{"id":"https://openalex.org/W4412824955","doi":"https://doi.org/10.1186/s13040-025-00468-3","title":"circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data","display_name":"circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4412824955","doi":"https://doi.org/10.1186/s13040-025-00468-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/40751272"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00468-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00468-3","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00468-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00468-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089537120","display_name":"Petr Ry\u0161av\u00fd","orcid":"https://orcid.org/0000-0002-6597-6616"},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Petr Ry\u0161av\u00fd","raw_affiliation_strings":["Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic. petr.rysavy@fel.cvut.cz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic. petr.rysavy@fel.cvut.cz","institution_ids":["https://openalex.org/I44504214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117711875","display_name":"Alikhan Anuarbekov","orcid":null},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Alikhan Anuarbekov","raw_affiliation_strings":["Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic","institution_ids":["https://openalex.org/I44504214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068736593","display_name":"Michaela Dost\u00e1lov\u00e1 Merkerov\u00e1","orcid":"https://orcid.org/0000-0002-6345-9180"},"institutions":[{"id":"https://openalex.org/I4210096318","display_name":"Institute of Haematology and Blood Transfusion","ror":"https://ror.org/00n6rde07","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I4210096318"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Michaela Dost\u00e1lov\u00e1 Merkerov\u00e1","raw_affiliation_strings":["Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice, 12800, Prague, Prague, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice, 12800, Prague, Prague, Czech Republic","institution_ids":["https://openalex.org/I4210096318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080019407","display_name":"J\u01d0\u0155\u0131 Kl\u00e9ma","orcid":"https://orcid.org/0000-0003-1753-9435"},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ji\u0159\u00ed Kl\u00e9ma","raw_affiliation_strings":["Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Technick\u00e1, 16627, Prague, Prague, Czech Republic","institution_ids":["https://openalex.org/I44504214"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14959309,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987000226974487,"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":0.9987000226974487,"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/annotation","display_name":"Annotation","score":0.7293422818183899},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6202483177185059},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6178150773048401},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47645071148872375},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42082738876342773},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3936973214149475},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35038667917251587},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22431206703186035},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19968357682228088}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7293422818183899},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6202483177185059},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6178150773048401},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47645071148872375},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42082738876342773},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3936973214149475},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35038667917251587},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22431206703186035},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19968357682228088},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00468-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00468-3","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00468-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:40751272","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40751272","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:e6806ead8ccd47f2875c4032fe2be799","is_oa":true,"landing_page_url":"https://doaj.org/article/e6806ead8ccd47f2875c4032fe2be799","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":"BioData Mining, Vol 18, Iss 1, Pp 1-32 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12317645","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12317645","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00468-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00468-3","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00468-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1471787206","display_name":null,"funder_award_id":"SGS23/184/OHK3/3T/13","funder_id":"https://openalex.org/F4320309972","funder_display_name":"\u010cesk\u00e9 Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Praze"},{"id":"https://openalex.org/G2044203393","display_name":null,"funder_award_id":"NU20-03-00412","funder_id":"https://openalex.org/F4320321798","funder_display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky"},{"id":"https://openalex.org/G5366248502","display_name":null,"funder_award_id":"90254","funder_id":"https://openalex.org/F4320321798","funder_display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky"},{"id":"https://openalex.org/G6247895005","display_name":null,"funder_award_id":"NU20-03-00412","funder_id":"https://openalex.org/F4320325869","funder_display_name":"Agentura Pro Zdravotnick\u00fd V\u00fdzkum \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G7223443805","display_name":null,"funder_award_id":"AZV NU20-03-00412","funder_id":"https://openalex.org/F4320321798","funder_display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky"}],"funders":[{"id":"https://openalex.org/F4320309972","display_name":"\u010cesk\u00e9 Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Praze","ror":"https://ror.org/03kqpb082"},{"id":"https://openalex.org/F4320321798","display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","ror":"https://ror.org/00y6khe77"},{"id":"https://openalex.org/F4320325869","display_name":"Agentura Pro Zdravotnick\u00fd V\u00fdzkum \u010cesk\u00e9 Republiky","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412824955.pdf","grobid_xml":"https://content.openalex.org/works/W4412824955.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W192831050","https://openalex.org/W1966327575","https://openalex.org/W1968817103","https://openalex.org/W2003091453","https://openalex.org/W2020541351","https://openalex.org/W2026134786","https://openalex.org/W2053003053","https://openalex.org/W2060705109","https://openalex.org/W2061554433","https://openalex.org/W2097948046","https://openalex.org/W2103017472","https://openalex.org/W2104806799","https://openalex.org/W2110065044","https://openalex.org/W2115662330","https://openalex.org/W2134629862","https://openalex.org/W2145708195","https://openalex.org/W2159675211","https://openalex.org/W2210577735","https://openalex.org/W2551383706","https://openalex.org/W2558702637","https://openalex.org/W2770983033","https://openalex.org/W2808610674","https://openalex.org/W2884943532","https://openalex.org/W2885229294","https://openalex.org/W2899867782","https://openalex.org/W2907492528","https://openalex.org/W2951739649","https://openalex.org/W2981316968","https://openalex.org/W3013288409","https://openalex.org/W3047927730","https://openalex.org/W3103008448","https://openalex.org/W3117084002","https://openalex.org/W3168396907","https://openalex.org/W3179922387","https://openalex.org/W3217387659","https://openalex.org/W3217673092","https://openalex.org/W4213236868","https://openalex.org/W4213277551","https://openalex.org/W4288902530","https://openalex.org/W4297200000","https://openalex.org/W4297458751","https://openalex.org/W4300526689","https://openalex.org/W4367675086","https://openalex.org/W4383302735","https://openalex.org/W4386620529","https://openalex.org/W4386946778","https://openalex.org/W4388000718","https://openalex.org/W4388870409","https://openalex.org/W4391296859","https://openalex.org/W4394773567","https://openalex.org/W4394841745","https://openalex.org/W4401812687","https://openalex.org/W4408682802","https://openalex.org/W6815805937"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W4405124681","https://openalex.org/W1533177136","https://openalex.org/W4380994516"],"abstract_inverted_index":{"Circular":[0],"RNAs":[1,22,37],"play":[2],"a":[3,44,107],"crucial":[4],"role":[5],"in":[6,13,87,153],"cell":[7],"development":[8],"and":[9,32,38,60,117],"serve":[10],"as":[11],"biomarkers":[12],"many":[14,20,64],"diseases.":[15],"Nevertheless,":[16],"the":[17,84,94,97,99,113,140,146,154],"function":[18,26],"of":[19,96],"circular":[21],"remains":[23],"unknown.":[24],"This":[25],"can":[27],"be":[28],"inferred":[29],"from":[30],"sponging":[31],"silencing":[33],"interactions":[34,56,62],"with":[35,139],"micro":[36],"messenger":[39],"RNAs.":[40],"We":[41,110],"recently":[42],"proposed":[43],"network-based":[45],"circRNA":[46],"functional":[47,90],"annotation":[48,156],"tool,":[49],"circGPA.":[50],"However,":[51],"validation":[52],"data":[53,81],"for":[54],"RNA":[55],"are":[57],"often":[58],"sparse":[59],"predicted":[61],"contain":[63],"false":[65],"positives.":[66],"To":[67,92],"address":[68],"this":[69],"issue,":[70],"we":[71,149],"propose":[72],"an":[73],"extended":[74],"algorithm":[75,123],"named":[76],"circGPAcorr,":[77],"which":[78],"uses":[79],"expression":[80,131],"to":[82,105],"weight":[83],"interactions,":[85],"resulting":[86],"more":[88],"precise":[89],"annotation.":[91],"assess":[93],"significance":[95],"results,":[98],"p-value":[100],"is":[101,115,124],"calculated":[102],"using":[103],"reduction":[104],"circGPA,":[106],"generating-polynomial-based":[108],"method.":[109],"show":[111],"that":[112,137],"problem":[114],"#P-hard,":[116],"thus":[118],"computationally":[119],"difficult.":[120],"The":[121],"circGPAcorr":[122],"tested":[125],"on":[126,142],"publicly":[127],"available":[128],"myelodysplastic":[129,143],"syndromes":[130],"data,":[132],"providing":[133],"gene":[134],"ontology":[135],"annotations":[136],"align":[138],"literature":[141],"syndromes.":[144],"At":[145],"same":[147],"time,":[148],"demonstrate":[150],"its":[151],"performance":[152],"circRNA-disease":[155],"task.":[157]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
