{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T21:03:27Z","timestamp":1774559007891,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T00:00:00Z","timestamp":1766534400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Deutsche Forschungsgemeinschaft (DFG) Research Training Group","award":["325443116"],"award-info":[{"award-number":["325443116"]}]},{"name":"Federal Ministry of Research, Technology and Space (BMFTR) via the German Network for Bioinformatics Infrastructure"},{"name":"Projekt DEAL"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>RNA\u2013protein interactions play essential roles in every living organism, with RNA transcription, processing, and translation being just a few examples. Therefore, determining the set of RNAs that are bound by individual RNA-binding proteins, as well as the precise location of the interaction, is crucial for biological understanding. CLIP (UV-cross-linking and immunoprecipitation) is a method developed to study these interactions. Several variations of the CLIP protocol have been developed, e.g. iCLIP (individual-nucleotide resolution CLIP), which offers nucleotide-precise resolution of the cross-linking event.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations, and several additional steps, which can be used to detect specific characteristics, e.g. definite distances between cross-link events or identify binding motifs. Additionally, results are visualized as statistical plots for a quick overview and as standardized bioinformatics file formats, which can be used for further analysis steps.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PARANOiD is published under the MIT license and is available from https:\/\/github.com\/patrick-barth\/PARANOiD. The documentation is available at https:\/\/paranoid.readthedocs.io\/en\/latest\/index.html.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf673","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T06:54:12Z","timestamp":1766559252000},"source":"Crossref","is-referenced-by-count":0,"title":["PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9156-9694","authenticated-orcid":false,"given":"Patrick","family":"Barth","sequence":"first","affiliation":[{"name":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4166-5423","authenticated-orcid":false,"given":"Frank","family":"F\u00f6rster","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 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