{"id":"https://openalex.org/W4409077135","doi":"https://doi.org/10.1109/tcbbio.2025.3556876","title":"Protein-Binding RNA Prediction Based on Integrated Sequence-Structure-Function Pre-Training","display_name":"Protein-Binding RNA Prediction Based on Integrated Sequence-Structure-Function Pre-Training","publication_year":2025,"publication_date":"2025-04-01","ids":{"openalex":"https://openalex.org/W4409077135","doi":"https://doi.org/10.1109/tcbbio.2025.3556876","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811318"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3556876","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3556876","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 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":null,"display_name":"Lin Gan","orcid":"https://orcid.org/0009-0005-1337-4188"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Gan","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0009-0005-1337-4188","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061601272","display_name":"Xinyi Wang","orcid":"https://orcid.org/0000-0001-8740-0469"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyi Wang","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-8740-0469","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065789169","display_name":"Yi Zhou","orcid":"https://orcid.org/0000-0001-9024-7514"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhou","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]},{"author_position":"last","author":{"id":null,"display_name":"Min Zhu","orcid":"https://orcid.org/0000-0002-5664-1558"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Zhu","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0002-5664-1558","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03826113,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","first_page":"1441","last_page":"1452"},"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":0.9995999932289124,"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":0.9987999796867371,"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/sequence","display_name":"Sequence (biology)","score":0.6264902353286743},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6216968297958374},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5129958987236023},{"id":"https://openalex.org/keywords/training","display_name":"Training (meteorology)","score":0.4845110774040222},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.42973199486732483},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4213283658027649},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.42042970657348633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.413432776927948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34754663705825806},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3433910012245178},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2761850655078888},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2420150637626648},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13328292965888977},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10801130533218384},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09090444445610046}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6264902353286743},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6216968297958374},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5129958987236023},{"id":"https://openalex.org/C2777211547","wikidata":"https://www.wikidata.org/wiki/Q17141490","display_name":"Training (meteorology)","level":2,"score":0.4845110774040222},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.42973199486732483},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4213283658027649},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.42042970657348633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.413432776927948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34754663705825806},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3433910012245178},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2761850655078888},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2420150637626648},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13328292965888977},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10801130533218384},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09090444445610046},{"id":"https://openalex.org/C153294291","wikidata":"https://www.wikidata.org/wiki/Q25261","display_name":"Meteorology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3556876","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3556876","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811318","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811318","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G6043036435","display_name":null,"funder_award_id":"62172289","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1842452185","https://openalex.org/W1969156759","https://openalex.org/W1997535872","https://openalex.org/W2009215595","https://openalex.org/W2102017611","https://openalex.org/W2103375140","https://openalex.org/W2154241726","https://openalex.org/W2159249646","https://openalex.org/W2159324718","https://openalex.org/W2336509392","https://openalex.org/W2801121099","https://openalex.org/W2805813392","https://openalex.org/W2896457183","https://openalex.org/W2917724292","https://openalex.org/W2951748044","https://openalex.org/W2954102902","https://openalex.org/W2962784628","https://openalex.org/W2980708516","https://openalex.org/W3014677172","https://openalex.org/W3036197410","https://openalex.org/W3041434156","https://openalex.org/W3046003662","https://openalex.org/W3081249922","https://openalex.org/W3112745729","https://openalex.org/W3120031819","https://openalex.org/W3125850677","https://openalex.org/W3127238141","https://openalex.org/W4225014121","https://openalex.org/W4225917625","https://openalex.org/W4290546063","https://openalex.org/W4294811379","https://openalex.org/W4309890087","https://openalex.org/W4323065787","https://openalex.org/W4385245566","https://openalex.org/W4388488977","https://openalex.org/W4391892621","https://openalex.org/W6755207826"],"related_works":["https://openalex.org/W230091440","https://openalex.org/W2233261550","https://openalex.org/W2810751659","https://openalex.org/W258997015","https://openalex.org/W2997094352","https://openalex.org/W4412817058","https://openalex.org/W3216976533","https://openalex.org/W100620283","https://openalex.org/W2495260952","https://openalex.org/W4366179611"],"abstract_inverted_index":{"RNA":[0,79,128],"binding":[1,104],"proteins":[2],"(RBPs)":[3],"play":[4],"a":[5,59,66,89],"crucial":[6],"role":[7],"in":[8],"regulating":[9],"biological":[10],"functions":[11],"through":[12],"their":[13],"interactions":[14],"with":[15,65,99],"specific":[16],"RNAs,":[17],"significantly":[18],"impacting":[19],"various":[20],"life":[21],"processes.":[22],"High-throughput":[23],"experiments":[24],"provide":[25],"substantial":[26],"data,":[27],"facilitating":[28],"the":[29],"development":[30],"of":[31,113],"computational":[32],"predictions.":[33],"However,":[34],"current":[35],"methods":[36],"struggle":[37],"to":[38],"effectively":[39],"integrate":[40],"multi-level":[41,114],"semantic":[42,92],"information":[43,77],"and":[44,85,103,126],"require":[45],"enhanced":[46],"predictive":[47],"accuracy":[48],"on":[49,132],"small-sample":[50],"datasets.":[51,134],"To":[52],"address":[53],"these":[54],"limitations,":[55],"we":[56],"propose":[57],"MTP-RBP,":[58],"method":[60,71],"that":[61,119],"integrates":[62],"multi-task":[63],"pre-training":[64,107],"robust":[67],"pre-trained":[68],"encoder.":[69],"This":[70],"not":[72],"only":[73],"extracts":[74],"deep":[75],"contextual":[76],"from":[78],"sequences":[80],"but":[81],"also":[82],"incorporates":[83],"structural":[84],"functional":[86],"knowledge":[87],"for":[88],"more":[90],"comprehensive":[91],"representation.":[93],"By":[94],"enhancing":[95],"masked":[96],"language":[97,129],"modeling":[98],"secondary":[100],"structure":[101],"construction":[102],"function":[105],"prediction":[106],"tasks,":[108],"MTP-RBP":[109,120],"enables":[110],"better":[111],"fusion":[112],"features.":[115],"Experimental":[116],"results":[117],"show":[118],"achieves":[121],"state-of-the-art":[122],"performance,":[123],"surpassing":[124],"baseline":[125],"existing":[127],"models,":[130],"particularly":[131],"small":[133]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}