{"id":"https://openalex.org/W4381307511","doi":"https://doi.org/10.1093/bib/bbad225","title":"C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data","display_name":"C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data","publication_year":2023,"publication_date":"2023-06-19","ids":{"openalex":"https://openalex.org/W4381307511","doi":"https://doi.org/10.1093/bib/bbad225","pmid":"https://pubmed.ncbi.nlm.nih.gov/37337745"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad225","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad225","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5092211361","display_name":"Mandy Ib\u00e9n\u00e9","orcid":null},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Mandy Ib\u00e9n\u00e9","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007319005","display_name":"Audrey Legendre","orcid":"https://orcid.org/0000-0001-6219-0100"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Audrey Legendre","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055433325","display_name":"Guillaume Postic","orcid":"https://orcid.org/0000-0002-0380-0092"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Guillaume Postic","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020198009","display_name":"\u00c9ric Angel","orcid":null},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eric Angel","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I277688954"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091493314","display_name":"Fariza Tahi","orcid":"https://orcid.org/0000-0002-3975-5668"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fariza Tahi","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020, Evry-Courcouronnes , France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I277688954"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5092211361"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210107733"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25336028,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":"4","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":1.0,"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":1.0,"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":0.9987000226974487,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944999814033508,"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":0.6636137962341309},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4375646114349365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41872408986091614},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.373891681432724},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37344616651535034},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3386922776699066},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10067257285118103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.05647331476211548}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6636137962341309},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4375646114349365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41872408986091614},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.373891681432724},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37344616651535034},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3386922776699066},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10067257285118103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.05647331476211548},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad225","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad225","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37337745","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37337745","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-04173835v1","is_oa":false,"landing_page_url":"https://hal.science/hal-04173835","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 2023, 24 (4), ⟨10.1093/bib/bbad225⟩","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1501644705","https://openalex.org/W1519185585","https://openalex.org/W1972760347","https://openalex.org/W1989020100","https://openalex.org/W2000775854","https://openalex.org/W2003841667","https://openalex.org/W2017370325","https://openalex.org/W2043653977","https://openalex.org/W2071883352","https://openalex.org/W2082603400","https://openalex.org/W2086561953","https://openalex.org/W2109553965","https://openalex.org/W2120974004","https://openalex.org/W2131462431","https://openalex.org/W2133203832","https://openalex.org/W2134943543","https://openalex.org/W2137356209","https://openalex.org/W2150882562","https://openalex.org/W2159117141","https://openalex.org/W2161159766","https://openalex.org/W2162224067","https://openalex.org/W2290893604","https://openalex.org/W2501301043","https://openalex.org/W2783814264","https://openalex.org/W2808844301","https://openalex.org/W2906841844","https://openalex.org/W2935340325","https://openalex.org/W2953380662","https://openalex.org/W2958013639","https://openalex.org/W2999081115","https://openalex.org/W3022948658","https://openalex.org/W3126773939","https://openalex.org/W4205118936","https://openalex.org/W4206897099","https://openalex.org/W4280509920","https://openalex.org/W4282929726","https://openalex.org/W4289599043","https://openalex.org/W4302362590","https://openalex.org/W4401946675","https://openalex.org/W6632011196"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"RNAs":[0,62],"can":[1,63,90],"interact":[2],"with":[3,19],"other":[4,14],"molecules":[5],"in":[6,43],"their":[7,66],"environment,":[8],"such":[9],"as":[10,140],"ions,":[11],"proteins":[12],"or":[13,94],"RNAs,":[15],"to":[16],"form":[17],"complexes":[18,30,45],"important":[20,34],"biological":[21],"roles.":[22],"The":[23],"prediction":[24,76,134],"of":[25,28,47,77,117,125],"the":[26,60,75,115,118,122,133,148],"structure":[27],"these":[29],"is":[31,97,137],"therefore":[32],"an":[33,71,105,141],"issue":[35],"and":[36,86,121,129,144],"a":[37,100],"difficult":[38],"task.":[39],"We":[40,54,69],"are":[41],"interested":[42],"RNA":[44,78],"composed":[46],"several":[48],"(more":[49],"than":[50],"two)":[51],"interacting":[52],"RNAs.":[53],"show":[55,114],"how":[56],"available":[57,139],"knowledge":[58,85,128],"on":[59,99,132,147],"considered":[61],"help":[64],"predict":[65],"secondary":[67],"structure.":[68],"propose":[70],"interactive":[72],"tool":[73],"for":[74],"complexes,":[79],"called":[80],"C-RCPRed,":[81],"that":[82],"considers":[83],"user":[84,127],"probing":[87,130],"data":[88,131],"(which":[89],"be":[91],"generated":[92],"experimentally":[93],"artificially).":[95],"C-RCPred":[96,136],"based":[98],"multi-objective":[101,119],"optimization":[102],"algorithm.":[103],"Through":[104],"extensive":[106],"benchmarking":[107],"procedure,":[108],"which":[109],"includes":[110],"state-of-the-art":[111],"methods,":[112],"we":[113],"efficiency":[116],"approach":[120],"positive":[123],"impact":[124],"considering":[126],"results.":[135],"freely":[138],"open-source":[142],"program":[143],"web":[145],"server":[146],"EvryRNA":[149],"website":[150],"(https://evryrna.ibisc.univ-evry.fr).":[151]},"counts_by_year":[],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2023-06-21T00:00:00"}