{"id":"https://openalex.org/W4225082641","doi":"https://doi.org/10.1093/bioinformatics/btac302","title":"Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq","display_name":"Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq","publication_year":2022,"publication_date":"2022-04-25","ids":{"openalex":"https://openalex.org/W4225082641","doi":"https://doi.org/10.1093/bioinformatics/btac302","pmid":"https://pubmed.ncbi.nlm.nih.gov/35482518"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac302","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3037/43857861/btac302.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3037/43857861/btac302.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100689490","display_name":"Hongfei Liu","orcid":"https://orcid.org/0000-0003-4637-9151"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Liu","raw_affiliation_strings":["College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073781634","display_name":"Zhanerke Akhatayeva","orcid":"https://orcid.org/0000-0003-2624-1833"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhanerke Akhatayeva","raw_affiliation_strings":["College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080944216","display_name":"Chuanying Pan","orcid":"https://orcid.org/0000-0002-9461-6740"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuanying Pan","raw_affiliation_strings":["College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060605576","display_name":"Mingzhi Liao","orcid":"https://orcid.org/0000-0002-5216-5742"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mingzhi Liao","raw_affiliation_strings":["College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":"https://orcid.org/0000-0002-5216-5742","affiliations":[{"raw_affiliation_string":"College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081219554","display_name":"Xianyong Lan","orcid":"https://orcid.org/0000-0003-2254-5805"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xianyong Lan","raw_affiliation_strings":["College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5060605576","https://openalex.org/A5081219554"],"corresponding_institution_ids":["https://openalex.org/I89652312"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3358,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.52990784,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"38","issue":"11","first_page":"3037","last_page":"3043"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","score":0.738099992275238,"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/T11765","display_name":"Circular RNAs in diseases","score":0.738099992275238,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.1387999951839447,"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/T10604","display_name":"RNA Research and Splicing","score":0.06030000001192093,"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":0.6712405681610107},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.472443163394928},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4570872485637665},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.443676233291626},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36039605736732483},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.339419960975647},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13017848134040833},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1115068793296814},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.102201908826828},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09582096338272095},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08179989457130432}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6712405681610107},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.472443163394928},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4570872485637665},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.443676233291626},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36039605736732483},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.339419960975647},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13017848134040833},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1115068793296814},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.102201908826828},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09582096338272095},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08179989457130432}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac302","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3037/43857861/btac302.pdf","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:35482518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35482518","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":{"id":"doi:10.1093/bioinformatics/btac302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac302","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3037/43857861/btac302.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6266675966","display_name":null,"funder_award_id":"61772431","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6501996369","display_name":"\u57fa\u4e8e\u591a\u7ec4\u5b66\u7684\u52a8\u7269\u4ea7\u524d\u57fa\u56e0\u7ec4\u9009\u62e9\u8ba1\u7b97\u6a21\u578b\u7814\u7a76","funder_award_id":"62072377","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8512658715","display_name":null,"funder_award_id":"31872331","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1566841623","https://openalex.org/W1981726010","https://openalex.org/W2017919052","https://openalex.org/W2051477788","https://openalex.org/W2058835062","https://openalex.org/W2089891619","https://openalex.org/W2103441770","https://openalex.org/W2115662330","https://openalex.org/W2126144698","https://openalex.org/W2139399606","https://openalex.org/W2157539385","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2194134194","https://openalex.org/W2196247406","https://openalex.org/W2238930303","https://openalex.org/W2261488440","https://openalex.org/W2286014095","https://openalex.org/W2464424326","https://openalex.org/W2599812844","https://openalex.org/W2622004629","https://openalex.org/W2791184452","https://openalex.org/W2791808804","https://openalex.org/W2903812443","https://openalex.org/W2950811896","https://openalex.org/W2951912016","https://openalex.org/W2955067089","https://openalex.org/W2964331590","https://openalex.org/W2996796392","https://openalex.org/W3009173724","https://openalex.org/W3020614442","https://openalex.org/W3082710919","https://openalex.org/W3135065548","https://openalex.org/W3208194349"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2544423928","https://openalex.org/W4200033037","https://openalex.org/W2053286651","https://openalex.org/W2181743346","https://openalex.org/W3213655218","https://openalex.org/W2187401768","https://openalex.org/W2181413294","https://openalex.org/W1971332228"],"abstract_inverted_index":{"MOTIVATION:":[0],"Circular":[1],"RNA":[2],"is":[3],"generally":[4],"formed":[5],"by":[6,64,154],"the":[7,11,16,21,24,45,48,80,105,133,137,168,189],"'back-splicing'":[8],"process":[9],"between":[10,86],"upstream":[12],"splice":[13],"acceptor":[14],"and":[15,32,39,83,125,139,146,158,173,182,203],"downstream":[17],"donor":[18],"in/not":[19],"in":[20,116],"regulation":[22],"of":[23,47,100,109,141,188],"corresponding":[25],"RNA-binding":[26],"proteins":[27],"or":[28,192],"cis-elements.":[29],"Therefore,":[30],"more":[31,33,183],"software":[34,57,87],"packages":[35],"have":[36],"been":[37],"developed":[38,55],"they":[40],"are":[41,215],"mostly":[42],"based":[43,89,170,175],"on":[44,90,176],"identification":[46],"back-spliced":[49],"junction":[50],"reads.":[51],"However,":[52],"recent":[53],"studies":[54],"two":[56,98,117],"tools":[58,88,96],"that":[59,165],"can":[60,206],"detect":[61],"circRNA":[62],"candidates":[63],"constructing":[65],"k-mer":[66,169],"table":[67],"or/and":[68],"de":[69],"Bruijn":[70],"graph":[71],"rather":[72],"than":[73],"reads":[74,177],"mapping.":[75],"RESULTS:":[76],"Here,":[77],"we":[78,163],"compared":[79,166],"precision,":[81],"sensitivity":[82,138],"detection":[84,95,126,185],"efficiency":[85,127],"different":[91],"algorithms.":[92],"Eleven":[93],"representative":[94],"with":[97],"types":[99],"algorithm":[101],"were":[102,129,151],"selected":[103],"for":[104],"overall":[106],"pipeline":[107],"analysis":[108],"RNA-seq":[110],"datasets":[111],"with/without":[112],"RNase":[113,148,193],"R":[114,149,194],"treatment":[115,150],"cell":[118,190],"lines.":[119],"Precision,":[120],"sensitivity,":[121],"AUC,":[122],"F1":[123],"score":[124],"metrics":[128],"assessed":[130],"to":[131,167],"compare":[132],"prediction":[134],"tools.":[135],"Meanwhile,":[136],"distribution":[140],"highly":[142],"expressed":[143],"circRNAs":[144],"before":[145],"after":[147],"also":[152],"revealed":[153],"their":[155],"enrichment,":[156],"unaffected":[157],"depleted":[159],"candidate":[160],"frequencies.":[161],"Eventually,":[162],"found":[164],"tools,":[171],"CIRI2":[172],"KNIFE":[174],"mapping":[178],"had":[179],"relatively":[180],"superior":[181],"balanced":[184],"performance":[186],"regardless":[187],"line":[191],"(-/+)":[195],"datasets.":[196],"AVAILABILITY":[197],"AND":[198],"IMPLEMENTATION:":[199],"All":[200],"predicted":[201],"results":[202],"source":[204],"codes":[205],"be":[207],"retrieved":[208],"from":[209],"https://github.com/luffy563/circRNA_tools_comparison.":[210],"SUPPLEMENTARY":[211],"INFORMATION:":[212],"Supplementary":[213],"data":[214],"available":[216],"at":[217],"Bioinformatics":[218],"online.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}