{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T23:30:41Z","timestamp":1789601441788,"version":"build-2803163510"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2022,6,10]],"date-time":"2022-06-10T00:00:00Z","timestamp":1654819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006219","name":"KWF","doi-asserted-by":"publisher","award":["NKI-2016-10535"],"award-info":[{"award-number":["NKI-2016-10535"]}],"id":[{"id":"10.13039\/100006219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006219","name":"KWF","doi-asserted-by":"publisher","award":["NKI-2021-13878"],"award-info":[{"award-number":["NKI-2021-13878"]}],"id":[{"id":"10.13039\/100006219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"NWO","doi-asserted-by":"publisher","award":["OCENW.KLEIN.263"],"award-info":[{"award-number":["OCENW.KLEIN.263"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Recent studies have revealed multiple mechanisms that can lead to heterogeneity in ribosomal composition. This heterogeneity can lead to preferential translation of specific panels of mRNAs, and is defined in large part by the ribosomal protein (RP) content, amongst other things. However, it is currently unknown to what extent ribosomal composition is heterogeneous across tissues, which is compounded by a lack of tools available to study it. Here we present dripARF, a method for detecting differential RP incorporation into the ribosome using Ribosome Profiling (Ribo-seq) data. We combine the \u2018waste\u2019 rRNA fragment data generated in Ribo-seq with the known 3D structure of the human ribosome to predict differences in the composition of ribosomes in the material being studied. We have validated this approach using publicly available data, and have revealed a potential role for eS25\/RPS25 in development. Our results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new method to study this phenomenon. Furthermore, with dripARF, previously published Ribo-seq data provides a wealth of new information, allowing the identification of RPs of interest in many disease and normal contexts. dripARF is available as part of the ARF R package and can be accessed through https:\/\/github.com\/fallerlab\/ARF.<\/jats:p>","DOI":"10.1093\/nar\/gkac484","type":"journal-article","created":{"date-parts":[[2022,6,10]],"date-time":"2022-06-10T15:04:08Z","timestamp":1654873448000},"page":"e95-e95","source":"Crossref","is-referenced-by-count":28,"title":["Identifying ribosome heterogeneity using ribosome profiling"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6709-9605","authenticated-orcid":false,"given":"Ferhat","family":"Alkan","sequence":"first","affiliation":[{"name":"Division of Oncogenomics, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3334-0568","authenticated-orcid":false,"given":"Oscar G","family":"Wilkins","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute , London, UK"},{"name":"UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology , UCL, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"Hern\u00e1ndez-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9091-2657","authenticated-orcid":false,"given":"Sofia","family":"Ramalho","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5301-1799","authenticated-orcid":false,"given":"Joana","family":"Silva","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jernej","family":"Ule","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute , London, UK"},{"name":"UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology , UCL, London, UK"},{"name":"UK Dementia Research Institute Centre, King\u2019s College London , London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0738-2254","authenticated-orcid":false,"given":"William\u00a0J","family":"Faller","sequence":"additional","affiliation":[{"name":"Division of Oncogenomics, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,10]]},"reference":[{"key":"2022090823585977900_B1","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.tibs.2021.07.001","article-title":"Translational control through ribosome heterogeneity and functional specialization","volume":"47","author":"Gay","year":"2021","journal-title":"Trends Biochem. 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