{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T20:26:27Z","timestamp":1770582387161,"version":"3.49.0"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,7,9]],"date-time":"2024-07-09T00:00:00Z","timestamp":1720483200000},"content-version":"vor","delay-in-days":47,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019478","name":"FPU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019478","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023561","name":"Spanish Ministerio de Universidades","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023561","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023561","name":"Spanish Ministerio de Universidades","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023561","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministerio de Educaci\u00f3n y Ciencia","award":["BFU2017-86152-P"],"award-info":[{"award-number":["BFU2017-86152-P"]}]},{"name":"Ministerio de Educaci\u00f3n y Ciencia","award":["PID2020-117820GB-I00"],"award-info":[{"award-number":["PID2020-117820GB-I00"]}]},{"DOI":"10.13039\/501100003030","name":"AGAUR","doi-asserted-by":"publisher","award":["2021-SGR00372-GRC"],"award-info":[{"award-number":["2021-SGR00372-GRC"]}],"id":[{"id":"10.13039\/501100003030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Around 50\u00a0years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and artificial intelligence (AI), we focus on an elusive and intriguing mechanism of gene function regulation, RNA editing, in which a single nucleotide from an RNA molecule is changed, with a remarkable impact in the increase of the complexity of the transcriptome and proteome. We present a new generation approach to assess the functional conservation of the RNA-editing targeting mechanism using two AI learning algorithms, random forest (RF) and bidirectional long short-term memory (biLSTM) neural networks with an attention layer. These algorithms, combined with RNA-editing data coming from databases and variant calling from same-individual RNA and DNA-seq experiments from different species, allowed us to predict RNA-editing events using both primary sequence and secondary structure. Then, we devised a method for assessing conservation or divergence in the molecular mechanisms of editing completely in silico: the cross-testing analysis. This novel method not only helps to understand the conservation of the editing mechanism through evolution but could set the basis for achieving a better understanding of the adenosine-targeting mechanism in other fields.<\/jats:p>","DOI":"10.1093\/bib\/bbae332","type":"journal-article","created":{"date-parts":[[2024,7,9]],"date-time":"2024-07-09T15:06:38Z","timestamp":1720537598000},"source":"Crossref","is-referenced-by-count":2,"title":["Exploring functional conservation <i>in silico<\/i>: a new machine learning approach to RNA-editing"],"prefix":"10.1093","volume":"25","author":[{"given":"Micha\u0142","family":"Zawisza-\u00c1lvarez","sequence":"first","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Institut de Biomedicina (IBUB), Universitat de Barcelona , Av. Diagonal 643, 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"Pe\u00f1uela-Melero","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esteban","family":"Vegas","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III , Calle Sinesio Delgado 4, 28029 Madrid , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ferran","family":"Reverter","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jordi","family":"Garcia-Fern\u00e0ndez","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Institut de Biomedicina (IBUB), Universitat de Barcelona , Av. Diagonal 643, 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2334-9470","authenticated-orcid":false,"given":"Carlos","family":"Herrera-\u00dabeda","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Facultat de Biologia, Universitat de Barcelona , Microbiologia i Estad\u00edstica, , Av. Digonal 643, 08028 Barcelona , Spain"},{"name":"Institut de Biomedicina (IBUB), Universitat de Barcelona , Av. Diagonal 643, 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,7,9]]},"reference":[{"key":"2024070914033357900_ref1","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2017.05.045","article-title":"Dynamic RNA modifications in gene expression regulation","volume":"169","author":"Roundtree","year":"2017","journal-title":"Cell"},{"key":"2024070914033357900_ref2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s42977-022-00142-3","article-title":"The role of post-transcriptional modifications during development","volume":"74","author":"Hamar","year":"2023","journal-title":"Biol Futur"},{"key":"2024070914033357900_ref3","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.ceb.2012.03.005","article-title":"Alternative splicing: decoding an expansive regulatory layer","volume":"24","author":"Irimia","year":"2012","journal-title":"Curr Opin Cell Biol"},{"key":"2024070914033357900_ref4","first-page":"5319","article-title":"Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain","author":"Irimia","year":"2011"},{"key":"2024070914033357900_ref5","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.cell.2017.03.025","article-title":"Trade-off between transcriptome plasticity and genome evolution in