{"id":"https://openalex.org/W4412191260","doi":"https://doi.org/10.1186/s12859-025-06197-y","title":"RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA\u2013protein binding sites prediction","display_name":"RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA\u2013protein binding sites prediction","publication_year":2025,"publication_date":"2025-07-11","ids":{"openalex":"https://openalex.org/W4412191260","doi":"https://doi.org/10.1186/s12859-025-06197-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/40646507"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06197-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06197-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06197-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/s12859-025-06197-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076402089","display_name":"Jiangbo Zhang","orcid":"https://orcid.org/0000-0002-5546-7949"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiangbo Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082796473","display_name":"Yunhui Peng","orcid":"https://orcid.org/0000-0001-9768-4127"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunhui Peng","raw_affiliation_strings":["School of Physics Science and Technology, Central China Normal University, Wuhan, 430000, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics Science and Technology, Central China Normal University, Wuhan, 430000, Hubei, China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061028143","display_name":"Feifei Cui","orcid":"https://orcid.org/0000-0001-7055-3813"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feifei Cui","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353028","display_name":"Zilong Zhang","orcid":"https://orcid.org/0000-0002-4934-1258"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilong Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016741865","display_name":"Shankai Yan","orcid":"https://orcid.org/0000-0003-0369-4979"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shankai Yan","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China. skyan@hainanu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China. skyan@hainanu.edu.cn","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063023682","display_name":"Qingchen Zhang","orcid":"https://orcid.org/0000-0003-1160-9922"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingchen Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China. zhangqingchen@hainanu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, 570100, Hainan, China. zhangqingchen@hainanu.edu.cn","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2652,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.79001559,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"176","last_page":"176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10604","display_name":"RNA Research and Splicing","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"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9955000281333923,"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/rna","display_name":"RNA","score":0.5939586758613586},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5136813521385193},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5135160088539124},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.47359874844551086},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39046767354011536},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37150755524635315},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28114286065101624},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2620159983634949},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2457534670829773}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5939586758613586},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5136813521385193},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5135160088539124},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.47359874844551086},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39046767354011536},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37150755524635315},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28114286065101624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2620159983634949},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2457534670829773}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001517","descriptor_name":"Coleoptera","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001517","descriptor_name":"Coleoptera","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001517","descriptor_name":"Coleoptera","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06197-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06197-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06197-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40646507","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40646507","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:doaj.org/article:1297251989f847b28a441da4baf663b9","is_oa":true,"landing_page_url":"https://doaj.org/article/1297251989f847b28a441da4baf663b9","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":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-21 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12247420","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12247420","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06197-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06197-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06197-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6297944654","display_name":null,"funder_award_id":"62202128","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/F4320323370","display_name":"Hainan University","ror":"https://ror.org/03q648j11"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412191260.pdf","grobid_xml":"https://content.openalex.org/works/W4412191260.