{"id":"https://openalex.org/W3187121296","doi":"https://doi.org/10.1093/bib/bbab285","title":"A systematic evaluation of the computational tools for lncRNA identification","display_name":"A systematic evaluation of the computational tools for lncRNA identification","publication_year":2021,"publication_date":"2021-07-05","ids":{"openalex":"https://openalex.org/W3187121296","doi":"https://doi.org/10.1093/bib/bbab285","mag":"3187121296","pmid":"https://pubmed.ncbi.nlm.nih.gov/34368833"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab285","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab285","pdf_url":null,"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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060522316","display_name":"Hansi Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hansi Zheng","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, Orlando, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007638508","display_name":"Amlan Talukder","orcid":"https://orcid.org/0000-0001-7457-8268"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amlan Talukder","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, Orlando, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100669881","display_name":"Xiaoman Li","orcid":"https://orcid.org/0000-0002-9209-458X"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoman Li","raw_affiliation_strings":["Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101762276","display_name":"Haiyan Hu","orcid":"https://orcid.org/0000-0002-4580-5975"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Haiyan Hu","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, Orlando, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100669881","https://openalex.org/A5101762276"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2249,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.76527582,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"22","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"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":1.0,"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":0.9800999760627747,"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":0.9585000276565552,"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/identification","display_name":"Identification (biology)","score":0.8123534917831421},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7882753610610962},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5225754976272583},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.516484260559082},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5053873062133789},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4447852075099945},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4177592396736145},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34440964460372925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09829160571098328},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.05997470021247864}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.8123534917831421},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7882753610610962},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5225754976272583},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.516484260559082},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5053873062133789},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4447852075099945},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4177592396736145},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34440964460372925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09829160571098328},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.05997470021247864},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"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":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab285","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab285","pdf_url":null,"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:34368833","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34368833","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3198000179","display_name":null,"funder_award_id":"2015838","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G5862447349","display_name":null,"funder_award_id":"1661414","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":126,"referenced_works":["https://openalex.org/W51532682","https://openalex.org/W386206782","https://openalex.org/W1536680647","https://openalex.org/W1601667204","https://openalex.org/W1750059056","https://openalex.org/W1810679038","https://openalex.org/W1963604994","https://openalex.org/W1965555277","https://openalex.org/W1966580635","https://openalex.org/W1970569349","https://openalex.org/W1976067040","https://openalex.org/W1978811100","https://openalex.org/W1988896110","https://openalex.org/W1992605446","https://openalex.org/W1998422171","https://openalex.org/W1999746344","https://openalex.org/W2001841820","https://openalex.org/W2007006753","https://openalex.org/W2019160435","https://openalex.org/W2024329298","https://openalex.org/W2029173942","https://openalex.org/W2032183472","https://openalex.org/W2039816251","https://openalex.org/W2041741035","https://openalex.org/W2048194168","https://openalex.org/W2056227286","https://openalex.org/W2061548680","https://openalex.org/W2062313490","https://openalex.org/W2062502437","https://openalex.org/W2063950568","https://openalex.org/W2