cephalopods","volume":"169","author":"Liscovitch-Brauer","year":"2017","journal-title":"Cell"},{"key":"2024070914033357900_ref6","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.molcel.2012.05.002","article-title":"Nascent-seq indicates widespread cotranscriptional RNA editing in drosophila","volume":"47","author":"Rodriguez","year":"2012","journal-title":"Mol Cell"},{"key":"2024070914033357900_ref7","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1261\/rna.404407","article-title":"The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript","volume":"13","author":"Ryman","year":"2007","journal-title":"RNA"},{"key":"2024070914033357900_ref8","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1186\/s13059-017-1315-y","article-title":"Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance","volume":"18","author":"Porath","year":"2017","journal-title":"Genome Biol"},{"key":"2024070914033357900_ref9","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1101\/gr.199877.115","article-title":"Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes","volume":"26","author":"Liu","year":"2016","journal-title":"Genome Res"},{"key":"2024070914033357900_ref10","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1146\/annurev-genet-111212-133519","article-title":"RNA editing in plants and its evolution","volume":"47","author":"Takenaka","year":"2013","journal-title":"Annu Rev Genet"},{"key":"2024070914033357900_ref11","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/gb-2012-13-12-252","article-title":"The ADAR protein family","volume":"13","author":"Savva","year":"2012","journal-title":"Genome Biol"},{"key":"2024070914033357900_ref12","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s12862-015-0279-3","article-title":"The origin of the ADAR gene family and animal RNA editing","volume":"15","author":"Grice","year":"2015","journal-title":"BMC Evol Biol"},{"key":"2024070914033357900_ref13","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1002\/iub.207","article-title":"Origins and evolution of ADAR-mediated RNA editing","volume":"61","author":"Jin","year":"2009","journal-title":"IUBMB Life"},{"key":"2024070914033357900_ref14","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.3390\/genes11121440","article-title":"The ADAR family in amphioxus: RNA editing and conserved orthologous site predictions","volume":"11","author":"Zawisza-\u00c1lvarez","year":"2020","journal-title":"Genes (Basel)"},{"key":"2024070914033357900_ref15","doi-asserted-by":"crossref","first-page":"10801","DOI":"10.1093\/nar\/gkz815","article-title":"RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024070914033357900_ref16","doi-asserted-by":"crossref","first-page":"31795","DOI":"10.1074\/jbc.271.50.31795","article-title":"RED2, a brain-specific member of the RNA-specific adenosine deaminase family","volume":"271","author":"Melcher","year":"1996","journal-title":"J Biol Chem"},{"key":"2024070914033357900_ref17","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nrm.2015.4","article-title":"A-to-I editing of coding and non-coding RNAs by ADARs","volume":"17","author":"Nishikura","year":"2016","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024070914033357900_ref18","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.3389\/fimmu.2019.01763","article-title":"ADAR1: \u201cEditor-in-Chief\u201d of cytoplasmic innate immunity","volume":"10","author":"Lamers","year":"2019","journal-title":"Front Immunol"},{"key":"2024070914033357900_ref19","doi-asserted-by":"crossref","first-page":"5848","DOI":"10.1093\/nar\/gkp604","article-title":"Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection","volume":"37","author":"Doria","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024070914033357900_ref20","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1126\/science.1118265","article-title":"The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C","volume":"311","author":"Kishore","year":"2006","journal-title":"Science"},{"key":"2024070914033357900_ref21","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1016\/j.neurobiolaging.2014.02.018","article-title":"Hippocampus-specific deficiency in RNA editing of GluA2 in Alzheimer\u2019s disease","volume":"35","author":"Gaisler-Salomon","year":"2014","journal-title":"Neurobiol Aging"},{"key":"2024070914033357900_ref22","doi-asserted-by":"crossref","first-page":"321","DOI":"10.4161\/rna.23343","article-title":"RNA editing of the GLI1 transcription factor modulates the output of hedgehog signaling","volume":"10","author":"Shimokawa","year":"2013","journal-title":"RNA Biol"},{"key":"2024070914033357900_ref23","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nm.3043","article-title":"Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma","volume":"19","author":"Chen","year":"2013","journal-title":"Nat Med"},{"key":"2024070914033357900_ref24","doi-asserted-by":"crossref","first-page":"1525","DOI":"10.1261\/rna.041533.113","article-title":"ADAR1 regulates ARHGAP26 gene expression through RNA editing by disrupting miR-30b-3p and miR-573 binding","volume":"19","author":"Wang","year":"2013","journal-title":"RNA"},{"key":"2024070914033357900_ref25","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1126\/science.7992055","article-title":"Control of kinetic properties of AMPA receptor channels by nuclear RNA