{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:10:39Z","timestamp":1772172639115,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007227","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T00:00:00Z","timestamp":1567123200000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2019,8,19]],"date-time":"2019-08-19T00:00:00Z","timestamp":1566172800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007227","type":"journal-article","created":{"date-parts":[[2019,8,19]],"date-time":"2019-08-19T13:35:10Z","timestamp":1566221710000},"page":"e1007227","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3894-6902","authenticated-orcid":true,"given":"Jianan","family":"Lin","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8986-0354","authenticated-orcid":true,"given":"Yuping","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Wayne N.","family":"Frankel","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2842-8503","authenticated-orcid":true,"given":"Zhengqing","family":"Ouyang","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,8,19]]},"reference":[{"issue":"7","key":"pcbi.1007227.ref001","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nrg2111","article-title":"RNA regulons: coordination of post-transcriptional events","volume":"8","author":"JD Keene","year":"2007","journal-title":"Nat Rev Genet"},{"issue":"2","key":"pcbi.1007227.ref002","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1002\/jnr.21485","article-title":"New implications for the QUAKING RNA binding protein in human disease","volume":"86","author":"CA Chenard","year":"2008","journal-title":"J Neurosci Res"},{"issue":"3","key":"pcbi.1007227.ref003","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/j.molcel.2011.06.008","article-title":"Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR","volume":"43","author":"S Lebedeva","year":"2011","journal-title":"Mol Cell"},{"issue":"2","key":"pcbi.1007227.ref004","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.molcel.2014.05.022","article-title":"Direct binding of Ataxin-2 to distinct elements in 3' UTRs promotes mRNA stability and protein expression","volume":"55","author":"M Yokoshi","year":"2014","journal-title":"Mol Cell"},{"issue":"7221","key":"pcbi.1007227.ref005","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/nature07488","article-title":"HITS-CLIP yields genome-wide insights into brain alternative RNA processing","volume":"456","author":"DD Licatalosi","year":"2008","journal-title":"Nature"},{"issue":"2","key":"pcbi.1007227.ref006","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1038\/nrg3141","article-title":"Protein-RNA interactions: new genomic technologies and perspectives","volume":"13","author":"J Konig","year":"2012","journal-title":"Nat Rev Genet"},{"issue":"1","key":"pcbi.1007227.ref007","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.cell.2010.03.009","article-title":"Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP","volume":"141","author":"M Hafner","year":"2010","journal-title":"Cell"},{"issue":"7","key":"pcbi.1007227.ref008","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nsmb.1838","article-title":"iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution","volume":"17","author":"J Konig","year":"2010","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"pcbi.1007227.ref009","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1093\/bfgp\/elu047","article-title":"High-throughput characterization of protein-RNA interactions","volume":"14","author":"KB Cook","year":"2015","journal-title":"Briefings in functional genomics"},{"issue":"1","key":"pcbi.1007227.ref010","doi-asserted-by":"crossref","first-page":"R18","DOI":"10.1186\/gb-2014-15-1-r18","article-title":"PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis","volume":"15","author":"B Chen","year":"2014","journal-title":"Genome Biol"},{"issue":"1","key":"pcbi.1007227.ref011","doi-asserted-by":"crossref","first-page":"R11","DOI":"10.1186\/gb-2014-15-1-r11","article-title":"dCLIP: a computational approach for comparative CLIP-seq analyses","volume":"15","author":"T Wang","year":"2014","journal-title":"Genome Biol"},{"issue":"4","key":"pcbi.1007227.ref012","doi-asserted-by":"crossref","first-page":"e93248","DOI":"10.1371\/journal.pone.0093248","article-title":"A model-based approach to identify binding sites in CLIP-Seq data","volume":"9","author":"T Wang","year":"2014","journal-title":"PLoS One"},{"issue":"12","key":"pcbi.1007227.ref013","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1038\/nsmb.2699","article-title":"Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges","volume":"20","author":"MT Lovci","year":"2013","journal-title":"Nat Struct Mol Biol"},{"issue":"24","key":"pcbi.1007227.ref014","doi-asserted-by":"crossref","first-page":"3333","DOI":"10.1093\/bioinformatics\/btr570","article-title":"Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data","volume":"27","author":"S Althammer","year":"2011","journal-title":"Bioinformatics"},{"issue":"23","key":"pcbi.1007227.ref015","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1093\/bioinformatics\/bts569","article-title":"Site