{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T04:05:40Z","timestamp":1783483540114,"version":"3.55.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":256,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30\u2009bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a na\u00efve mapping.<\/jats:p>\n                  <jats:p>Availability and implementation: Ribomap is available as open source at http:\/\/www.cs.cmu.edu\/\u223cckingsf\/software\/ribomap.<\/jats:p>\n                  <jats:p>Contact: \u00a0carlk@cs.cmu.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw085","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T21:13:34Z","timestamp":1455570814000},"page":"1880-1882","source":"Crossref","is-referenced-by-count":40,"title":["Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap"],"prefix":"10.1093","volume":"32","author":[{"given":"Hao","family":"Wang","sequence":"first","affiliation":[{"name":"1 Computational Biology Department, School of Computer Science and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel","family":"McManus","sequence":"additional","affiliation":[{"name":"1 Computational Biology Department, School of Computer Science and"},{"name":"2 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carl","family":"Kingsford","sequence":"additional","affiliation":[{"name":"1 Computational Biology Department, School of Computer Science and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,2,15]]},"reference":[{"key":"2023020112312589600_btw085-B1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020112312589600_btw085-B2","doi-asserted-by":"crossref","DOI":"10.1038\/nmeth.3208","article-title":"Quantitative profiling of initiating ribosomes in vivo.","author":"Gao","year":"2015","journal-title":"Nat. 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