Georgia, Athens, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"[Institute of Bioinformatics, University of Georgia, Athens, USA]","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031339632","display_name":"Ying-Wai Li","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying-Wai Li","raw_affiliation_strings":["Center for Simulational Physics, University of Georgia, Athens, Georgia, 30602, USA","Center for Simulational Physics, University of Georgia, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Simulational Physics, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Center for Simulational Physics, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081591724","display_name":"Russell L. Malmberg","orcid":"https://orcid.org/0000-0002-7448-5034"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell L Malmberg","raw_affiliation_strings":["Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA","Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","Institute of Bioinformatics, University of Georgia, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012513857","display_name":"Liming Cai","orcid":"https://orcid.org/0000-0002-8982-2435"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liming Cai","raw_affiliation_strings":["Department of Computer Science, University of Georgia, Athens, Georgia, 30602, USA","Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","Institute of Bioinformatics, University of Georgia, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5005662495"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.7468,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.84266324,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S5","first_page":"S1","last_page":"S1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9668999910354614,"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":0.9668999910354614,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00860000029206276,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.005799999926239252,"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/non-coding-rna","display_name":"Non-coding RNA","score":0.7136585116386414},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.6820436716079712},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.640846848487854},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6232302188873291},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6034179925918579},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5911268591880798},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.5582964420318604},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5299329161643982},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5287100076675415},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44417884945869446},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38465479016304016},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3361991047859192},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.233879953622818}],"concepts":[{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.7136585116386414},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6820436716079712},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.640846848487854},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6232302188873291},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6034179925918579},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5911268591880798},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.5582964420318604},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5299329161643982},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5287100076675415},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44417884945869446},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38465479016304016},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3361991047859192},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.233879953622818},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":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":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-13-s5-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s5-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S5-S1","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:22537005","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22537005","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:doaj.org/article:c7983cbc964a4d52bb3b140f30cd3e19","is_oa":true,"landing_page_url":"https://doaj.org/article/c7983cbc964a4d52bb3b140f30cd3e19","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss Suppl 5, p S1 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3358654","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3358654","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s5-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s5-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S5-S1","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":[],"awards":[{"id":"https://openalex.org/G4797020615","display_name":"MRI: Acquisition of a Computer Cluster for Bioinformatics Research at UGA","funder_award_id":"0821263","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8092658006","display_name":"III: Small: Accurate Protein Threading via Tree-Decomposable Graph Modeling","funder_award_id":"0916250","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2092777420.pdf","grobid_xml":"https://content.openalex.org/works/W2092777420.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W636462510","https://openalex.org/W1542426682","https://openalex.org/W1543796220","https://openalex.org/W1622263187","https://openalex.org/W1902809146","https://openalex.org/W1950410402","https://openalex.org/W1984675364","https://openalex.org/W1988884185","https://openalex.org/W2003787247","https://openalex.org/W2009215595","https://openalex.org/W2009570821","https://openalex.org/W2012714413","https://openalex.org/W2025763720","https://openalex.org/W2042881722","https://openalex.org/W2044595289","https://openalex.org/W2053783019","https://openalex.org/W2061011128","https://openalex.org/W2084720293","https://openalex.org/W2084875499","https://openalex.org/W2094386736","https://openalex.org/W2102110811","https://openalex.org/W2102749300","https://openalex.org/W2103250001","https://openalex.org/W2111741055","https://openalex.org/W2121918723","https://openalex.org/W2124162379","https://openalex.org/W2134664665","https://openalex.org/W2137640371","https://openalex.org/W2140302584","https://openalex.org/W2149159794","https://openalex.org/W2152327613","https://openalex.org/W2153140501","https://openalex.org/W2158826174","https://openalex.org/W2163638609","https://openalex.org/W2167955222","https://openalex.org/W2294604761","https://openalex.org/W2950747312","https://openalex.org/W3008021358","https://openalex.org/W3041815373","https://openalex.org/W4245668478","https://openalex.org/W4249186015"],"related_works":["https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W3047450301","https://openalex.org/W2345156963","https://openalex.org/W1978187259","https://openalex.org/W4318218930","https://openalex.org/W2057388609","https://openalex.org/W2159621058","https://openalex.org/W2412575231","https://openalex.org/W2001187219"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"computational":[2],"identification":[3,11],"of":[4,12,14,32,41,46,107,144,153,174,202,215],"RNAs":[5,35],"in":[6,30,89,121,131,135,183],"genomic":[7],"sequences":[8],"requires":[9],"the":[10,38,44,57,69,83,104,142,145,151,158,184,200],"signals":[13],"RNA":[15,25],"sequences.":[16,77,195],"Shannon":[17],"base":[18,48,108,125,154,162],"pairing":[19,109,163],"entropy":[20,64,84,110],"is":[21,50],"an":[22,63],"indicator":[23],"for":[24,72,186],"secondary":[26,42,118,146,212],"structure":[27,97,119,147,213],"fold":[28],"certainty":[29],"detection":[31],"structural,":[33],"non-coding":[34],"(ncRNAs).":[36],"Under":[37],"Boltzmann":[39],"ensemble":[40,120],"structures,":[43],"probability":[45],"a":[47,116,136],"pair":[49],"estimated":[51],"from":[52,75],"its":[53],"frequency":[54],"across":[55],"all":[56,187],"alternative":[58],"equilibrium":[59],"structures.":[60],"However,":[61],"such":[62],"has":[65],"yet":[66],"to":[67,81,129,157,193],"deliver":[68],"desired":[70],"performance":[71,86,106],"distinguishing":[73],"ncRNAs":[74],"random":[76],"Developing":[78],"novel":[79],"methods":[80,209],"improve":[82],"measure":[85],"may":[87,149],"result":[88],"more":[90],"effective":[91,204],"ncRNA":[92,190,206],"gene":[93,207],"finding":[94,208],"based":[95],"on":[96],"detection.":[98],"RESULTS:":[99],"This":[100,138],"paper":[101],"shows":[102],"that":[103],"measuring":[105],"can":[111],"be":[112],"significantly":[113],"improved":[114],"with":[115,166],"constrained":[117,168],"which":[122],"only":[123],"canonical":[124],"pairs":[126,155],"are":[127],"assumed":[128],"occur":[130],"energetically":[132],"stable":[133],"stems":[134],"fold.":[137,160],"constraint":[139],"actually":[140],"reduces":[141],"space":[143],"and":[148],"lower":[150],"probabilities":[152],"unfavorable":[156],"native":[159],"Indeed,":[161],"entropies":[164],"computed":[165],"this":[167],"model":[169],"demonstrate":[170],"substantially":[171],"narrowed":[172],"gaps":[173],"Z-scores":[175],"between":[176],"ncRNAs,":[177],"as":[178,180],"well":[179],"drastic":[181],"increases":[182],"Z-score":[185],"13":[188],"tested":[189],"sets,":[191],"compared":[192],"shuffled":[194],"CONCLUSIONS:":[196],"These":[197],"results":[198],"suggest":[199],"viability":[201],"developing":[203],"structure-based":[205],"by":[210],"investigating":[211],"ensembles":[214],"ncRNAs.":[216]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}