{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T15:16:31Z","timestamp":1779894991808,"version":"3.53.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":63,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the EU Marie Curie ITN framework","award":["(Grant # PITN-GA-2012-316861 to GR)"],"award-info":[{"award-number":["(Grant # PITN-GA-2012-316861 to GR)"]}]},{"name":"National Cancer Institute","award":["(R01-CA142798-01 to HGW)"],"award-info":[{"award-number":["(R01-CA142798-01 to HGW)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case\u2013control studies are needed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>RiboDiff webpage http:\/\/bioweb.me\/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http:\/\/github.com\/ratschlab\/ribodiff.<\/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\/btw585","type":"journal-article","created":{"date-parts":[[2016,9,15]],"date-time":"2016-09-15T20:10:35Z","timestamp":1473970235000},"page":"139-141","source":"Crossref","is-referenced-by-count":173,"title":["RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints"],"prefix":"10.1093","volume":"33","author":[{"given":"Yi","family":"Zhong","sequence":"first","affiliation":[{"name":"Computational Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theofanis","family":"Karaletsos","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Drewe","sequence":"additional","affiliation":[{"name":"Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vipin T","family":"Sreedharan","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Kuo","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kamini","family":"Singh","sequence":"additional","affiliation":[{"name":"Cancer Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Guido","family":"Wendel","sequence":"additional","affiliation":[{"name":"Cancer Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Sloan Kettering Institute, New York, NY, USA"},{"name":"Department of Computer Science, ETH Zurich, Universitatsstrasse 6, Zrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,9,14]]},"reference":[{"key":"2023020204202191500_btw585-B1","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2023020204202191500_btw585-B2","doi-asserted-by":"crossref","first-page":"5189","DOI":"10.1093\/nar\/gkt211","article-title":"Accurate detection of differential RNA processing","volume":"41","author":"Drewe","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020204202191500_btw585-B3","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","article-title":"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes","volume":"147","author":"Ingolia","year":"2011","journal-title":"Cell"},{"key":"2023020204202191500_btw585-B4","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1038\/nprot.2012.086","article-title":"The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments","volume":"7","author":"Ingolia","year":"2012","journal-title":"Nat. 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