{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T05:18:47Z","timestamp":1773119927748,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,3,15]],"date-time":"2021-03-15T00:00:00Z","timestamp":1615766400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dutch Cancer Society (KWF Kankerbestrijding) Project","award":["NKI-2016-10535"],"award-info":[{"award-number":["NKI-2016-10535"]}]},{"name":"EMBO Long Term Fellowship","award":["210-2018"],"award-info":[{"award-number":["210-2018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of rRNA fragments. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, they may perform suboptimally in Ribo-seq. In order to overcome this, it is possible to use custom biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we first show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a \u2018one-size-fits-all\u2019 approach may be inefficient. Therefore we developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We experimentally show that Ribo-ODDR designed oligos outperform commercially available kits and lead to a significant increase in rRNA depletion in Ribo-seq.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Ribo-ODDR is freely accessible at https:\/\/github.com\/fallerlab\/Ribo-ODDR.<\/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\/btab171","type":"journal-article","created":{"date-parts":[[2021,3,10]],"date-time":"2021-03-10T07:17:44Z","timestamp":1615360664000},"page":"2659-2667","source":"Crossref","is-referenced-by-count":14,"title":["<i>Ribo-ODDR<\/i>\n                    : oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6709-9605","authenticated-orcid":false,"given":"Ferhat","family":"Alkan","sequence":"first","affiliation":[{"name":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"}]},{"given":"Joana","family":"Silva","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"}]},{"given":"Eric","family":"Pint\u00f3 Barber\u00e0","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0738-2254","authenticated-orcid":false,"given":"William J.","family":"Faller","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2021,3,15]]},"reference":[{"key":"2023051609172700900_btab171-B1","first-page":"e60","article-title":"RIsearch2: suffix array-based large-scale prediction of RNA\u2013RNA interactions and siRNA off-targets","volume":"45","author":"Alkan","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023051609172700900_btab171-B2","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nature06196","article-title":"Identification of stem cells in small intestine and colon by marker gene Lgr5","volume":"449","author":"Barker","year":"2007","journal-title":"Nature"},{"key":"2023051609172700900_btab171-B3","doi-asserted-by":"crossref","first-page":"11005","DOI":"10.1038\/s41598-019-47424-w","article-title":"Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker\u2019s yeast","volume":"9","author":"Blevins","year":"2019","journal-title":"Sci. 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