{"id":"https://openalex.org/W7130601810","doi":"https://doi.org/10.1093/bioinformatics/btag088","title":"A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins","display_name":"A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins","publication_year":2026,"publication_date":"2026-02-19","ids":{"openalex":"https://openalex.org/W7130601810","doi":"https://doi.org/10.1093/bioinformatics/btag088","pmid":"https://pubmed.ncbi.nlm.nih.gov/41712756"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag088","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag088","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000688174","display_name":"Serena Rosignoli","orcid":"https://orcid.org/0000-0002-0164-8998"},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Serena Rosignoli","raw_affiliation_strings":["Centre for Regenerative Medicine \u201cStefano Ferrari\u201d, Department of Life Sciences, University of Modena and Reggio Emilia , Modena 41125,"],"affiliations":[{"raw_affiliation_string":"Centre for Regenerative Medicine \u201cStefano Ferrari\u201d, Department of Life Sciences, University of Modena and Reggio Emilia , Modena 41125,","institution_ids":["https://openalex.org/I122346577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018360998","display_name":"S. Taraglio","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sophie Taraglio","raw_affiliation_strings":["Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014577770","display_name":"Francesco Di Luzio","orcid":"https://orcid.org/0009-0001-4279-3761"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Di Luzio","raw_affiliation_strings":["Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome , Rome 00184,"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome , Rome 00184,","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093838917","display_name":"Elisa Lustrino","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Elisa Lustrino","raw_affiliation_strings":["Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010273076","display_name":"Dario F. Marzella","orcid":"https://orcid.org/0000-0002-0043-3055"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Dario Marzella","raw_affiliation_strings":["Medical BioSciences Department, Radboud University Medical Center , Nijmegen 6500,"],"affiliations":[{"raw_affiliation_string":"Medical BioSciences Department, Radboud University Medical Center , Nijmegen 6500,","institution_ids":["https://openalex.org/I2802934949","https://openalex.org/I145872427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126406912","display_name":"Arne Elofsson","orcid":null},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Arne Elofsson","raw_affiliation_strings":["Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University , Solna 171 21,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University , Solna 171 21,","institution_ids":["https://openalex.org/I2800139495"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Massimo Panella","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimo Panella","raw_affiliation_strings":["Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome , Rome 00184,"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome , Rome 00184,","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067090345","display_name":"Alessandro Paiardini","orcid":"https://orcid.org/0000-0001-9078-7545"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Paiardini","raw_affiliation_strings":["Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , Rome 00185,","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5000688174"],"corresponding_institution_ids":["https://openalex.org/I122346577"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.40837891,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.3319999873638153,"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":0.3319999873638153,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.1891999989748001,"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/T12610","display_name":"RNA regulation and disease","score":0.11680000275373459,"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/deep-learning","display_name":"Deep learning","score":0.819599986076355},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.484499990940094},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.35580000281333923},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.33239999413490295},{"id":"https://openalex.org/keywords/human-proteins","display_name":"Human proteins","score":0.2825999855995178}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.819599986076355},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6861000061035156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.682699978351593},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5105999708175659},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.484499990940094},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.400299996137619},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.33239999413490295},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2879999876022339},{"id":"https://openalex.org/C2911029443","wikidata":"https://www.wikidata.org/wiki/Q21296145","display_name":"Human proteins","level":3,"score":0.2825999855995178},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27559998631477356},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2639999985694885},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2587999999523163}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"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":"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":"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":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btag088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag088","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41712756","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41712756","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},{"id":"pmh:oai:iris.uniroma1.it:11573/1761984","is_oa":true,"landing_page_url":"https://hdl.handle.net/11573/1761984","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.ubn.ru.nl:2066/329811","is_oa":false,"landing_page_url":"https://hdl.handle.net/2066/329811","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag088","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4246042104","display_name":null,"funder_award_id":"RM1221815D52AB32","funder_id":"https://openalex.org/F4320322510","funder_display_name":"Sapienza Universit\u00e0 di Roma"}],"funders":[{"id":"https://openalex.org/F4320310982","display_name":"Associazione Italiana per la Lotta al Neuroblastoma","ror":"https://ror.org/02zn32y15"},{"id":"https://openalex.org/F4320322510","display_name":"Sapienza Universit\u00e0 di Roma","ror":"https://ror.org/02be6w209"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1778505584","https://openalex.org/W1986911150","https://openalex.org/W2027657574","https://openalex.org/W2041737563","https://openalex.org/W2100232590","https://openalex.org/W2101313056","https://openalex.org/W2122846880","https://openalex.org/W2201995907","https://openalex.org/W2463879412","https://openalex.org/W2548306987","https://openalex.org/W2619324489","https://openalex.org/W2745257241","https://openalex.org/W2821700122","https://openalex.org/W2891388683","https://openalex.org/W2913145970","https://openalex.org/W2953008890","https://openalex.org/W2964121744","https://openalex.org/W2969283119","https://openalex.org/W2969774962","https://openalex.org/W3009101585","https://openalex.org/W3097878558","https://openalex.org/W3108562892","https://openalex.org/W3113024442","https://openalex.org/W3123384049","https://openalex.org/W3147286443","https://openalex.org/W3155442940","https://openalex.org/W3202075453","https://openalex.org/W3211436564","https://openalex.org/W3212326044","https://openalex.org/W4224226524","https://openalex.org/W4225147145","https://openalex.org/W4283069545","https://openalex.org/W4296778358","https://openalex.org/W4297734170","https://openalex.org/W4308616073","https://openalex.org/W4309506674","https://openalex.org/W4317549025","https://openalex.org/W4327550249","https://openalex.org/W4383550359","https://openalex.org/W4388567027","https://openalex.org/W4391538864","https://openalex.org/W4391682171","https://openalex.org/W4393094534","https://openalex.org/W4396721167","https://openalex.org/W4396858334","https://openalex.org/W4396939000","https://openalex.org/W4403275633","https://openalex.org/W4403824354","https://openalex.org/W4406758820"],"related_works":[],"abstract_inverted_index":{"Source":[0],"code":[1],"for":[2],"the":[3],"G4REP":[4,16],"Model":[5],"training":[6],"and":[7,13],"evaluation":[8],"is":[9,18],"available":[10],"at:":[11,20],"https://github.com/G4REP/G4REPmodel":[12],"at":[14],"https://doi.org/10.5281/zenodo.17963046.":[15],"Server":[17],"hosted":[19],"https://schubert.bio.uniroma1.it/g4/.":[21]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2026-02-20T00:00:00"}