{"id":"https://openalex.org/W2169271641","doi":"https://doi.org/10.1093/bib/bbp022","title":"An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes","display_name":"An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes","publication_year":2009,"publication_date":"2009-04-21","ids":{"openalex":"https://openalex.org/W2169271641","doi":"https://doi.org/10.1093/bib/bbp022","mag":"2169271641","pmid":"https://pubmed.ncbi.nlm.nih.gov/19383843"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp022","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bib/bbp022","pdf_url":"https://academic.oup.com/bib/article-pdf/10/5/475/565771/bbp022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/10/5/475/565771/bbp022.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051867363","display_name":"Giulia Sold\u00e0","orcid":"https://orcid.org/0000-0003-0972-610X"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"G. Solda","raw_affiliation_strings":["Department of Biology and Genetics for Medical Sciences, University of Milano, 20133 Milan, Italy. giulia.solda@unimi.it"],"affiliations":[{"raw_affiliation_string":"Department of Biology and Genetics for Medical Sciences, University of Milano, 20133 Milan, Italy. giulia.solda@unimi.it","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057816946","display_name":"Igor V. Makunin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I. V. Makunin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039717404","display_name":"Osman U\u011fur Sezerman","orcid":"https://orcid.org/0000-0003-0905-6783"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"O. U. Sezerman","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070594419","display_name":"Alberto Corradin","orcid":"https://orcid.org/0000-0003-2605-9492"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Corradin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052141168","display_name":"Giorgio Corti","orcid":"https://orcid.org/0000-0001-6379-4117"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"G. Corti","raw_affiliation_strings":["Istituto Oncologico Candiolo"],"affiliations":[{"raw_affiliation_string":"Istituto Oncologico Candiolo","institution_ids":["https://openalex.org/I4210151091"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018950136","display_name":"Alessandro Guffanti","orcid":"https://orcid.org/0000-0003-1517-9392"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Guffanti","raw_affiliation_strings":["Department of Medical Statistics"],"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5051867363"],"corresponding_institution_ids":["https://openalex.org/I189158943"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2797,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82456427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"5","first_page":"475","last_page":"489"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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":0.9991000294685364,"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":0.7587727308273315},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6439002156257629},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6141449809074402},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5825819373130798},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.526084303855896},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4526977837085724},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4408568739891052},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29054132103919983}],"concepts":[{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.7587727308273315},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6439002156257629},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6141449809074402},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5825819373130798},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.526084303855896},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4526977837085724},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4408568739891052},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29054132103919983},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","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":"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":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbp022","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bib/bbp022","pdf_url":"https://academic.oup.com/bib/article-pdf/10/5/475/565771/bbp022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19383843","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19383843","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:research.sabanciuniv.edu:13238","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402254","display_name":"Sabanci University","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134235054","host_organization_name":"Sabanc\u0131 \u00dcniversitesi","host_organization_lineage":["https://openalex.org/I134235054"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:zenodo.org:14313033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp022","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbp022","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bib/bbp022","pdf_url":"https://academic.oup.com/bib/article-pdf/10/5/475/565771/bbp022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169271641.pdf","grobid_xml":"https://content.openalex.org/works/W2169271641.grobid-xml"},"referenced_works_count":89,"referenced_works":["https://openalex.org/W1822105579","https://openalex.org/W1845151788","https://openalex.org/W1975437957","https://openalex.org/W1976021976","https://openalex.org/W1986234964","https://openalex.org/W1992361112","https://openalex.org/W1993158258","https://openalex.org/W1994658343","https://openalex.org/W1995073275","https://openalex.org/W2002357485","https://openalex.org/W2005636452","https://openalex.org/W2006079840","https://openalex.org/W2012363927","https://openalex.org/W2012739246","https://openalex.org/W2016066165","https://openalex.org/W2020678193","https://openalex.org/W2022523272","https://openalex.org/W2025605104","https://openalex.org/W2025794959","https://openalex.org/W2026980372","https://openalex.org/W2027780439","https://openalex.org/W2029506861","https://openalex.org/W2032766715","https://openalex.org/W2033094967","https://openalex.org/W2044832480","https://openalex.org/W2049339234","https://openalex.org/W2053078446","https://openalex.org/W2053150867","https://openalex.org/W2053490054","https://openalex.org/W2058044724","https://openalex.org/W2062313490","https://openalex.org/W2070571588","https://openalex.org/W2071051311","https://openalex.org/W2073136316","https://openalex.org/W2075320162","https://openalex.org/W2080551186","https://openalex.org/W2082826363","https://openalex.org/W2086255487","https://openalex.org/W2088017477","https://openalex.org/W2088431202","https://openalex.org/W2088938573","https://openalex.org/W2091802341","https://openalex.org/W2092758029","https://openalex.org/W2093956979","https://openalex.org/W2094722357","https://openalex.org/W2097493491","https://openalex.org/W2099101991","https://openalex.org/W2099741455","https://openalex.org/W2100806094","https://openalex.org/W2102749300","https://openalex.org/W2105292164","https://openalex.org/W2105846417","https://openalex.org/W2106348976","https://openalex.org/W2106554405","https://openalex.org/W2107959716","https://openalex.org/W2108292745","https://openalex.org/W2109968848","https://openalex.org/W2111741055","https://openalex.org/W2112001233","https://openalex.org/W2114973325","https://openalex.org/W2115441328","https://openalex.org/W2120893338","https://openalex.org/W2123067735","https://openalex.org/W2127981985","https://openalex.org/W2128066844","https://openalex.org/W2129974507","https://openalex.org/W2130599655","https://openalex.org/W2134597758","https://openalex.org/W2138664009","https://openalex.org/W2139347946","https://openalex.org/W2140302584","https://openalex.org/W2142187732","https://openalex.org/W2144603545","https://openalex.org/W2145628933","https://openalex.org/W2147154770","https://openalex.org/W2147495091","https://openalex.org/W2149146453","https://openalex.org/W2149785901","https://openalex.org/W2151804955","https://openalex.org/W2152327613","https://openalex.org/W2152419282","https://openalex.org/W2154688988","https://openalex.org/W2154916602","https://openalex.org/W2156186883","https://openalex.org/W2158826174","https://openalex.org/W2159006685","https://openalex.org/W2160913143","https://openalex.org/W2165699964","https://openalex.org/W4233163680"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2058984380","https://openalex.org/W1988125422","https://openalex.org/W2900182103","https://openalex.org/W4365136234","https://openalex.org/W3183769948","https://openalex.org/W3184762873","https://openalex.org/W2010385783","https://openalex.org/W2600828970"],"abstract_inverted_index":{"Non-protein":[0],"coding":[1],"RNAs":[2],"(ncRNAs)":[3],"have":[4,27],"emerged":[5],"as":[6,132,134],"a":[7,33],"vast":[8],"and":[9,30,44,89,105,119,141,145],"heterogeneous":[10],"portion":[11],"of":[12,35,72,92,94,109,116],"eukaryotic":[13],"transcriptomes.":[14],"Several":[15],"ncRNA":[16,59,84,126,143],"families,":[17],"either":[18],"short":[19,142],"(<200":[20],"nucleotides,":[21],"nt)":[22],"or":[23],"long":[24,140],"(>200":[25],"nt),":[26],"been":[28],"described":[29],"implicated":[31],"in":[32,69],"variety":[34],"biological":[36],"processes,":[37],"from":[38,64],"translation":[39],"to":[40,53,82],"gene":[41],"expression":[42],"regulation":[43],"nuclear":[45],"trafficking.":[46],"Most":[47],"probably,":[48],"other":[49],"families":[50],"are":[51],"still":[52],"be":[54],"discovered.":[55],"Computational":[56],"methods":[57,118],"for":[58,101,124,139],"research":[60],"require":[61],"different":[62,136],"approaches":[63,137],"the":[65,70,95,103,106,129,135],"ones":[66],"normally":[67],"used":[68],"prediction":[71,104],"protein-coding":[73],"genes.":[74],"Indeed,":[75],"primary":[76],"sequence":[77],"alone":[78],"is":[79],"often":[80],"insufficient":[81],"infer":[83],"functionality,":[85],"whereas":[86],"secondary":[87],"structure":[88],"local":[90],"conservation":[91],"portions":[93],"transcript":[96],"could":[97],"provide":[98],"useful":[99],"information":[100],"both":[102],"functional":[107],"annotation":[108],"ncRNAs.":[110],"Here":[111],"we":[112],"present":[113],"an":[114],"overview":[115],"computational":[117],"bioinformatics":[120],"resources":[121],"currently":[122],"available":[123],"studying":[125],"genes,":[127],"introducing":[128],"common":[130],"themes":[131],"well":[133],"required":[138],"identification":[144],"annotation.":[146]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
