{"id":"https://openalex.org/W3214075907","doi":"https://doi.org/10.1093/bioinformatics/btab768","title":"<scp>Verna</scp>l: a tool for mining fuzzy network motifs in RNA","display_name":"<scp>Verna</scp>l: a tool for mining fuzzy network motifs in RNA","publication_year":2021,"publication_date":"2021-11-09","ids":{"openalex":"https://openalex.org/W3214075907","doi":"https://doi.org/10.1093/bioinformatics/btab768","mag":"3214075907"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab768","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab768","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"],"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/I4210164802","display_name":"Mila - Quebec Artificial Intelligence Institute","ror":"https://ror.org/05c22rx21","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210164802"]},{"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":"Carlos Oliver","raw_affiliation_strings":["Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada","School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"affiliations":[{"raw_affiliation_string":"Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada","institution_ids":["https://openalex.org/I4210164802"]},{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, 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/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":["Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology , Paris 75272, France","Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 , Paris, France"],"affiliations":[{"raw_affiliation_string":"Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology , Paris 75272, France","institution_ids":["https://openalex.org/I70768539"]},{"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/I157536573","https://openalex.org/I1294671590"]}]},{"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"],"affiliations":[{"raw_affiliation_string":"Department of Physics, McGill University , Montr\u00e9al, QC H3A 2T8, 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/I4210164802","display_name":"Mila - Quebec Artificial Intelligence Institute","ror":"https://ror.org/05c22rx21","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210164802"]},{"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":"William L Hamilton","raw_affiliation_strings":["Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada","School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"affiliations":[{"raw_affiliation_string":"Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada","institution_ids":["https://openalex.org/I4210164802"]},{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, 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":true,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000881484"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4869,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.628256,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"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":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/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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":0.9998999834060669,"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":0.7058331370353699},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6974022388458252},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4756217300891876},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4572335183620453},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4286327362060547},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4218497574329376},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.416864812374115},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3869290351867676},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33812451362609863},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.31416067481040955},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22453966736793518},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14884936809539795}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7058331370353699},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6974022388458252},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4756217300891876},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4572335183620453},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4286327362060547},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4218497574329376},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.416864812374115},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3869290351867676},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33812451362609863},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.31416067481040955},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22453966736793518},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14884936809539795},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btab768","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab768","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1863324516","https://openalex.org/W1951403192","https://openalex.org/W2007615447","https://openalex.org/W2013902881","https://openalex.org/W2023013439","https://openalex.org/W2023209608","https://openalex.org/W2032338144","https://openalex.org/W2036131961","https://openalex.org/W2040447892","https://openalex.org/W2070136856","https://openalex.org/W2106478835","https://openalex.org/W2108096294","https://openalex.org/W2119274978","https://openalex.org/W2126295301","https://openalex.org/W2136556521","https://openalex.org/W2137309356","https://openalex.org/W2147128567","https://openalex.org/W2150404344","https://openalex.org/W2152379980","https://openalex.org/W2158381555","https://openalex.org/W2187089797","https://openalex.org/W2222512263","https://openalex.org/W2402481807","https://openalex.org/W2604314403","https://openalex.org/W2795053763","https://openalex.org/W2919373301","https://openalex.org/W2949965166","https://openalex.org/W2990138404","https://openalex.org/W3041118201","https://openalex.org/W3164771453","https://openalex.org/W6780807301","https://openalex.org/W7075630220"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368037387","https://openalex.org/W2368410102","https://openalex.org/W3021477453","https://openalex.org/W2364249514","https://openalex.org/W3113308218","https://openalex.org/W2610941444","https://openalex.org/W2132757463","https://openalex.org/W4288366168","https://openalex.org/W1967686998"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"RNA":[2,41,110,133],"3D":[3],"motifs":[4,28,111],"are":[5,16,184,208],"recurrent":[6],"substructures,":[7],"modeled":[8],"as":[9,84,167,169],"networks":[10],"of":[11,24,40,52,63,96,100,109,120,147,165],"base":[12],"pair":[13],"interactions,":[14],"which":[15],"crucial":[17],"for":[18],"understanding":[19],"structure\u2013function":[20],"relationships.":[21],"The":[22,177],"task":[23],"automatically":[25],"identifying":[26],"such":[27],"is":[29,157],"computationally":[30],"hard,":[31],"and":[32,44,66,89,107,126,151,161,175,181,194,200],"remains":[33],"a":[34,64,85,118,182,191,195],"key":[35],"challenge":[36],"in":[37,61,112],"the":[38,53,58,68,80,97,105],"field":[39],"structural":[42,59],"biology":[43],"network":[45],"analysis.":[46],"State-of-the-art":[47],"methods":[48,125],"solve":[49],"special":[50],"cases":[51],"motif":[54,81,127,148],"problem":[55,83],"by":[56,78,142],"constraining":[57],"variability":[60,108],"occurrences":[62],"motif,":[65],"narrowing":[67],"substructure":[69],"search":[70],"space.":[71],"Results":[72],"Here,":[73],"we":[74],"relax":[75],"these":[76],"constraints":[77],"posing":[79],"finding":[82],"graph":[86,101],"representation":[87],"learning":[88],"clustering":[90,124],"task.":[91],"This":[92],"framing":[93],"takes":[94],"advantage":[95],"continuous":[98],"nature":[99],"representations":[102],"to":[103,130,144,159,170,198],"model":[104],"flexibility":[106],"an":[113],"efficient":[114],"manner.":[115],"We":[116,153,188],"propose":[117,171],"set":[119],"node":[121],"similarity":[122],"functions,":[123],"construction":[128],"algorithms":[129],"recover":[131],"flexible":[132,192],"motifs.":[134,173],"Our":[135],"tool,":[136],"Vernal":[137,156],"can":[138],"be":[139],"easily":[140],"customized":[141],"users":[143],"desired":[145],"levels":[146],"flexibility,":[149],"abundance":[150],"size.":[152],"show":[154],"that":[155],"able":[158],"retrieve":[160],"expand":[162],"known":[163],"classes":[164],"motifs,":[166],"well":[168],"novel":[172],"Availability":[174],"implementation":[176],"source":[178],"code,":[179],"data":[180,207],"webserver":[183,197],"available":[185,209],"at":[186,210],"vernal.cs.mcgill.ca.":[187],"also":[189],"provide":[190],"interface":[193],"user-friendly":[196],"browse":[199],"download":[201],"our":[202],"results.":[203],"Supplementary":[204,206],"information":[205],"Bioinformatics":[211],"online.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2021-11-22T00:00:00"}
