{"id":"https://openalex.org/W2889525593","doi":"https://doi.org/10.1093/bioinformatics/bty765","title":"RNAdetect: efficient computational detection of novel non-coding RNAs","display_name":"RNAdetect: efficient computational detection of novel non-coding RNAs","publication_year":2018,"publication_date":"2018-08-30","ids":{"openalex":"https://openalex.org/W2889525593","doi":"https://doi.org/10.1093/bioinformatics/bty765","mag":"2889525593","pmid":"https://pubmed.ncbi.nlm.nih.gov/30169792"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty765","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty765","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/A5100629596","display_name":"Chun\u2010Chi Chen","orcid":"https://orcid.org/0000-0002-7459-5591"},"institutions":[{"id":"https://openalex.org/I173268674","display_name":"Texas A&M University System","ror":"https://ror.org/0034eay46","country_code":"US","type":"education","lineage":["https://openalex.org/I173268674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chun-Chi Chen","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I173268674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073946580","display_name":"Xiaoning Qian","orcid":"https://orcid.org/0000-0002-4347-2476"},"institutions":[{"id":"https://openalex.org/I173268674","display_name":"Texas A&M University System","ror":"https://ror.org/0034eay46","country_code":"US","type":"education","lineage":["https://openalex.org/I173268674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoning Qian","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I173268674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081620315","display_name":"Byung-Jun Yoon","orcid":"https://orcid.org/0000-0001-9328-1101"},"institutions":[{"id":"https://openalex.org/I173268674","display_name":"Texas A&M University System","ror":"https://ror.org/0034eay46","country_code":"US","type":"education","lineage":["https://openalex.org/I173268674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Byung-Jun Yoon","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I173268674"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081620315"],"corresponding_institution_ids":["https://openalex.org/I173268674","https://openalex.org/I91045830"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.371,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.60860862,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"35","issue":"7","first_page":"1133","last_page":"1141"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.5056999921798706,"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":0.5056999921798706,"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":0.33559998869895935,"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":0.04910000041127205,"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/computer-science","display_name":"Computer science","score":0.5872327089309692},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.5454190969467163},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5437610745429993},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5372021198272705},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4421236515045166},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2513846755027771},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22778591513633728},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.21066099405288696},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13290145993232727}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5872327089309692},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.5454190969467163},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5437610745429993},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5372021198272705},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4421236515045166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2513846755027771},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22778591513633728},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.21066099405288696},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13290145993232727}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty765","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty765","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30169792","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30169792","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6499999761581421,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G712506091","display_name":null,"funder_award_id":"CCF-1149544","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7527124865","display_name":null,"funder_award_id":"CCF-1447235","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W573845210","https://openalex.org/W1530144005","https://openalex.org/W1542426682","https://openalex.org/W1543796220","https://openalex.org/W1605441808","https://openalex.org/W1822105579","https://openalex.org/W1974736226","https://openalex.org/W1977937947","https://openalex.org/W1984675364","https://openalex.org/W1991022130","https://openalex.org/W1996640618