{"id":"https://openalex.org/W4225014121","doi":"https://doi.org/10.1109/tcbb.2022.3170367","title":"MCNN: Multiple Convolutional Neural Networks for RNA-Protein Binding Sites Prediction","display_name":"MCNN: Multiple Convolutional Neural Networks for RNA-Protein Binding Sites Prediction","publication_year":2022,"publication_date":"2022-04-26","ids":{"openalex":"https://openalex.org/W4225014121","doi":"https://doi.org/10.1109/tcbb.2022.3170367","pmid":"https://pubmed.ncbi.nlm.nih.gov/35471886"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3170367","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3170367","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5036870534","display_name":"Zhengsen Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengsen Pan","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060143865","display_name":"Shusen Zhou","orcid":"https://orcid.org/0000-0002-1081-2542"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shusen Zhou","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":"https://orcid.org/0000-0002-1081-2542","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100462440","display_name":"Hailin Zou","orcid":"https://orcid.org/0000-0003-3000-4945"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hailin Zou","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":"https://orcid.org/0000-0003-3000-4945","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001777432","display_name":"Chanjuan Liu","orcid":"https://orcid.org/0000-0003-3686-0451"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chanjuan Liu","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005413901","display_name":"Mujun Zang","orcid":"https://orcid.org/0000-0001-5868-6023"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mujun Zang","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":"https://orcid.org/0000-0001-5868-6023","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392605","display_name":"Tong Liu","orcid":"https://orcid.org/0000-0001-5497-8117"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":"https://orcid.org/0000-0001-5497-8117","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100686407","display_name":"Qingjun Wang","orcid":"https://orcid.org/0009-0004-3516-1514"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingjun Wang","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, China","institution_ids":["https://openalex.org/I182707071"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7796,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68477526,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"2","first_page":"1180","last_page":"1187"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9997000098228455,"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":0.9994999766349792,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6854836940765381},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6410919427871704},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5508496761322021},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5229737758636475},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41624945402145386},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4126695394515991},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10426512360572815},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06054452061653137}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6854836940765381},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6410919427871704},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5508496761322021},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5229737758636475},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41624945402145386},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4126695394515991},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10426512360572815},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06054452061653137},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3170367","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3170367","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35471886","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35471886","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2570003996","display_name":null,"funder_award_id":"61300155","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3445548413","display_name":null,"funder_award_id":"ZR2020MF134","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1951403192","https://openalex.org/W1965286266","https://openalex.org/W1997535872","https://openalex.org/W2025150647","https://openalex.org/W2039816251","https://openalex.org/W2041440237","https://openalex.org/W2041509376","https://openalex.org/W2053003053","https://openalex.org/W2103375140","https://openalex.org/W2104806799","https://openalex.org/W2105694586","https://openalex.org/W2112796928","https://openalex.org/W2132863465","https://openalex.org/W2789367970","https://openalex.org/W2799487719","https://openalex.org/W2919115771","https://openalex.org/W2950463913","https://openalex.org/W2951748044","https://openalex.org/W3036197410","https://openalex.org/W3183966140"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4313906399","https://openalex.org/W4321487865","https://openalex.org/W2811106690","https://openalex.org/W4239306820","https://openalex.org/W2947043951","https://openalex.org/W2318112981","https://openalex.org/W4312417841","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"Computational":[0],"prediction":[1],"of":[2,40,101,140,175],"the":[3,37,130,137],"RBP":[4],"bound":[5],"sites":[6,62,121,170],"using":[7],"features":[8,127],"learned":[9],"from":[10,75,160],"existing":[11],"annotation":[12],"knowledge":[13],"is":[14,43,163],"an":[15,164],"effective":[16,165],"method":[17,166,179],"because":[18],"high-throughput":[19],"experiments":[20],"are":[21],"complex,":[22],"expensive":[23],"and":[24,128],"time-consuming.":[25],"Many":[26],"methods":[27,154],"have":[28],"been":[29],"proposed":[30,145,177],"to":[31],"predict":[32],"RNA-protein":[33,60,119,168],"binding":[34,61,99,120,126,169],"sites.":[35],"However,":[36],"partial":[38],"information":[39,73,117,138],"RNA":[41,71,87,114],"sequence":[42,72,116,125],"not":[44],"fully":[45],"used.":[46],"In":[47],"this":[48],"study,":[49],"we":[50],"propose":[51],"multiple":[52,65,83,107],"convolutional":[53,66],"neural":[54,67],"networks":[55,68],"(MCNN)":[56],"method,":[57],"which":[58,123,162],"predicts":[59,129],"by":[63,70,90,103],"integrating":[64],"constructed":[69],"extracted":[74,89],"windows":[76],"with":[77,132,152],"different":[78,91],"lengths.":[79,93],"First,":[80],"MCNN":[81,95,111,146,178],"trains":[82],"CNNs":[84,108],"base":[85,115],"on":[86,155],"sequences":[88],"window":[92],"Second,":[94],"can":[96,180],"extract":[97],"more":[98],"patterns":[100],"RBPs":[102],"combining":[104],"these":[105],"trained":[106],"previously.":[109],"Third,":[110],"only":[112],"uses":[113],"for":[118,167],"prediction,":[122],"extracts":[124],"result":[131],"same":[133],"architecture.":[134],"This":[135],"avoids":[136],"loss":[139],"feature":[141],"extraction":[142],"step.":[143],"Our":[144],"demonstrates":[147],"a":[148,156],"competitive":[149],"performance":[150],"comparing":[151],"other":[153],"large-scale":[157],"dataset":[158],"derived":[159],"CLIP-seq,":[161],"prediction.":[171],"The":[172],"source":[173],"code":[174],"our":[176],"be":[181],"found":[182],"in":[183],"https://github.com/biomg/MCNN.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
