{"id":"https://openalex.org/W1622263187","doi":"https://doi.org/10.1186/1471-2105-7-173","title":"Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change","display_name":"Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change","publication_year":2006,"publication_date":"2006-03-27","ids":{"openalex":"https://openalex.org/W1622263187","doi":"https://doi.org/10.1186/1471-2105-7-173","mag":"1622263187","pmid":"https://pubmed.ncbi.nlm.nih.gov/16566836"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-173","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-173","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-173","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/10.1186/1471-2105-7-173","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029416625","display_name":"Andrew Uzilov","orcid":"https://orcid.org/0000-0002-5411-9280"},"institutions":[{"id":"https://openalex.org/I28792581","display_name":"University of Rochester Medical Center","ror":"https://ror.org/00trqv719","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I28792581","https://openalex.org/I5388228"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew V Uzilov","raw_affiliation_strings":["Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA. andrew.uzilov@gmail.com","Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA. andrew.uzilov@gmail.com","institution_ids":["https://openalex.org/I28792581","https://openalex.org/I5388228"]},{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025183011","display_name":"Joshua M. Keegan","orcid":null},"institutions":[{"id":"https://openalex.org/I28792581","display_name":"University of Rochester Medical Center","ror":"https://ror.org/00trqv719","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I28792581","https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua M Keegan","raw_affiliation_strings":["Center for Pediatric Biomedical Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pediatric Biomedical Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002272329","display_name":"David H. Mathews","orcid":"https://orcid.org/0000-0002-2907-6557"},"institutions":[{"id":"https://openalex.org/I28792581","display_name":"University of Rochester Medical Center","ror":"https://ror.org/00trqv719","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I28792581","https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David H Mathews","raw_affiliation_strings":["Center for Pediatric Biomedical Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pediatric Biomedical Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York, 14642, USA","institution_ids":["https://openalex.org/I28792581"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5029416625"],"corresponding_institution_ids":["https://openalex.org/I28792581","https://openalex.org/I5388228"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.27,"has_fulltext":true,"cited_by_count":212,"citation_normalized_percentile":{"value":0.97252922,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"173","last_page":"173"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9460999965667725,"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":0.9460999965667725,"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":0.007300000172108412,"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":0.007000000216066837,"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":0.7438066005706787},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6287870407104492},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.533735454082489},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5133837461471558},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5027782917022705},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.445425420999527},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41736122965812683},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3311637043952942},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32872068881988525},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3148114085197449},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1579773724079132}],"concepts":[{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.7438066005706787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6287870407104492},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.533735454082489},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5133837461471558},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5027782917022705},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.445425420999527},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41736122965812683},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3311637043952942},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32872068881988525},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3148114085197449},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1579773724079132}],"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"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}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-173","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-173","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-173","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:16566836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16566836","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:4c08c315f1d24524b31697f723d5055d","is_oa":true,"landing_page_url":"https://doaj.org/article/4c08c315f1d24524b31697f723d5055d","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":"BMC Bioinformatics, Vol 7, Iss 1, p 173 