{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T01:57:54Z","timestamp":1775267874697,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["BA 2168\/11-1 SPP 1738,"],"award-info":[{"award-number":["BA 2168\/11-1 SPP 1738,"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["BA2168\/11-2 SPP 1738"],"award-info":[{"award-number":["BA2168\/11-2 SPP 1738"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","award":["RNAProNet-031L0164B"],"award-info":[{"award-number":["RNAProNet-031L0164B"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"DFG under Germany\u2019s Excellence Strategy"},{"name":"CIBSS\u2014EXC-2189-Project","award":["390939984"],"award-info":[{"award-number":["390939984"]}]}],"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>CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by tools termed peak callers. Many RBPs bind to a spliced RNA (i.e. transcript) context, but all currently available peak callers only consider and report the genomic context. To accurately model protein binding behavior, a tool is needed for the individual context assignment to CLIP-seq peak regions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present Peakhood, the first tool that utilizes CLIP-seq peak regions identified by peak callers, in tandem with CLIP-seq read information and genomic annotations, to determine which context applies, individually for each peak region. For sites assigned to transcript context, it further determines the most likely splice variant, and merges results for any number of datasets to obtain a comprehensive collection of transcript context binding sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Peakhood is freely available under MIT license at: https:\/\/github.com\/BackofenLab\/Peakhood.<\/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\/btab755","type":"journal-article","created":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T19:12:04Z","timestamp":1635534724000},"page":"1139-1140","source":"Crossref","is-referenced-by-count":3,"title":["Peakhood: individual site context extraction for CLIP-seq peak regions"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9563-4991","authenticated-orcid":false,"given":"Michael","family":"Uhl","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6701-7753","authenticated-orcid":false,"given":"Dominik","family":"Rabsch","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9564-7525","authenticated-orcid":false,"given":"Florian","family":"Eggenhofer","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg im Breisgau, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,11,4]]},"reference":[{"key":"2023020108514253600_btab755-B1","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":"Hafner","year":"2010","journal-title":"Cell"},{"key":"2023020108514253600_btab755-B2","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":"K\u00f6nig","year":"2010","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023020108514253600_btab755-B3","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1186\/s13059-017-1364-2","article-title":"PureCLIP: capturing target-specific protein\u2013RNA interaction footprints from single-nucleotide CLIP-seq data","volume":"18","author":"Krakau","year":"2017","journal-title":"Genome Biol"},{"key":"2023020108514253600_btab755-B4","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":"Licatalosi","year":"2008","journal-title":"Nature"},{"key":"2023020108514253600_btab755-B5","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":"Lovci","year":"2013","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023020108514253600_btab755-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-020-07297-0","article-title":"Improving CLIP-seq data analysis by incorporating transcript information","volume":"21","author":"Uhl","year":"2020","journal-title":"BMC Genomics"},{"key":"2023020108514253600_btab755-B7","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1093\/bioinformatics\/bts569","article-title":"Site identification in high-throughput RNA\u2013protein interaction data","volume":"28","author":"Uren","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020108514253600_btab755-B8","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":"Van Nostrand","year":"2016","journal-title":"Nat. Methods"},{"key":"2023020108514253600_btab755-B9","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/s41586-020-2077-3","article-title":"A large-scale binding and functional map of human RNA-binding proteins","volume":"583","author":"Van Nostrand","year":"2020","journal-title":"Nature"},{"key":"2023020108514253600_btab755-B10","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s13059-020-01982-9","article-title":"Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins","volume":"21","author":"Van Nostrand","year":"2020","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab755\/41075206\/btab755.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1139\/49008003\/btab755.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1139\/49008003\/btab755.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:10:12Z","timestamp":1675282212000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/4\/1139\/6420697"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,11,4]]},"references-count":10,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,1,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab755","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,15]]},"published":{"date-parts":[[2021,11,4]]}}}