","https://openalex.org/W2009818318","https://openalex.org/W2011567514","https://openalex.org/W2012960603","https://openalex.org/W2015672706","https://openalex.org/W2020021066","https://openalex.org/W2025305823","https://openalex.org/W2025763720","https://openalex.org/W2029939029","https://openalex.org/W2037871728","https://openalex.org/W2039925764","https://openalex.org/W2041257508","https://openalex.org/W2050256969","https://openalex.org/W2073865971","https://openalex.org/W2080140462","https://openalex.org/W2086159470","https://openalex.org/W2086561953","https://openalex.org/W2088938573","https://openalex.org/W2092777420","https://openalex.org/W2098571862","https://openalex.org/W2104465908","https://openalex.org/W2105133080","https://openalex.org/W2108230379","https://openalex.org/W2111272410","https://openalex.org/W2113816707","https://openalex.org/W2120768154","https://openalex.org/W2121918723","https://openalex.org/W2123047239","https://openalex.org/W2123552972","https://openalex.org/W2124050695","https://openalex.org/W2125615424","https://openalex.org/W2135106139","https://openalex.org/W2137015675","https://openalex.org/W2137677639","https://openalex.org/W2140302584","https://openalex.org/W2140818786","https://openalex.org/W2141152740","https://openalex.org/W2141249964","https://openalex.org/W2150965110","https://openalex.org/W2153635508","https://openalex.org/W2158381555","https://openalex.org/W2158826174","https://openalex.org/W2160226414","https://openalex.org/W2166812441","https://openalex.org/W2167708455","https://openalex.org/W2179575365","https://openalex.org/W2335480701","https://openalex.org/W2998216295","https://openalex.org/W4249465073","https://openalex.org/W4285719527","https://openalex.org/W4300746236","https://openalex.org/W6636160900","https://openalex.org/W6680272842","https://openalex.org/W7066667914"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W2010385783","https://openalex.org/W2600828970"],"abstract_inverted_index":{"MOTIVATION:":[0],"Non-coding":[1],"RNAs":[2],"(ncRNAs)":[3],"are":[4,57,194],"known":[5,58,206],"to":[6,29,33,59,110,185,196,205],"play":[7],"crucial":[8],"roles":[9],"in":[10,90,133,266],"various":[11],"biological":[12],"processes,":[13],"and":[14,177,235,243,261],"there":[15],"is":[16],"a":[17,61,79,91,105,122,140,186],"pressing":[18],"need":[19],"for":[20,51,70,87,128,259],"accurate":[21,129],"computational":[22,71,123],"detection":[23,99,130,215],"methods":[24,100],"that":[25,47,78,199,218,239],"could":[26,48],"be":[27,49,85,270],"used":[28,50,195,265],"efficiently":[30],"scan":[31],"genomes":[32,237],"detect":[34,146,245],"novel":[35,126,154,246],"ncRNAs.":[36],"However,":[37],"unlike":[38],"coding":[39],"genes,":[40],"ncRNAs":[41,56,89,132,151,217],"often":[42],"lack":[43],"distinctive":[44],"sequence":[45,141,203],"features":[46,127,156,198],"recognizing":[52],"them.":[53],"Although":[54],"many":[55,224],"have":[60,219],"well":[62],"conserved":[63],"secondary":[64],"structure,":[65],"which":[66,166],"provides":[67],"useful":[68],"cues":[69],"prediction,":[72],"it":[73],"has":[74],"been":[75],"also":[76],"shown":[77],"structure-based":[80,102],"approach":[81,109],"alone":[82],"may":[83],"not":[84],"sufficient":[86],"detecting":[88],"single":[92],"sequence.":[93],"Currently,":[94],"the":[95,112,147,159,168,178,181,214,232,249,262],"most":[96],"effective":[97],"ncRNA":[98,207],"combine":[101],"techniques":[103],"with":[104,135,223],"comparative":[106,136],"genome":[107,137],"analysis":[108],"improve":[111],"prediction":[113],"performance.":[114],"RESULTS:":[115],"In":[116],"this":[117,267],"paper,":[118],"we":[119],"propose":[120],"RNAdetect,":[121],"method":[124],"incorporating":[125,153],"of":[131,149,161,170,180,210,216],"combination":[134],"analysis.":[138],"Given":[139],"alignment,":[142],"RNAdetect":[143,240,260],"can":[144,200,212,241,269],"accurately":[145,242],"presence":[148],"functional":[150],"by":[152],"predictive":[155],"based":[157,230],"on":[158,231],"concept":[160],"generalized":[162],"ensemble":[163],"defect":[164],"(GED),":[165],"assesses":[167],"degree":[169],"structure":[171],"conservation":[172],"across":[173],"multiple":[174],"related":[175],"sequences":[176],"conformation":[179],"individual":[182],"folding":[183,221],"structures":[184,222],"common":[187],"consensus":[188],"structure.":[189],"Furthermore,":[190],"n-gram":[191],"models":[192],"(NGMs)":[193],"extract":[197],"effectively":[201],"capture":[202],"homology":[204],"families.":[208],"Utilization":[209],"NGMs":[211],"enhance":[213],"sparse":[220],"unpaired":[225],"bases.":[226],"Extensive":[227],"performance":[228],"evaluation":[229],"Rfam":[233],"database":[234],"bacterial":[236],"demonstrate":[238],"reliably":[244],"ncRNAs,":[247],"outperforming":[248],"current":[250],"state-of-the-art":[251],"methods.":[252],"AVAILABILITY":[253],"AND":[254],"IMPLEMENTATION:":[255],"The":[256],"source":[257],"code":[258],"benchmark":[263],"data":[264],"paper":[268],"downloaded":[271],"at":[272],"https://github.com/bjyoontamu/RNAdetect.":[273]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