064675550","https://openalex.org/W2075320162","https://openalex.org/W2080356693","https://openalex.org/W2081530255","https://openalex.org/W2085220756","https://openalex.org/W2086607018","https://openalex.org/W2087001748","https://openalex.org/W2100495367","https://openalex.org/W2102649026","https://openalex.org/W2110957978","https://openalex.org/W2112001233","https://openalex.org/W2117677974","https://openalex.org/W2123067735","https://openalex.org/W2123462814","https://openalex.org/W2125484161","https://openalex.org/W2127230663","https://openalex.org/W2131774270","https://openalex.org/W2136922672","https://openalex.org/W2141831115","https://openalex.org/W2142580593","https://openalex.org/W2143426320","https://openalex.org/W2149706766","https://openalex.org/W2153268494","https://openalex.org/W2154431984","https://openalex.org/W2156392314","https://openalex.org/W2160333540","https://openalex.org/W2161311669","https://openalex.org/W2163605009","https://openalex.org/W2165312739","https://openalex.org/W2166810745","https://openalex.org/W2176555004","https://openalex.org/W2237493771","https://openalex.org/W2259938310","https://openalex.org/W2291340556","https://openalex.org/W2395238275","https://openalex.org/W2519244818","https://openalex.org/W2557660291","https://openalex.org/W2559275412","https://openalex.org/W2559953833","https://openalex.org/W2562379668","https://openalex.org/W2567665210","https://openalex.org/W2571489439","https://openalex.org/W2604951703","https://openalex.org/W2615786037","https://openalex.org/W2727545883","https://openalex.org/W2749576358","https://openalex.org/W2761249484","https://openalex.org/W2784570320","https://openalex.org/W2805219020","https://openalex.org/W2805467558","https://openalex.org/W2805813857","https://openalex.org/W2806037935","https://openalex.org/W2806980026","https://openalex.org/W2807607992","https://openalex.org/W2883632755","https://openalex.org/W2886900083","https://openalex.org/W2903139824","https://openalex.org/W2904944681","https://openalex.org/W2914698725","https://openalex.org/W2919115771","https://openalex.org/W2922602740","https://openalex.org/W2922701384","https://openalex.org/W2923387381","https://openalex.org/W2927243169","https://openalex.org/W2933231366","https://openalex.org/W2936562571","https://openalex.org/W2939800568","https://openalex.org/W2943835743","https://openalex.org/W2947017644","https://openalex.org/W2951162249","https://openalex.org/W2951579118","https://openalex.org/W2963150697","https://openalex.org/W2963608065","https://openalex.org/W2968830255","https://openalex.org/W2972083913","https://openalex.org/W2984943906","https://openalex.org/W3003753408","https://openalex.org/W3008496114","https://openalex.org/W3027742040","https://openalex.org/W3045332767","https://openalex.org/W3081278968","https://openalex.org/W3081791314","https://openalex.org/W3088693971","https://openalex.org/W3093327767","https://openalex.org/W3111419662","https://openalex.org/W3115880421","https://openalex.org/W3134616030","https://openalex.org/W3134802634","https://openalex.org/W4236137412","https://openalex.org/W4245643014","https://openalex.org/W6684191040","https://openalex.org/W6711757063","https://openalex.org/W6731700065","https://openalex.org/W6761079606","https://openalex.org/W6782440588","https://openalex.org/W6787073073"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2046435967","https://openalex.org/W4231775656","https://openalex.org/W2611989081","https://openalex.org/W4230611425","https://openalex.org/W2731899572","https://openalex.org/W2383646825","https://openalex.org/W4304166257","https://openalex.org/W4294635752","https://openalex.org/W4380075502"],"abstract_inverted_index":{"The":[0],"computational":[1],"identification":[2],"of":[3,19,34,49,64,76,96,123],"long":[4],"non-coding":[5],"RNAs":[6],"(lncRNAs)":[7],"is":[8,30],"important":[9],"to":[10,26,107],"study":[11,142],"lncRNAs":[12],"and":[13,40,46,99,128,153],"their":[14,44],"functions.":[15],"Despite":[16],"the":[17,47,50,62,74,77,81,86,91,100,108,113,121,129],"existence":[18],"many":[20],"computation":[21],"tools":[22,36,66,89,125,132,152],"for":[23,150,155],"lncRNA":[24,156],"identification,":[25],"our":[27],"knowledge,":[28],"there":[29],"no":[31,41,134],"systematic":[32],"evaluation":[33],"these":[35],"on":[37,67],"common":[38,69],"datasets":[39],"consensus":[42],"regarding":[43],"performance":[45,63,93,122],"importance":[48,75],"features":[51,78,102,154],"used.":[52],"To":[53],"fill":[54],"this":[55,58],"gap,":[56],"in":[57,94,115],"study,":[59],"we":[60],"assessed":[61],"17":[65],"several":[68],"datasets.":[70],"We":[71,83],"also":[72],"investigated":[73],"used":[79],"by":[80],"tools.":[82,140],"found":[84],"that":[85],"deep":[87,130],"learning-based":[88,131],"have":[90],"best":[92],"terms":[95],"identifying":[97],"lncRNAs,":[98],"peptide":[101],"do":[103],"not":[104],"contribute":[105],"much":[106],"tool":[109],"accuracy.":[110],"Moreover,":[111],"when":[112],"transcripts":[114],"a":[116],"cell":[117],"type":[118],"were":[119,133],"considered,":[120],"all":[124],"significantly":[126],"dropped,":[127],"longer":[135],"as":[136,138,145],"good":[137],"other":[139],"Our":[141],"will":[143],"serve":[144],"an":[146],"excellent":[147],"starting":[148],"point":[149],"selecting":[151],"identification.":[157]},"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":2},{"year":2022,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
