{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T07:57:42Z","timestamp":1771919862379,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T00:00:00Z","timestamp":1598832000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["C10701\/A15181"],"award-info":[{"award-number":["C10701\/A15181"]}],"id":[{"id":"10.13039\/501100000289","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"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"WT-MRC Cambridge Stem Cell Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n CONCUR is written in Perl and is freely available at https:\/\/github.com\/susbo\/concur.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa733","type":"journal-article","created":{"date-parts":[[2020,8,22]],"date-time":"2020-08-22T11:13:27Z","timestamp":1598094807000},"page":"717-719","source":"Crossref","is-referenced-by-count":8,"title":["CONCUR: quick and robust calculation of codon usage from ribosome profiling data"],"prefix":"10.1093","volume":"37","author":[{"given":"Michaela","family":"Frye","sequence":"first","affiliation":[{"name":"Cell Biology and Tumor Biology, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"}]},{"given":"Susanne","family":"Bornel\u00f6v","sequence":"additional","affiliation":[{"name":"Wellcome \u2013 MRC Cambridge Stem Cell Institute, University of Cambridge , Cambridge CB2 0AW, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,8,31]]},"reference":[{"key":"2023051704111079600_btaa733-B1","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s13059-019-1726-z","article-title":"Codon usage optimization in pluripotent embryonic stem cells","volume":"20","author":"Bornel\u00f6v","year":"2019","journal-title":"Genome Biol"},{"key":"2023051704111079600_btaa733-B2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2023051704111079600_btaa733-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":"2023051704111079600_btaa733-B4","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/j.cell.2015.05.022","article-title":"Optimization of codon translation rates via tRNA modification maintains proteome integrity","volume":"161","author":"Nedialkova","year":"2015","journal-title":"Cell"},{"key":"2023051704111079600_btaa733-B5","doi-asserted-by":"crossref","first-page":"12915","DOI":"10.1038\/ncomms12915","article-title":"Comparative survey of the relative impact of mRNA features on local ribosome profiling read density","volume":"7","author":"O\u2019Connor","year":"2016","journal-title":"Nat. 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Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa733\/34036762\/btaa733.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/5\/717\/50356709\/btaa733.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/5\/717\/50356709\/btaa733.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T04:11:41Z","timestamp":1684296701000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/5\/717\/5899719"}},"subtitle":[],"editor":[{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,31]]},"references-count":6,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,5,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa733","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,3,1]]},"published":{"date-parts":[[2020,8,31]]}}}