{"id":"https://openalex.org/W3172858537","doi":"https://doi.org/10.1093/bioinformatics/btab435","title":"AQUARIUM: accurate quantification of circular isoforms using model-based strategy","display_name":"AQUARIUM: accurate quantification of circular isoforms using model-based strategy","publication_year":2021,"publication_date":"2021-06-08","ids":{"openalex":"https://openalex.org/W3172858537","doi":"https://doi.org/10.1093/bioinformatics/btab435","mag":"3172858537","pmid":"https://pubmed.ncbi.nlm.nih.gov/34115093"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab435","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab435","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/A5080791569","display_name":"Guoxia Wen","orcid":"https://orcid.org/0000-0001-6544-8242"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]},{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoxia Wen","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023236942","display_name":"Musheng Li","orcid":null},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Musheng Li","raw_affiliation_strings":["Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine , Reno, Nevada 89557, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine , Reno, Nevada 89557, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052523104","display_name":"Fuyu Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuyu Li","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103980331","display_name":"Zengyan Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]},{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zengyan Yang","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055436613","display_name":"Tong Zhou","orcid":"https://orcid.org/0000-0003-2361-1931"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tong Zhou","raw_affiliation_strings":["Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine , Reno, Nevada 89557, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine , Reno, Nevada 89557, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102781094","display_name":"Wanjun Gu","orcid":"https://orcid.org/0000-0003-4501-0539"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]},{"id":"https://openalex.org/I131434179","display_name":"Nanjing University of Chinese Medicine","ror":"https://ror.org/04523zj19","country_code":"CN","type":"education","lineage":["https://openalex.org/I131434179"]},{"id":"https://openalex.org/I4210117216","display_name":"Jiangsu Provincial Center for Disease Control and Prevention","ror":"https://ror.org/02ey6qs66","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210117216"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wanjun Gu","raw_affiliation_strings":["Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine , Nanjing, Jiangsu 210023, China","School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine , Nanjing, Jiangsu 210023, China","State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China"],"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine , Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210117216"]},{"raw_affiliation_string":"School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine , Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I131434179"]},{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University , Nanjing, Jiangsu 210096, China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5055436613","https://openalex.org/A5102781094"],"corresponding_institution_ids":["https://openalex.org/I131434179","https://openalex.org/I134113660","https://openalex.org/I4210117216","https://openalex.org/I4387154005","https://openalex.org/I76569877"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2413,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.52019824,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"37","issue":"24","first_page":"4879","last_page":"4881"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","score":1.0,"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":1.0,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9945999979972839,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/circular-rna","display_name":"Circular RNA","score":0.7446949481964111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6179209351539612},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5278194546699524},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.510330855846405},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5101814270019531},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.508562445640564},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4898766875267029},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.4745510518550873},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38833528757095337},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20283982157707214},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19075363874435425},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.16827711462974548},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15770366787910461},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.07683056592941284}],"concepts":[{"id":"https://openalex.org/C2775893923","wikidata":"https://www.wikidata.org/wiki/Q17113455","display_name":"Circular RNA","level":4,"score":0.7446949481964111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6179209351539612},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5278194546699524},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.510330855846405},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5101814270019531},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.508562445640564},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4898766875267029},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.4745510518550873},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38833528757095337},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20283982157707214},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19075363874435425},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.16827711462974548},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15770366787910461},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.07683056592941284}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","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},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab435","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab435","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:34115093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34115093","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":[{"id":"https://metadata.un.org/sdg/14","score":0.4000000059604645,"display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G1730841757","display_name":null,"funder_award_id":"61571109","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2065456227","display_name":null,"funder_award_id":"2018YFC1314902","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3692157422","display_name":null,"funder_award_id":"2242017K3DN04","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7181415362","display_name":null,"funder_award_id":"2018YFC1314900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1566841623","https://openalex.org/W2105875994","https://openalex.org/W2126938291","https://openalex.org/W2147625377","https://openalex.org/W2464424326","https://openalex.org/W2592207155","https://openalex.org/W2592811885","https://openalex.org/W2599812844","https://openalex.org/W2782794356","https://openalex.org/W2909481667","https://openalex.org/W2996796392","https://openalex.org/W2998081701","https://openalex.org/W3003850032","https://openalex.org/W3020855961","https://openalex.org/W3093781399","https://openalex.org/W3095098757","https://openalex.org/W3118996612","https://openalex.org/W3135065548","https://openalex.org/W6719195283","https://openalex.org/W6784436155","https://openalex.org/W6791767855"],"related_works":["https://openalex.org/W1540936366","https://openalex.org/W2079625624","https://openalex.org/W2004254765","https://openalex.org/W2126407448","https://openalex.org/W2906670751","https://openalex.org/W2169001731","https://openalex.org/W4365151374","https://openalex.org/W2900469846","https://openalex.org/W3113577179","https://openalex.org/W4207033213"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}