{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:23:56Z","timestamp":1763810636492,"version":"3.37.3"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T00:00:00Z","timestamp":1636934400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fonds de Recherche du Qu\u00e9bec Nature et technologies"},{"name":"INCEPTION project","award":["PIA\/ANR-16-CONV-0005"],"award-info":[{"award-number":["PIA\/ANR-16-CONV-0005"]}]},{"name":"Center for Research and Interdisciplinarity"},{"name":"Discovery grant from the Natural Sciences and Engineering Research Council of Canada"},{"name":"Qu\u00e9bec \u2013 Nature et technologies","award":["FRQ-NT PR-284708"],"award-info":[{"award-number":["FRQ-NT PR-284708"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure\u2013function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab768","type":"journal-article","created":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T20:18:03Z","timestamp":1636489083000},"page":"970-976","source":"Crossref","is-referenced-by-count":8,"title":["<scp>Verna<\/scp>l: a tool for mining fuzzy network motifs in RNA"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8742-8795","authenticated-orcid":false,"given":"Carlos","family":"Oliver","sequence":"first","affiliation":[{"name":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"},{"name":"Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4664-754X","authenticated-orcid":false,"given":"Vincent","family":"Mallet","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 , Paris, France"},{"name":"Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology , Paris 75272, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pericles","family":"Philippopoulos","sequence":"additional","affiliation":[{"name":"Department of Physics, McGill University , Montr\u00e9al, QC H3A 2T8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William L","family":"Hamilton","sequence":"additional","affiliation":[{"name":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"},{"name":"Montreal Institute for Learning Algorithms (MILA) , Montr\u00e9al, QC H2S 3H1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2561-7117","authenticated-orcid":false,"given":"J\u00e9r\u00f4me","family":"Waldisp\u00fchl","sequence":"additional","affiliation":[{"name":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,15]]},"reference":[{"key":"2023020108515390300_btab768-B1","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1261\/rna.853208","article-title":"Analysis and classification of RNA tertiary structures","volume":"14","author":"Abraham","year":"2008","journal-title":"RNA"},{"first-page":"996","year":"2008","author":"Bunke","key":"2023020108515390300_btab768-B2"},{"key":"2023020108515390300_btab768-B3","doi-asserted-by":"crossref","first-page":"D123","DOI":"10.1093\/nar\/gkt1084","article-title":"RNA bricks\u2014a database of RNA 3D motifs and their interactions","volume":"42","author":"Chojnowski","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020108515390300_btab768-B4","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.1603","article-title":"Sequence-based identification of 3d structural modules in RNA with rmdetect","volume":"8","author":"Cruz","year":"2011","journal-title":"Nat. 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