identification in high-throughput RNA-protein interaction data","volume":"28","author":"PJ Uren","year":"2012","journal-title":"Bioinformatics"},{"key":"pcbi.1007227.ref016","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s12859-015-0470-y","article-title":"Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data","volume":"16","author":"F Comoglio","year":"2015","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"pcbi.1007227.ref017","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2011-12-8-r79","article-title":"PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data","volume":"12","author":"DL Corcoran","year":"2011","journal-title":"Genome Biol"},{"issue":"2","key":"pcbi.1007227.ref018","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nprot.2014.012","article-title":"Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis","volume":"9","author":"MJ Moore","year":"2014","journal-title":"Nat Protoc"},{"issue":"4","key":"pcbi.1007227.ref019","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1093\/bioinformatics\/btw653","article-title":"CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data","volume":"33","author":"A Shah","year":"2017","journal-title":"Bioinformatics"},{"issue":"7","key":"pcbi.1007227.ref020","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2013-14-7-r79","article-title":"PARma: identification of microRNA target sites in AGO-PAR-CLIP data","volume":"14","author":"F Erhard","year":"2013","journal-title":"Genome Biol"},{"key":"pcbi.1007227.ref021","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.mcn.2013.04.002","article-title":"CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders","volume":"56","author":"M Modic","year":"2013","journal-title":"Mol Cell Neurosci"},{"issue":"5","key":"pcbi.1007227.ref022","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1016\/j.celrep.2017.04.028","article-title":"High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43","volume":"19","author":"G Rot","year":"2017","journal-title":"Cell Rep"},{"issue":"3","key":"pcbi.1007227.ref023","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.molcel.2011.06.007","article-title":"Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability","volume":"43","author":"N Mukherjee","year":"2011","journal-title":"Mol Cell"},{"issue":"3\u20134","key":"pcbi.1007227.ref024","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1159\/000066619","article-title":"Identification and characterization of murine Brunol4, a new member of the elav\/bruno family","volume":"97","author":"M Meins","year":"2002","journal-title":"Cytogenet Genome Res"},{"issue":"7","key":"pcbi.1007227.ref025","doi-asserted-by":"crossref","first-page":"e124","DOI":"10.1371\/journal.pgen.0030124","article-title":"Complex seizure disorder caused by Brunol4 deficiency in mice","volume":"3","author":"Y Yang","year":"2007","journal-title":"PLoS Genet"},{"issue":"12","key":"pcbi.1007227.ref026","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1038\/ejhg.2012.92","article-title":"Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity","volume":"20","author":"C Halgren","year":"2012","journal-title":"European journal of human genetics: EJHG"},{"issue":"6","key":"pcbi.1007227.ref027","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1002\/ajmg.a.38205","article-title":"Familial 18q12.2 deletion supports the role of RNA-binding protein CELF4 in autism spectrum disorders","volume":"173","author":"R Barone","year":"2017","journal-title":"American journal of medical genetics Part A"},{"issue":"7","key":"pcbi.1007227.ref028","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1111\/j.1601-183X.2011.00717.x","article-title":"Etiology of a genetically complex seizure disorder in Celf4 mutant mice","volume":"10","author":"JL Wagnon","year":"2011","journal-title":"Genes, brain, and behavior"},{"issue":"11","key":"pcbi.1007227.ref029","doi-asserted-by":"crossref","first-page":"e1003067","DOI":"10.1371\/journal.pgen.1003067","article-title":"CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function","volume":"8","author":"JL Wagnon","year":"2012","journal-title":"PLoS Genet"},{"issue":"1","key":"pcbi.1007227.ref030","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/hmg\/5.1.115","article-title":"Novel proteins with binding specificity for DNA CTG repeats and RNA CUG repeats: implications for myotonic dystrophy","volume":"5","author":"LT Timchenko","year":"1996","journal-title":"Hum Mol Genet"},{"issue":"51","key":"pcbi.1007227.ref031","doi-asserted-by":"crossref","first-page":"20333","DOI":"10.1073\/pnas.0809045105","article-title":"A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart","volume":"105","author":"A Kalsotra","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pcbi.1007227.ref032","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1002\/dvdy.20382","article-title":"Dynamic balance between activation and repression regulates pre-mRNA alternative splicing