{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:24Z","timestamp":1772138064067,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["United Kingdom"],"award-info":[{"award-number":["United Kingdom"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["104640"],"award-info":[{"award-number":["104640"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["207498"],"award-info":[{"award-number":["207498"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["0292096"],"award-info":[{"award-number":["0292096"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>RNA (ribonucleic acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analyzing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https:\/\/CRAN.R-project.org\/package=rnaCrosslinkOO. The software is supported on Linux, macOS, and Windows platforms.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae193","type":"journal-article","created":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T13:25:38Z","timestamp":1712582738000},"source":"Crossref","is-referenced-by-count":1,"title":["rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6554-5667","authenticated-orcid":false,"given":"Jonathan L","family":"Price","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Cambridge , Cambridge, CB2 1GA, United Kingdom"}]},{"given":"Omer","family":"Ziv","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Cambridge , Cambridge, CB2 1GA, United Kingdom"},{"name":"Eleven Therapeutics , Cambridge, CB2 0RE, United Kingdom"}]},{"given":"Malte L","family":"Pinckert","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cambridge , Cambridge, CB2 1QP, United Kingdom"}]},{"given":"Andrew","family":"Lim","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Cambridge , Cambridge, CB2 1GA, United Kingdom"}]},{"given":"Eric A","family":"Miska","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Cambridge , Cambridge, CB2 1GA, United Kingdom"}]}],"member":"286","published-online":{"date-parts":[[2024,4,10]]},"reference":[{"key":"2024043023463387200_btae193-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2016.04.028","article-title":"In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation","volume":"62","author":"Aw","year":"2016","journal-title":"Mol Cell"},{"key":"2024043023463387200_btae193-B2","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1126\/science.289.5481.905","article-title":"The complete atomic structure of the large ribosomal subunit at 2.4 a resolution","volume":"289","author":"Ban","year":"2000","journal-title":"Science"},{"key":"2024043023463387200_btae193-B3","author":"Cs\u00e1rdi","year":"2023"},{"key":"2024043023463387200_btae193-B4","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2024043023463387200_btae193-B5","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1038\/nprot.2016.011","article-title":"Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE","volume":"11","author":"Flynn","year":"2016","journal-title":"Nat Protoc"},{"key":"2024043023463387200_btae193-B6","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1111\/j.1471-4159.2010.07016.x","article-title":"Involvement of the 3\u2019-untranslated region of the brain-derived neurotrophic factor gene in activity-dependent mRNA stabilization","volume":"115","author":"Fukuchi","year":"2010","journal-title":"J Neurochem"},{"key":"2024043023463387200_btae193-B7","first-page":"956","article-title":"Global mapping of RNA homodimers in living cells","volume":"32","author":"Gabryelska","year":"2022","journal-title":"Genome Res"},{"key":"2024043023463387200_btae193-B8","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1128\/MCB.01149-10","article-title":"RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5\u2032 splice Site","volume":"31","author":"Kar","year":"2011","journal-title":"Mol Cell Biol"},{"key":"2024043023463387200_btae193-B9","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA Package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol Biol"},{"key":"2024043023463387200_btae193-B10","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/978-1-4939-7213-5_4","article-title":"PARIS: psoralen analysis of RNA interactions and structures with high throughput and resolution","volume":"1649","author":"Lu","year":"2018","journal-title":"Methods Mol Biol (Clifton, NJ)"},{"key":"2024043023463387200_btae193-B11","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nrg3681","article-title":"Insights into RNA structure and function from genome-wide studies","volume":"15","author":"Mortimer","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2024043023463387200_btae193-B12","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/nature07598","article-title":"A stress-responsive RNA switch regulates VEGFA expression","volume":"457","author":"Ray","year":"2009","journal-title":"Nature"},{"key":"2024043023463387200_btae193-B13","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.molcel.2016.04.030","article-title":"Global mapping of human RNA\u2013RNA interactions","volume":"62","author":"Sharma","year":"2016","journal-title":"Mol Cell"},{"key":"2024043023463387200_btae193-B14","doi-asserted-by":"crossref","first-page":"e70","DOI":"10.1093\/nar\/gkv1505","article-title":"TopDom: an efficient and deterministic method for identifying topological domains in genomes","volume":"44","author":"Shin","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024043023463387200_btae193-B15","doi-asserted-by":"crossref","first-page":"bbac112","DOI":"10.1093\/bib\/bbac112","article-title":"Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives","volume":"23","author":"Solayman","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024043023463387200_btae193-B16","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/s41576-022-00546-w","article-title":"Probing the dynamic RNA structurome and its functions","volume":"24","author":"Spitale","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2024043023463387200_btae193-B17","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1126\/science.1192002","article-title":"Long noncoding RNA as modular scaffold of histone modification complexes","volume":"329","author":"Tsai","year":"2010","journal-title":"Science"},{"key":"2024043023463387200_btae193-B18","doi-asserted-by":"crossref","first-page":"e2112677119","DOI":"10.1073\/pnas.2112677119","article-title":"Thoughts on how to think (and talk) about RNA structure","volume":"119","author":"Vicens","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024043023463387200_btae193-B19","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/nrg3049","article-title":"Understanding the transcriptome through RNA structure","volume":"12","author":"Wan","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2024043023463387200_btae193-B20","first-page":"1","article-title":"KARR-seq reveals cellular higher-order RNA structures and RNA\u2013RNA interactions","volume":"12","author":"Wu","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2024043023463387200_btae193-B21","first-page":"968","article-title":"Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers","volume":"32","author":"Zhang","year":"2022","journal-title":"Genome Res"},{"key":"2024043023463387200_btae193-B22","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41592-018-0121-0","article-title":"COMRADES determines in vivo RNA structures and interactions","volume":"15","author":"Ziv","year":"2018","journal-title":"Nat Methods"},{"key":"2024043023463387200_btae193-B23","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/j.molcel.2020.11.004","article-title":"The short- and long-range RNA\u2013RNA interactome of SARS-CoV-2","volume":"80","author":"Ziv","year":"2020","journal-title":"Mol Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae193\/57206600\/btae193.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/4\/btae193\/57364578\/btae193.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/4\/btae193\/57364578\/btae193.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,30]],"date-time":"2024-04-30T19:47:01Z","timestamp":1714506421000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae193\/7643507"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,3,29]]},"references-count":23,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,3,29]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae193","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.12.12.563348","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,4,1]]},"published":{"date-parts":[[2024,3,29]]},"article-number":"btae193"}}