{"id":"https://openalex.org/W3082513267","doi":"https://doi.org/10.1093/bioinformatics/btab768","title":"Vernal: a tool for mining fuzzy network motifs in RNA.","display_name":"Vernal: a tool for mining fuzzy network motifs in RNA.","publication_year":2022,"publication_date":"2022-01-27","ids":{"openalex":"https://openalex.org/W3082513267","doi":"https://doi.org/10.1093/bioinformatics/btab768","mag":"3082513267","pmid":"https://pubmed.ncbi.nlm.nih.gov/34791045"},"language":"en","primary_location":{"id":"pmid:34791045","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34791045","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},"type":"article","indexed_in":["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/A5003324363","display_name":"Carlos Oliver","orcid":"https://orcid.org/0000-0001-8742-8795"},"institutions":[{"id":"https://openalex.org/I4210099593","display_name":"Computer Algorithms for Medicine","ror":"https://ror.org/00zky6d38","country_code":"AT","type":"facility","lineage":["https://openalex.org/I4210099593"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["AT","CA"],"is_corresponding":false,"raw_author_name":"Carlos Oliver","raw_affiliation_strings":["School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","Montreal Institute for Learning Algorithms (MILA), Montr\u00e9al, QC H2S 3H1, Canada","School of Computer Science, McGill University, Montr\u00e9al QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Montreal Institute for Learning Algorithms (MILA), Montr\u00e9al, QC H2S 3H1, Canada","institution_ids":["https://openalex.org/I4210099593"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al QC, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103104178","display_name":"Vincent Mallet","orcid":"https://orcid.org/0000-0003-4664-754X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I4387156267","display_name":"Biologie Mol\u00e9culaire Structurale et Processus Infectieux","ror":"https://ror.org/009b91528","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I4387156267"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Mallet","raw_affiliation_strings":["Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756, Paris, France","Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology, Paris 75272, France","Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756, Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I4387156267"]},{"raw_affiliation_string":"Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology, Paris 75272, France","institution_ids":["https://openalex.org/I190752583","https://openalex.org/I70768539"]},{"raw_affiliation_string":"Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology, Paris, France","institution_ids":["https://openalex.org/I190752583","https://openalex.org/I70768539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045365503","display_name":"Pericles Philippopoulos","orcid":"https://orcid.org/0000-0002-8783-5574"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pericles Philippopoulos","raw_affiliation_strings":["Department of Physics, McGill University, Montr\u00e9al, QC H3A 2T8, Canada","Department of Physics, McGill University, Montreal, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, McGill University, Montr\u00e9al, QC H3A 2T8, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Physics, McGill University, Montreal, QC, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004542284","display_name":"William L. Hamilton","orcid":"https://orcid.org/0000-0002-3330-353X"},"institutions":[{"id":"https://openalex.org/I4210099593","display_name":"Computer Algorithms for Medicine","ror":"https://ror.org/00zky6d38","country_code":"AT","type":"facility","lineage":["https://openalex.org/I4210099593"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["AT","CA"],"is_corresponding":false,"raw_author_name":"William L Hamilton","raw_affiliation_strings":["School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","Montreal Institute for Learning Algorithms (MILA), Montr\u00e9al, QC H2S 3H1, Canada","School of Computer Science, McGill University, Montr\u00e9al QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Montreal Institute for Learning Algorithms (MILA), Montr\u00e9al, QC H2S 3H1, Canada","institution_ids":["https://openalex.org/I4210099593"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al QC, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000881484","display_name":"J\u00e9r\u00f4me Waldisp\u00fchl","orcid":"https://orcid.org/0000-0002-2561-7117"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","School of Computer Science, McGill University, Montr\u00e9al, QC Canada#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC Canada#TAB#","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.00133078,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":"38","issue":"4","first_page":"970","last_page":"976"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9577000141143799,"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":0.9577000141143799,"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":0.013899999670684338,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.004600000102072954,"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/motif","display_name":"Motif (music)","score":0.6891295313835144},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6588606834411621},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5475623607635498},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4821326434612274},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.45482969284057617},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4389244616031647},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43655964732170105},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4132075309753418},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38586926460266113},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3637353777885437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1973232924938202},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10969400405883789}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6891295313835144},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6588606834411621},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5475623607635498},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4821326434612274},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.45482969284057617},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4389244616031647},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43655964732170105},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4132075309753418},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38586926460266113},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3637353777885437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1973232924938202},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10969400405883789},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"pmid:34791045","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34791045","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":"mag:3082513267","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5196283127","display_name":"Institut Convergences pour l\u2019\u00e9tude de l\u2019Emergence des Pathologies au Travers des Individus et des populatiONs","funder_award_id":"ANR-16-CONV-0005","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3115130917","https://openalex.org/W3214075907","https://openalex.org/W3005678367","https://openalex.org/W782572168","https://openalex.org/W2528717069","https://openalex.org/W2902553674","https://openalex.org/W1553420678","https://openalex.org/W2794429201","https://openalex.org/W2013291425","https://openalex.org/W3154586454","https://openalex.org/W2162723124","https://openalex.org/W3101251439","https://openalex.org/W199864753","https://openalex.org/W2949444209","https://openalex.org/W2889813947","https://openalex.org/W1995176954","https://openalex.org/W2055007072","https://openalex.org/W2128142445","https://openalex.org/W2498086413","https://openalex.org/W2045373061"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA":[1,40,109,132],"3D":[2],"motifs":[3,27,110],"are":[4,15,183,207],"recurrent":[5],"substructures,":[6],"modeled":[7],"as":[8,83,166,168],"networks":[9],"of":[10,23,39,51,62,95,99,108,119,146,164],"base":[11],"pair":[12],"interactions,":[13],"which":[14],"crucial":[16],"for":[17],"understanding":[18],"structure-function":[19],"relationships.":[20],"The":[21,176],"task":[22],"automatically":[24],"identifying":[25],"such":[26],"is":[28,156],"computationally":[29],"hard,":[30],"and":[31,43,65,88,106,125,150,160,180,193,199],"remains":[32],"a":[33,63,84,117,181,190,194],"key":[34],"challenge":[35],"in":[36,60,111],"the":[37,52,57,67,79,96,104],"field":[38],"structural":[41,58],"biology":[42],"network":[44],"analysis.":[45],"State-of-the-art":[46],"methods":[47,124],"solve":[48],"special":[49],"cases":[50],"motif":[53,80,126,147],"problem":[54,82],"by":[55,77,141],"constraining":[56],"variability":[59,107],"occurrences":[61],"motif,":[64],"narrowing":[66],"substructure":[68],"search":[69],"space.":[70],"RESULTS:":[71],"Here,":[72],"we":[73],"relax":[74],"these":[75],"constraints":[76],"posing":[78],"finding":[81],"graph":[85,100],"representation":[86],"learning":[87],"clustering":[89,123],"task.":[90],"This":[91],"framing":[92],"takes":[93],"advantage":[94],"continuous":[97],"nature":[98],"representations":[101],"to":[102,129,143,158,169,197],"model":[103],"flexibility":[105],"an":[112],"efficient":[113],"manner.":[114],"We":[115,152,187],"propose":[116,170],"set":[118],"node":[120],"similarity":[121],"functions,":[122],"construction":[127],"algorithms":[128],"recover":[130],"flexible":[131,191],"motifs.":[133,172],"Our":[134],"tool,":[135],"Vernal":[136,155],"can":[137],"be":[138],"easily":[139],"customized":[140],"users":[142],"desired":[144],"levels":[145],"flexibility,":[148],"abundance":[149],"size.":[151],"show":[153],"that":[154],"able":[157],"retrieve":[159],"expand":[161],"known":[162],"classes":[163],"motifs,":[165],"well":[167],"novel":[171],"AVAILABILITY":[173],"AND":[174],"IMPLEMENTATION:":[175],"source":[177],"code,":[178],"data":[179,206],"webserver":[182,196],"available":[184,208],"at":[185,209],"vernal.cs.mcgill.ca.":[186],"also":[188],"provide":[189],"interface":[192],"user-friendly":[195],"browse":[198],"download":[200],"our":[201],"results.":[202],"SUPPLEMENTARY":[203],"INFORMATION:":[204],"Supplementary":[205],"Bioinformatics":[210],"online.":[211]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