editing","volume":"266","author":"Lomeli","year":"1994","journal-title":"Science"},{"key":"2024070914033357900_ref26","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/0092-8674(91)90568-J","article-title":"RNA editing in brain controls a determinant of ion flow in glutamate-gated channels","volume":"67","author":"Sommer","year":"1991","journal-title":"Cell"},{"key":"2024070914033357900_ref27","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1073\/pnas.90.2.755","article-title":"Ca2+ permeability of unedited and edited versions of the kainate selective glutamate receptor GluR6","volume":"90","author":"Egebjerg","year":"1993","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024070914033357900_ref28","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/0896-6273(93)90336-P","article-title":"Determinants of Ca2+ permeability in both TM1 and TM2 of high affinity kainate receptor channels: diversity by RNA editing","volume":"10","author":"K\u00f6hler","year":"1993","journal-title":"Neuron"},{"key":"2024070914033357900_ref29","doi-asserted-by":"crossref","first-page":"12","DOI":"10.4161\/rna.9.1.18387","article-title":"Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1","volume":"9","author":"Irimia","year":"2012","journal-title":"RNA Biol"},{"key":"2024070914033357900_ref30","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/35017558","article-title":"Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2","volume":"406","author":"Higuchi","year":"2000","journal-title":"Nature"},{"key":"2024070914033357900_ref31","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.stem.2020.04.016","article-title":"ADAR1-dependent RNA editing promotes MET and iPSC reprogramming by alleviating ER stress","volume":"27","author":"Guallar","year":"2020","journal-title":"Cell Stem Cell"},{"key":"2024070914033357900_ref32","doi-asserted-by":"crossref","first-page":"6025","DOI":"10.1093\/emboj\/cdf607","article-title":"RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans","volume":"21","author":"Tonkin","year":"2002","journal-title":"EMBO J"},{"key":"2024070914033357900_ref33","doi-asserted-by":"crossref","first-page":"4952","DOI":"10.1074\/jbc.M310162200","article-title":"Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene","volume":"279","author":"Wang","year":"2004","journal-title":"J Biol Chem"},{"key":"2024070914033357900_ref34","doi-asserted-by":"crossref","first-page":"e1007064","DOI":"10.1371\/journal.pgen.1007064","article-title":"The evolution and adaptation of A-to-I RNA editing","volume":"13","author":"Yablonovitch","year":"2017","journal-title":"PLoS Genet"},{"key":"2024070914033357900_ref35","doi-asserted-by":"crossref","first-page":"112112","DOI":"10.1016\/j.celrep.2023.112112","article-title":"On the origin and evolution of RNA editing in metazoans","volume":"42","author":"Zhang","year":"2023","journal-title":"Cell Rep"},{"key":"2024070914033357900_ref36","doi-asserted-by":"crossref","first-page":"1600187","DOI":"10.1002\/bies.201600187","article-title":"How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs","volume":"39","author":"Thomas","year":"2017","journal-title":"Bioessays"},{"key":"2024070914033357900_ref37","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1002\/wrna.10","article-title":"Substitutional A-to-I RNA editing","volume":"1","author":"Wulff","year":"2010","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2024070914033357900_ref38","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13742-016-0143-4","article-title":"RES-Scanner: a software package for genome-wide identification of RNA-editing sites","volume":"5","author":"Wang","year":"2016","journal-title":"Gigascience"},{"key":"2024070914033357900_ref39","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-023-02921-0","article-title":"DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing","volume":"24","author":"Chen","year":"2023","journal-title":"Genome Biol"},{"key":"2024070914033357900_ref40","doi-asserted-by":"crossref","first-page":"D750","DOI":"10.1093\/nar\/gkw767","article-title":"REDIportal: a comprehensive database of A-to-I RNA editing events in humans","volume":"45","author":"Picardi","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024070914033357900_ref41","doi-asserted-by":"crossref","first-page":"118","DOI":"10.12688\/wellcomeopenres.17813.1","article-title":"The genome sequence of the Atlantic horse mackerel, Trachurus trachurus (Linnaeus 1758)","volume":"7","author":"Genner","year":"2022","journal-title":"Wellcome Open Res"},{"key":"2024070914033357900_ref42","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/s12859-019-2996-x","article-title":"Magic-BLAST, an accurate RNA-seq aligner for long and short reads","volume":"20","author":"Boratyn","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2024070914033357900_ref43","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2024070914033357900_ref44","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","journal-title":"Gigascience"},{"key":"2024070914033357900_ref45","doi-asserted-by":"crossref","first-page":"i295","DOI":"10.1093\/bioinformatics\/btz375","article-title":"LinearFold: linear-time approximate RNA folding by 5\u2032-to-3\u2032 dynamic programming and beam