{"id":"https://openalex.org/W4378783433","doi":"https://doi.org/10.1186/s12859-023-05352-7","title":"CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization","display_name":"CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization","publication_year":2023,"publication_date":"2023-05-30","ids":{"openalex":"https://openalex.org/W4378783433","doi":"https://doi.org/10.1186/s12859-023-05352-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/37254080"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05352-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05352-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05352-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05352-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071008670","display_name":"Chao Cao","orcid":"https://orcid.org/0000-0001-6730-9422"},"institutions":[{"id":"https://openalex.org/I18570673","display_name":"Guangxi University of Science and Technology","ror":"https://ror.org/02fj6b627","country_code":"CN","type":"education","lineage":["https://openalex.org/I18570673"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Cao","raw_affiliation_strings":["School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China","institution_ids":["https://openalex.org/I18570673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111156960","display_name":"Shuhong Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I18570673","display_name":"Guangxi University of Science and Technology","ror":"https://ror.org/02fj6b627","country_code":"CN","type":"education","lineage":["https://openalex.org/I18570673"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuhong Yang","raw_affiliation_strings":["Key Laboratory of Guangxi Universities on Intelligent Computing and Distributed Information Processing, Guangxi University of Science and Technology, Liuzhou, China. ysh@hzu.edu.cn","Key Laboratory of Guangxi Universities on Intelligent Computing and Distributed Information Processing, Guangxi University of Science and Technology, Liuzhou, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Guangxi Universities on Intelligent Computing and Distributed Information Processing, Guangxi University of Science and Technology, Liuzhou, China. ysh@hzu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Key Laboratory of Guangxi Universities on Intelligent Computing and Distributed Information Processing, Guangxi University of Science and Technology, Liuzhou, China","institution_ids":["https://openalex.org/I18570673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101681183","display_name":"Mengli Li","orcid":"https://orcid.org/0000-0001-5881-2763"},"institutions":[{"id":"https://openalex.org/I4387153915","display_name":"Guilin University","ror":"https://ror.org/00jbpxw47","country_code":null,"type":"education","lineage":["https://openalex.org/I4387153915"]},{"id":"https://openalex.org/I38706770","display_name":"Guilin University of Technology","ror":"https://ror.org/03z391397","country_code":"CN","type":"education","lineage":["https://openalex.org/I38706770"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengli Li","raw_affiliation_strings":["School of Technology, Guilin University, Guilin, China"],"affiliations":[{"raw_affiliation_string":"School of Technology, Guilin University, Guilin, China","institution_ids":["https://openalex.org/I38706770","https://openalex.org/I4387153915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007074537","display_name":"Chungui Li","orcid":null},"institutions":[{"id":"https://openalex.org/I18570673","display_name":"Guangxi University of Science and Technology","ror":"https://ror.org/02fj6b627","country_code":"CN","type":"education","lineage":["https://openalex.org/I18570673"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chungui Li","raw_affiliation_strings":["School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China. liza4323@163.com","School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China. liza4323@163.com","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China","institution_ids":["https://openalex.org/I18570673"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111156960"],"corresponding_institution_ids":["https://openalex.org/I18570673"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.031,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.9154489,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"220","last_page":"220"},"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":0.9952999949455261,"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":0.9749000072479248,"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":0.798786461353302},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5607389211654663},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5261147618293762},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5064882040023804},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.42972663044929504},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.41719821095466614},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.41507619619369507},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4011651277542114},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.381692111492157},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08269357681274414}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.798786461353302},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5607389211654663},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5261147618293762},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5064882040023804},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.42972663044929504},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.41719821095466614},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.41507619619369507},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4011651277542114},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.381692111492157},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08269357681274414},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05352-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05352-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05352-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37254080","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37254080","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10230723","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10230723","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10230723/pdf/12859_2023_Article_5352.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:dd7f668554a843aeb0965586c62639c4","is_oa":true,"landing_page_url":"https://doaj.org/article/dd7f668554a843aeb0965586c62639c4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-19 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05352-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05352-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05352-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/1","score":0.47999998927116394,"display_name":"No poverty"}],"awards":[{"id":"https://openalex.org/G1210156861","display_name":null,"funder_award_id":"62061003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2802911279","display_name":null,"funder_award_id":"Young","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4020255992","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4470798686","display_name":null,"funder_award_id":"62062010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7033253288","display_name":null,"funder_award_id":"Grants","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"},{"id":"https://openalex.org/F4320323848","display_name":"Huizhou University","ror":null},{"id":"https://openalex.org/F4320327602","display_name":"Middle-aged and Young Teachers' Basic Ability Promotion Project of Guangxi","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4378783433.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1614298861","https://openalex.org/W1866220599","https://openalex.org/W1967791012","https://openalex.org/W2058835062","https://openalex.org/W2115662330","https://openalex.org/W2131744502","https://openalex.org/W2210577735","https://openalex.org/W2284415752","https://openalex.org/W2419834209","https://openalex.org/W2622079695","https://openalex.org/W2737722001","https://openalex.org/W2783029521","https://openalex.org/W2906592796","https://openalex.org/W2931923037","https://openalex.org/W2951748044","https://openalex.org/W2963212250","https://openalex.org/W2963542740","https://openalex.org/W2969715183","https://openalex.org/W2973586775","https://openalex.org/W2986421215","https://openalex.org/W2991019646","https://openalex.org/W3026425509","https://openalex.org/W3095596981","https://openalex.org/W3119787379","https://openalex.org/W3121523901","https://openalex.org/W3125993166","https://openalex.org/W3127238141","https://openalex.org/W3152830765","https://openalex.org/W3190152617","https://openalex.org/W3202624577","https://openalex.org/W4206826027","https://openalex.org/W4207079529","https://openalex.org/W4210444533","https://openalex.org/W4213019189","https://openalex.org/W4213099919","https://openalex.org/W4226085666","https://openalex.org/W4311225868","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W2140186469","https://openalex.org/W4390421286","https://openalex.org/W4280563792","https://openalex.org/W4318719684","https://openalex.org/W4389724018","https://openalex.org/W4318559728","https://openalex.org/W3183136280","https://openalex.org/W2775233965","https://openalex.org/W3114716045","https://openalex.org/W4360995913"],"abstract_inverted_index":{"In":[0],"conclusion,":[1],"CircSSNN":[2],"can":[3],"serve":[4],"as":[5],"an":[6],"appealing":[7],"circRNA-RBP":[8],"identification":[9,13],"tool":[10],"with":[11],"good":[12],"performance,":[14],"excellent":[15],"scalability,":[16],"and":[17],"wide":[18],"application":[19],"scope":[20],"without":[21],"the":[22,34],"need":[23],"for":[24,38],"task-oriented":[25],"fine-tuning":[26],"of":[27],"parameters,":[28],"which":[29],"is":[30],"expected":[31],"to":[32],"reduce":[33],"professional":[35],"threshold":[36],"required":[37],"hyperparameter":[39],"tuning":[40],"in":[41],"bioinformatics":[42],"analysis.":[43]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
