{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T16:49:18Z","timestamp":1783961358542,"version":"3.55.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2017,1,31]],"date-time":"2017-01-31T00:00:00Z","timestamp":1485820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HG006015"],"award-info":[{"award-number":["R01 HG006015"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample. Measurements of translation efficiency are generated when Ribo-seq data is analyzed in combination with matched RNA-seq gene expression profiles. Existing computational methods for identifying genes with differential translation across samples are based on sound principles, but require users to choose between accuracy and speed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Riborex, a computational tool for mapping genome-wide differences in translation efficiency. Riborex shares a similar mathematical structure with existing methods, but has a simplified implementation. Riborex directly leverages established RNA-seq analysis frameworks for all parameter estimation, providing users with a choice among robust engines for these computations. The result is a method that is dramatically faster than available methods without sacrificing accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/smithlabcode\/riborex<\/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\/btx047","type":"journal-article","created":{"date-parts":[[2017,1,30]],"date-time":"2017-01-30T13:28:22Z","timestamp":1485782902000},"page":"1735-1737","source":"Crossref","is-referenced-by-count":78,"title":["Riborex: fast and flexible identification of differential translation from Ribo-seq data"],"prefix":"10.1093","volume":"33","author":[{"given":"Wenzheng","family":"Li","sequence":"first","affiliation":[{"name":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weili","family":"Wang","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip J","family":"Uren","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz O F","family":"Penalva","sequence":"additional","affiliation":[{"name":"Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA"},{"name":"Children\u2019s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew D","family":"Smith","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,1,31]]},"reference":[{"key":"2023020205315751800_btx047-B1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1126\/science.1215704","article-title":"Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish","volume":"336","author":"Bazzini","year":"2012","journal-title":"Science"},{"key":"2023020205315751800_btx047-B2","first-page":"gkw207.","article-title":"Genome-wide analysis of Musashi-2 targets reveals novel functions in governing epithelial cell migration","volume":"1","author":"Bennett","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020205315751800_btx047-B3","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/ni.3115","article-title":"The RNA-binding protein HuR is essential for the B cell antibody response","volume":"16","author":"Diaz-Mu\u00f1oz","year":"2015","journal-title":"Nat. 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