during heart development","volume":"233","author":"AN Ladd","year":"2005","journal-title":"Dev Dyn"},{"issue":"19","key":"pcbi.1007227.ref033","doi-asserted-by":"crossref","first-page":"4625","DOI":"10.1016\/j.febslet.2006.07.042","article-title":"Inducible-NOS but not neuronal-NOS participate in the acute effect of TNF-alpha on hypothalamic insulin-dependent inhibition of food intake","volume":"580","author":"JC Moraes","year":"2006","journal-title":"FEBS Lett"},{"issue":"6","key":"pcbi.1007227.ref034","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1101\/gr.184390.114","article-title":"Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins","volume":"25","author":"ET Wang","year":"2015","journal-title":"Genome Res"},{"issue":"51","key":"pcbi.1007227.ref035","doi-asserted-by":"crossref","first-page":"21521","DOI":"10.1073\/pnas.0904863106","article-title":"ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells","volume":"106","author":"Z Ouyang","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"pcbi.1007227.ref036","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"issue":"6","key":"pcbi.1007227.ref037","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1007227.ref038","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1002\/wrna.107","article-title":"The importance of CELF control: molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins","volume":"3","author":"T Dasgupta","year":"2012","journal-title":"Wiley Interdiscip Rev RNA"},{"issue":"1","key":"pcbi.1007227.ref039","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/S1097-2765(03)00012-1","article-title":"Coupled mRNA stabilization and translational silencing of cyclooxygenase-2 by a novel RNA binding protein, CUGBP2","volume":"11","author":"D Mukhopadhyay","year":"2003","journal-title":"Mol Cell"},{"issue":"4","key":"pcbi.1007227.ref040","doi-asserted-by":"crossref","first-page":"G1025","DOI":"10.1152\/ajpgi.00602.2007","article-title":"Translation inhibition during cell cycle arrest and apoptosis: Mcl-1 is a novel target for RNA binding protein CUGBP2","volume":"294","author":"D Subramaniam","year":"2008","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"pcbi.1007227.ref041","first-page":"179648","article-title":"A Large-Scale Binding and Functional Map of Human RNA Binding Proteins","author":"EL Van Nostrand","year":"2018","journal-title":"bioRxiv"},{"issue":"6","key":"pcbi.1007227.ref042","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nmeth.3810","article-title":"Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)","volume":"13","author":"EL Van Nostrand","year":"2016","journal-title":"Nat Methods"},{"issue":"7414","key":"pcbi.1007227.ref043","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"EP Consortium","year":"2012","journal-title":"Nature"},{"issue":"12","key":"pcbi.1007227.ref044","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"6","key":"pcbi.1007227.ref045","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/j.molcel.2005.10.031","article-title":"Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping","volume":"20","author":"M Fenger-Gron","year":"2005","journal-title":"Mol Cell"},{"issue":"7","key":"pcbi.1007227.ref046","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1038\/ncb3189","article-title":"A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy","volume":"17","author":"G Hu","year":"2015","journal-title":"Nat Cell Biol"},{"issue":"7494","key":"pcbi.1007227.ref047","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/nature13007","article-title":"Poly(A)-tail profiling reveals an embryonic switch in translational control","volume":"508","author":"AO Subtelny","year":"2014","journal-title":"Nature"},{"issue":"6\u20137","key":"pcbi.1007227.ref048","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.bbagrm.2013.01.001","article-title":"CELFish ways to modulate mRNA decay","volume":"1829","author":"I Vlasova-St Louis","year":"2013","journal-title":"Biochim Biophys Acta"},{"issue":"5990","key":"pcbi.1007227.ref049","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1126\/science.1191150","article-title":"Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls","volume":"329","author":"C Zhang","year":"2010","journal-title":"Science"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007227","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T00:00:00Z","timestamp":1567123200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007227","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,19]],"date-time":"2023-09-19T03:19:53Z","timestamp":1695093593000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007227"}},"subtitle":[],"editor":[{"given":"Dina","family":"Schneidman-Duhovny","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,19]]},"references-count":49,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2019,8,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007227","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.736455944.793574308","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,19]]}}}