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:353692","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1570369","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1570369","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-173","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:10.1186/1471-2105-7-173","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-173","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-173","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":[{"id":"https://metadata.un.org/sdg/7","score":0.9100000262260437,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1622263187.pdf","grobid_xml":"https://content.openalex.org/works/W1622263187.grobid-xml"},"referenced_works_count":88,"referenced_works":["https://openalex.org/W1542426682","https://openalex.org/W1553934596","https://openalex.org/W1556119657","https://openalex.org/W1822105579","https://openalex.org/W1901451661","https://openalex.org/W1909512798","https://openalex.org/W1910105722","https://openalex.org/W1950410402","https://openalex.org/W1974736226","https://openalex.org/W1978242636","https://openalex.org/W1980410097","https://openalex.org/W1984136932","https://openalex.org/W1986234964","https://openalex.org/W1986385237","https://openalex.org/W1996423252","https://openalex.org/W2004945910","https://openalex.org/W2009818318","https://openalex.org/W2016707038","https://openalex.org/W2017313617","https://openalex.org/W2018216725","https://openalex.org/W2020021066","https://openalex.org/W2020195960","https://openalex.org/W2020865862","https://openalex.org/W2024799598","https://openalex.org/W2033907622","https://openalex.org/W2039244411","https://openalex.org/W2039925764","https://openalex.org/W2039951296","https://openalex.org/W2042881722","https://openalex.org/W2050256969","https://openalex.org/W2050426121","https://openalex.org/W2051713039","https://openalex.org/W2057850636","https://openalex.org/W2057998009","https://openalex.org/W2058044724","https://openalex.org/W2061981209","https://openalex.org/W2087347434","https://openalex.org/W2088938573","https://openalex.org/W2090030959","https://openalex.org/W2097654784","https://openalex.org/W2099319235","https://openalex.org/W2100167293","https://openalex.org/W2101399358","https://openalex.org/W2102225325","https://openalex.org/W2105133080","https://openalex.org/W2107282968","https://openalex.org/W2113966076","https://openalex.org/W2115215562","https://openalex.org/W2115457188","https://openalex.org/W2119821739","https://openalex.org/W2122035121","https://openalex.org/W2126924668","https://openalex.org/W2130032853","https://openalex.org/W2134153749","https://openalex.org/W2135146244","https://openalex.org/W2136654689","https://openalex.org/W2137677639","https://openalex.org/W2140302584","https://openalex.org/W2140651796","https://openalex.org/W2141144953","https://openalex.org/W2142056356","https://openalex.org/W2142066620","https://openalex.org/W2142768277","https://openalex.org/W2145928119","https://openalex.org/W2149429041","https://openalex.org/W2150770935","https://openalex.org/W2151464048","https://openalex.org/W2151922790","https://openalex.org/W2153635508","https://openalex.org/W2153758225","https://openalex.org/W2155913747","https://openalex.org/W2158033466","https://openalex.org/W2158381555","https://openalex.org/W2160226414","https://openalex.org/W2165230358","https://openalex.org/W2166745309","https://openalex.org/W2167557255","https://openalex.org/W2167673850","https://openalex.org/W2171746475","https://openalex.org/W2612812586","https://openalex.org/W2981209166","https://openalex.org/W3041019241","https://openalex.org/W4230501579","https://openalex.org/W4234879553","https://openalex.org/W4234887284","https://openalex.org/W4250052351","https://openalex.org/W4251866352","https://openalex.org/W4255207094"],"related_works":["https://openalex.org/W2058984380","https://openalex.org/W1988125422","https://openalex.org/W2900182103","https://openalex.org/W4365136234","https://openalex.org/W3183769948","https://openalex.org/W4385457841","https://openalex.org/W2581348958","https://openalex.org/W4367048159","https://openalex.org/W962838231","https://openalex.org/W2338408817"],"abstract_inverted_index":{"BACKGROUND:":[0],"Non-coding":[1],"RNAs":[2],"(ncRNAs)":[3],"have":[4,336],"a":[5,54,70,93,118,143,166,186,202,298,317],"multitude":[6],"of":[7,13,50,64,84,115,150,165,168,223],"roles":[8],"in":[9,27,41,175,233,268,308,322,333],"the":[10,82,107,111,140,145,160,206,269],"cell,":[11],"many":[12,235],"which":[14,105,234],"remain":[15],"to":[16,23,77,127,185,214],"be":[17,128,157,173,215,295],"discovered.":[18],"However,":[19],"it":[20],"is":[21,90,125,194,212,262],"difficult":[22],"detect":[24,39],"novel":[25,65],"ncRNAs":[26,40,236,267,321],"biochemical":[28],"screens.":[29],"To":[30,138],"advance":[31],"biological":[32],"knowledge,":[33],"computational":[34,58,94,241],"methods":[35,280,327],"that":[36,325],"can":[37,155,294],"accurately":[38],"sequenced":[42,323],"genomes":[43,324],"are":[44,237,243,281],"therefore":[45],"desirable.":[46],"The":[47,98,191,239,256],"increasing":[48],"number":[49],"genomic":[51,220,271,309],"sequences":[52,80],"provides":[53,316],"rich":[55],"dataset":[56],"for":[57,72,121,132,265,312,319],"comparative":[59],"sequence":[60,153,170,178,290],"analysis":[61],"and":[62,110,180,217,228,253,275,286],"detection":[63,96,250],"ncRNAs.":[66],"RESULTS:":[67],"Here,":[68],"Dynalign,":[69],"program":[71],"predicting":[73],"secondary":[74],"structures":[75],"common":[76,119],"two":[78,122,224,247],"RNA":[79,123],"on":[81,219],"basis":[83],"minimizing":[85],"folding":[86,116],"free":[87,102,112,147,162],"energy":[88,103,113,148,163],"change,":[89,104],"utilized":[91],"as":[92,142,183,297],"ncRNA":[95,134,221,249],"tool.":[97],"Dynalign-computed":[99],"optimal":[100],"total":[101,146,161],"scores":[106],"structural":[108],"alignment":[109],"change":[114,149],"into":[117],"structure":[120],"sequences,":[124],"shown":[126,213],"an":[129,151],"effective":[130],"measure":[131],"distinguishing":[133],"from":[135],"randomized":[136],"sequences.":[137],"make":[139],"classification":[141,187,207],"ncRNA,":[144],"input":[152,184],"pair":[154,291],"either":[156],"compared":[158,245],"with":[159,177,246],"changes":[164],"set":[167],"control":[169],"pairs,":[171],"or":[172,300,306],"used":[174,296],"combination":[176],"length":[179],"nucleotide":[181],"frequencies":[182],"support":[188,208,258],"vector":[189,209,259],"machine.":[190],"latter":[192],"method":[193,211,261,318],"much":[195],"faster,":[196],"but":[197],"slightly":[198],"less":[199],"sensitive":[200,216,264,283],"at":[201,288],"given":[203],"specificity.":[204],"Additionally,":[205,277],"machine":[210,260],"specific":[218],"screens":[222,272],"different":[225],"Escherichia":[226],"coli":[227],"Salmonella":[229],"typhi":[230],"genome":[231],"alignments,":[232],"known.":[238],"Dynalign":[240,293,315,334],"experiments":[242],"also":[244,337],"other":[248,326],"programs,":[251],"RNAz":[252,274,285,305],"QRNA.":[254,276],"CONCLUSION:":[255],"Dynalign-based":[257,279],"more":[263,282,301],"known":[266],"test":[270],"than":[273,284,304],"both":[278],"QRNA":[287,307],"low":[289],"identities.":[292],"comparable":[299],"accurate":[302],"tool":[303],"screens,":[310],"especially":[311],"low-identity":[313],"regions.":[314],"discovering":[320],"may":[328],"not":[329],"identify.":[330],"Significant":[331],"improvements":[332],"runtime":[335],"been":[338],"achieved.":[339]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