search","volume":"35","author":"Huang","year":"2019","journal-title":"Bioinformatics"},{"key":"2024070914033357900_ref46","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1162\/neco.1997.9.8.1735","article-title":"Long short-term memory","volume":"9","author":"Hochreiter","year":"1997","journal-title":"Neural Comput"},{"key":"2024070914033357900_ref47","article-title":"TensorFlow: large-scale machine learning on heterogeneous systems","author":"Abadi","year":"2015"},{"key":"2024070914033357900_ref48","article-title":"Keras","author":"Chollet","year":"2015"},{"key":"2024070914033357900_ref49","article-title":"Anaconda Software Distribution","year":"2020","journal-title":"Anaconda Documentation"},{"key":"2024070914033357900_ref50"},{"key":"2024070914033357900_ref51"},{"key":"2024070914033357900_ref52","volume-title":"CUDA Deep Neural Network (cuDNN)"},{"key":"2024070914033357900_ref53","volume-title":"Developer Documentation","author":"NVIDIA"},{"key":"2024070914033357900_ref54","first-page":"1","article-title":"PAI: predicting adenosine to inosine editing sites by using pseudo nucleotide compositions","volume":"6","author":"Chen","year":"2016","journal-title":"Sci Rep"},{"key":"2024070914033357900_ref55","doi-asserted-by":"crossref","first-page":"4208","DOI":"10.18632\/oncotarget.13758","article-title":"iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences","volume":"8","author":"Chen","year":"2016","journal-title":"Oncotarget"},{"key":"2024070914033357900_ref56","doi-asserted-by":"crossref","first-page":"052018","DOI":"10.1088\/1755-1315\/170\/5\/052018","article-title":"PAI-SAE: predicting adenosine to inosine editing sites based on hybrid features by using spare auto-encoder","volume":"170","author":"Xiao","year":"2018","journal-title":"IOP Conf Ser Earth Environ Sci"},{"key":"2024070914033357900_ref57","doi-asserted-by":"crossref","first-page":"3336","DOI":"10.1093\/bioinformatics\/btaa155","article-title":"iMRM: a platform for simultaneously identifying multiple kinds of RNA modifications","volume":"36","author":"Liu","year":"2020","journal-title":"Bioinformatics"},{"key":"2024070914033357900_ref58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bib\/bbad170","article-title":"ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species","volume":"24","author":"Chen","year":"2023","journal-title":"Brief Bioinform"},{"key":"2024070914033357900_ref59","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/ncomms1324","article-title":"Predicting sites of ADAR editing in double-stranded RNA","volume":"2","author":"Eggington","year":"2011","journal-title":"Nat Commun"},{"key":"2024070914033357900_ref60","doi-asserted-by":"crossref","first-page":"20715","DOI":"10.1073\/pnas.1009231107","article-title":"RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1","volume":"107","author":"Yeo","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024070914033357900_ref61","doi-asserted-by":"crossref","first-page":"7857","DOI":"10.1021\/bi4006539","article-title":"RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiae","volume":"52","author":"Eifler","year":"2013","journal-title":"Biochemistry"},{"key":"2024070914033357900_ref62","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nsmb1041","article-title":"Modulation of microRNA processing and expression through RNA editing by ADAR deaminases","volume":"13","author":"Yang","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"2024070914033357900_ref63","doi-asserted-by":"crossref","first-page":"31","DOI":"10.17849\/insm-47-01-31-39.1","article-title":"Random forest","volume":"47","author":"Rigatti","year":"2017","journal-title":"J Insur Med"},{"key":"2024070914033357900_ref64","doi-asserted-by":"crossref","first-page":"a003665","DOI":"10.1101\/cshperspect.a003665","article-title":"Folding and finding RNA secondary structure","volume":"2","author":"Mathews","year":"2010","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2024070914033357900_ref65","doi-asserted-by":"crossref","first-page":"D1012","DOI":"10.1093\/nar\/gkaa916","article-title":"REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments","volume":"49","author":"Mansi","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024070914033357900_ref66","doi-asserted-by":"crossref","first-page":"22071","DOI":"10.1073\/pnas.1900654116","article-title":"Definitions, methods, and applications in interpretable machine learning","volume":"116","author":"Murdoch","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024070914033357900_ref67","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1038\/s41588-023-01456-1","article-title":"Temperature-induced RNA recoding in octopus","volume":"55","author":"Anania","year":"2023","journal-title":"Nat Genet"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/4\/bbae332\/58482985\/bbae332.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/4\/bbae332\/58482985\/bbae332.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,9]],"date-time":"2024-07-09T15:07:20Z","timestamp":1720537640000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae332\/7709765"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,23]]},"references-count":67,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,5,23]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae332","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,5,23]]},"article-number":"bbae332"}}