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1941339056","https://openalex.org/W2086561953","https://openalex.org/W2799487719","https://openalex.org/W2799513065","https://openalex.org/W2802378359","https://openalex.org/W2958675005","https://openalex.org/W3004587664","https://openalex.org/W3007581139","https://openalex.org/W3036197410","https://openalex.org/W3134329288","https://openalex.org/W3165755255","https://openalex.org/W3202149807","https://openalex.org/W3203512539","https://openalex.org/W4221118730","https://openalex.org/W4225014121","https://openalex.org/W4226120253","https://openalex.org/W4286377464","https://openalex.org/W4296293027","https://openalex.org/W4296935222","https://openalex.org/W4321484068","https://openalex.org/W4323065787","https://openalex.org/W4323317329","https://openalex.org/W4394977592","https://openalex.org/W4406236666","https://openalex.org/W4408333202"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W4379233576","https://openalex.org/W2753172052","https://openalex.org/W3080365360","https://openalex.org/W1935063092"],"abstract_inverted_index":{"RNA-binding":[0],"proteins":[1],"(RBPs)":[2],"play":[3],"crucial":[4],"roles":[5],"in":[6,229],"gene":[7],"regulation.":[8],"Their":[9],"dysregulation":[10],"has":[11,226],"been":[12],"increasingly":[13],"linked":[14],"to":[15,54,169],"neurodegenerative":[16],"diseases,":[17],"liver":[18],"cancer,":[19],"and":[20,36,51,118,192,206,217,233],"lung":[21],"cancer.":[22],"Although":[23],"experimental":[24,210],"methods":[25],"like":[26],"CLIP-seq":[27,193],"accurately":[28],"identify":[29],"RNA-protein":[30,222],"binding":[31,150,185,204,223],"sites,":[32],"they":[33],"are":[34,63,76],"time-consuming":[35],"costly.":[37],"To":[38,85],"address":[39],"this,":[40],"we":[41,89],"propose":[42],"RMDNet-a":[43],"deep":[44],"learning":[45],"framework":[46],"that":[47,110,199],"integrates":[48],"CNN,":[49],"CNN-Transformer,":[50],"ResNet":[52],"branches":[53],"capture":[55],"features":[56,62],"at":[57],"multiple":[58,121],"sequence":[59],"scales.":[60],"These":[61],"fused":[64],"with":[65,83,209],"structural":[66],"representations":[67],"derived":[68],"from":[69,152],"RNA":[70],"secondary":[71],"structure":[72],"graphs.":[73],"The":[74,196,237],"graphs":[75],"processed":[77],"using":[78,187],"a":[79,188,215],"graph":[80],"neural":[81],"network":[82],"DiffPool.":[84],"optimize":[86],"feature":[87],"integration,":[88],"incorporate":[90],"an":[91],"improved":[92],"dung":[93],"beetle":[94],"optimization":[95],"algorithm,":[96],"which":[97],"adaptively":[98],"assigns":[99],"fusion":[100],"weights":[101],"during":[102],"inference.":[103],"Evaluations":[104],"on":[105,135,178,181],"the":[106,124,138,153,166,200],"RBP-24":[107],"benchmark":[108],"show":[109],"RMDNet":[111,213],"outperforms":[112],"state-of-the-art":[113],"models":[114],"including":[115],"GraphProt,":[116],"DeepRKE,":[117],"DeepDW":[119],"across":[120],"metrics.":[122],"On":[123],"RBP-31":[125],"dataset,":[126],"it":[127],"demonstrates":[128],"strong":[129],"generalization":[130],"ability,":[131],"while":[132],"ablation":[133],"studies":[134],"RBPsuite2.0":[136],"validate":[137],"contributions":[139],"of":[140],"individual":[141],"modules.":[142],"We":[143],"assess":[144],"biological":[145],"interpretability":[146],"by":[147],"extracting":[148],"candidate":[149],"motifs":[151,158],"first-layer":[154],"CNN":[155],"kernels.":[156],"Several":[157],"closely":[159],"match":[160],"experimentally":[161],"validated":[162],"RBP":[163],"motifs,":[164],"confirming":[165],"model's":[167],"capacity":[168],"learn":[170],"biologically":[171],"meaningful":[172],"patterns.":[173],"A":[174],"downstream":[175],"case":[176],"study":[177],"YTHDF1":[179],"focuses":[180],"analyzing":[182],"interpretable":[183,218],"spatial":[184,207],"patterns,":[186],"large-scale":[189],"prediction":[190],"dataset":[191],"peak":[194],"alignment.":[195],"results":[197],"confirm":[198],"model":[201],"captures":[202],"localized":[203],"signals":[205],"consistency":[208],"annotations.":[211],"Overall,":[212],"is":[214,240],"robust":[216],"tool":[219],"for":[220],"predicting":[221],"sites.":[224],"It":[225],"broad":[227],"potential":[228],"disease":[230],"mechanism":[231],"research":[232],"therapeutic":[234],"target":[235],"discovery.":[236],"source":[238],"code":[239],"available":[241],"https://github.com/cskyan/RMDNet":[242],".":[243]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
