{"id":"https://openalex.org/W4213072029","doi":"https://doi.org/10.1093/bioinformatics/btac106","title":"PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning","display_name":"PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning","publication_year":2022,"publication_date":"2022-02-15","ids":{"openalex":"https://openalex.org/W4213072029","doi":"https://doi.org/10.1093/bioinformatics/btac106","pmid":"https://pubmed.ncbi.nlm.nih.gov/35176130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac106","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac106","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/A5112480733","display_name":"Jun Zhang","orcid":"https://orcid.org/0009-0003-8185-4517"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101667939","display_name":"Ke Yan","orcid":"https://orcid.org/0000-0002-5326-4267"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ke Yan","raw_affiliation_strings":["School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101895423","display_name":"Qingcai Chen","orcid":"https://orcid.org/0000-0001-8473-7293"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingcai Chen","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"],"raw_orcid":"https://orcid.org/0000-0001-8473-7293","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100395591","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0003-3685-9469"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Liu","raw_affiliation_strings":["Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology , Beijing 100081, China","School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081, China","School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"],"raw_orcid":"https://orcid.org/0000-0003-3685-9469","affiliations":[{"raw_affiliation_string":"Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology , Beijing 100081, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100395591"],"corresponding_institution_ids":["https://openalex.org/I125839683","https://openalex.org/I204983213"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.1935,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.88539242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"38","issue":"8","first_page":"2135","last_page":"2143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8762000203132629,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8762000203132629,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0737999975681305,"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":0.017999999225139618,"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":0.6074530482292175},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.5992840528488159},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5656335949897766},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5267110466957092},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.46722185611724854},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4382937252521515},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4172550439834595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3732382655143738},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3142141103744507},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29926979541778564},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1631113588809967},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07256856560707092}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6074530482292175},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.5992840528488159},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5656335949897766},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5267110466957092},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.46722185611724854},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4382937252521515},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4172550439834595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3732382655143738},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3142141103744507},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29926979541778564},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1631113588809967},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07256856560707092}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac106","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac106","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:35176130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35176130","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":[{"display_name":"Life in Land","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3267686570","display_name":null,"funder_award_id":"62102030","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3425444037","display_name":null,"funder_award_id":"2018AAA0100100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6876496325","display_name":null,"funder_award_id":"JQ19019","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1593880960","https://openalex.org/W1892469892","https://openalex.org/W1984574291","https://openalex.org/W1997535872","https://openalex.org/W2033253992","https://openalex.org/W2046792302","https://openalex.org/W2055043387","https://openalex.org/W2062296203","https://openalex.org/W2067657160","https://openalex.org/W2096387274","https://openalex.org/W2103017472","https://openalex.org/W2125800162","https://openalex.org/W2130479394","https://openalex.org/W2143210482","https://openalex.org/W2148853951","https://openalex.org/W2156125289","https://openalex.org/W2158266834","https://openalex.org/W2158714788","https://openalex.org/W2182726182","https://openalex.org/W2253429366","https://openalex.org/W2336509392","https://openalex.org/W2480300184","https://openalex.org/W2521782266","https://openalex.org/W2528142478","https://openalex.org/W2561871078","https://openalex.org/W2582176104","https://openalex.org/W2748005921","https://openalex.org/W2766234610","https://openalex.org/W2777094228","https://openalex.org/W2781945186","https://openalex.org/W2782148675","https://openalex.org/W2785329615","https://openalex.org/W2850098960","https://openalex.org/W2889498145","https://openalex.org/W2914272550","https://openalex.org/W2949877712","https://openalex.org/W2951937481","https://openalex.org/W2952461195","https://openalex.org/W2969993699","https://openalex.org/W2972006361","https://openalex.org/W2982552606","https://openalex.org/W2984633739","https://openalex.org/W2989977616","https://openalex.org/W2990528340","https://openalex.org/W2997708032","https://openalex.org/W2999044305","https://openalex.org/W3046003662","https://openalex.org/W3086768476","https://openalex.org/W3112172360","https://openalex.org/W3116452748","https://openalex.org/W3124828689","https://openalex.org/W3128972055","https://openalex.org/W3133178585","https://openalex.org/W3136918052","https://openalex.org/W3142241514","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W3201126466","https://openalex.org/W4282827391","https://openalex.org/W2147993839","https://openalex.org/W1840103016","https://openalex.org/W2898732673","https://openalex.org/W54859794","https://openalex.org/W2057323302","https://openalex.org/W2028642547","https://openalex.org/W2410053581","https://openalex.org/W2569356794"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-binding":[1],"proteins":[2],"(RBPs)":[3],"play":[4],"crucial":[5],"roles":[6],"in":[7],"post-transcriptional":[8],"regulation.":[9],"Accurate":[10],"identification":[11],"of":[12,71,143,151],"RBPs":[13,39,64,112],"helps":[14],"to":[15,29,36,145],"understand":[16],"gene":[17],"expression,":[18],"regulation,":[19],"etc.":[20],"In":[21,51],"recent":[22],"years,":[23],"some":[24,41],"computational":[25,57,123],"methods":[26,34],"were":[27,75],"proposed":[28],"identify":[30,38,146],"RBPs.":[31,136],"However,":[32],"these":[33],"fail":[35],"accurately":[37],"from":[40,113],"specific":[42],"species":[43],"with":[44,79,88],"limited":[45],"data,":[46],"such":[47],"as":[48],"bacteria.":[49],"RESULTS:":[50],"this":[52],"study,":[53],"we":[54],"introduce":[55],"a":[56,131],"method":[58,133],"called":[59],"PreRBP-TL":[60,104,128,152],"for":[61,108,134],"identifying":[62,109,135],"species-specific":[63,91,111],"based":[65],"on":[66],"transfer":[67,96],"learning.":[68,97],"The":[69,98],"weights":[70],"the":[72,80,89,103,110,141,148],"prediction":[73],"model":[74],"initialized":[76],"by":[77,94],"pretraining":[78],"large":[81],"general":[82],"RBP":[83],"dataset":[84,93],"and":[85,118],"then":[86],"fine-tuned":[87],"small":[90],"RPB":[92],"using":[95],"experimental":[99],"results":[100],"show":[101],"that":[102],"achieves":[105],"better":[106],"performance":[107],"Human,":[114],"Arabidopsis,":[115],"Escherichia":[116],"coli":[117],"Salmonella,":[119],"outperforming":[120],"eight":[121],"state-of-the-art":[122],"methods.":[124],"It":[125],"is":[126],"anticipated":[127],"will":[129],"become":[130],"useful":[132],"AVAILABILITY":[137],"AND":[138],"IMPLEMENTATION:":[139],"For":[140],"convenience":[142],"researchers":[144],"RBPs,":[147],"web":[149],"server":[150],"was":[153],"established,":[154],"freely":[155],"available":[156,164],"at":[157,165],"http://bliulab.net/PreRBP-TL.":[158],"SUPPLEMENTARY":[159],"INFORMATION:":[160],"Supplementary":[161],"data":[162],"are":[163],"Bioinformatics":[166],"online.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":8}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
