{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:04:32Z","timestamp":1762459472016},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2017,2,22]],"date-time":"2017-02-22T00:00:00Z","timestamp":1487721600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA plays a critical role in gene expression and its regulation. RNA binding proteins (RBPs), in turn, are important regulators of RNA. Thanks to the availability of large scale data for RBP binding motifs and in vivo binding sites results in the form of eCLIP experiments, it is now possible to computationally predict RBP binding sites across the whole genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We describe MotifMap-RNA, an extension of MotifMap which predicts binding sites for RBP motifs across human and mouse genomes and allows large scale querying of predicted binding sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The data and corresponding web server are available from: http:\/\/motifmap-rna.ics.uci.edu\/ as part of the MotifMap web portal.<\/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\/btx087","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T08:58:08Z","timestamp":1487149088000},"page":"2029-2031","source":"Crossref","is-referenced-by-count":17,"title":["MotifMap-RNA: a genome-wide map of RBP binding sites"],"prefix":"10.1093","volume":"33","author":[{"given":"Yu","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sha","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Developmental and Cell Biology, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy","family":"Bredy","sequence":"additional","affiliation":[{"name":"Department of Neurobiology and Behavior, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcelo","family":"Wood","sequence":"additional","affiliation":[{"name":"Department of Neurobiology and Behavior, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert C","family":"Spitale","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and the Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Baldi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,22]]},"reference":[{"key":"2023020206012762700_btx087-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkq1069","article-title":"RBPDB: a database of RNA-binding specificities","volume":"39","author":"Cook","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020206012762700_btx087-B2","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1186\/1471-2105-12-495","article-title":"MotifMap: integrative genome-wide maps of regulatory motif sites for model species","volume":"12","author":"Daily","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020206012762700_btx087-B3","first-page":"1","volume-title":"Advances in Experimental Medicine and Biology","author":"Gerstberger","year":"2014"},{"key":"2023020206012762700_btx087-B4","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1016\/j.febslet.2008.03.004","article-title":"RNA-binding proteins and post-transcriptional gene regulation","volume":"582","author":"Glisovic","year":"2008","journal-title":"FEBS Lett"},{"key":"2023020206012762700_btx087-B5","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/nrm2178","article-title":"RNA-binding proteins: modular design for efficient function","volume":"8","author":"Lunde","year":"2007","journal-title":"Nat. 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