{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:11Z","timestamp":1772138051773,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T00:00:00Z","timestamp":1644796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/S018506\/1"],"award-info":[{"award-number":["BB\/S018506\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208779\/Z\/17\/Z"],"award-info":[{"award-number":["208779\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204804\/Z\/16\/Z"],"award-info":[{"award-number":["204804\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000848","name":"The University of Edinburgh","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000848","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation [DBI","award":["1936046"],"award-info":[{"award-number":["1936046"]}]},{"name":"National Science Foundation [DBI","award":["DBI 1936069"],"award-info":[{"award-number":["DBI 1936069"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35 GM124976"],"award-info":[{"award-number":["R35 GM124976"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 DK056645"],"award-info":[{"award-number":["R01 DK056645"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 DK109714"],"award-info":[{"award-number":["R01 DK109714"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 DK124369"],"award-info":[{"award-number":["R01 DK124369"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM132104"],"award-info":[{"award-number":["R01 GM132104"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Human Genetics Institute of New Jersey at Rutgers University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>riboviz 2 is freely available at github.com\/riboviz\/riboviz.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac093","type":"journal-article","created":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T15:14:23Z","timestamp":1644419663000},"page":"2358-2360","source":"Crossref","is-referenced-by-count":9,"title":["riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5756-7812","authenticated-orcid":false,"given":"Alexander L","family":"Cope","sequence":"first","affiliation":[{"name":"Department of Genetics, Rutgers University , Piscataway, NJ 08854-8082, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8778-6779","authenticated-orcid":false,"given":"Felicity","family":"Anderson","sequence":"additional","affiliation":[{"name":"Institute for Cell Biology and SynthSys, School 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School of Biological Sciences, The University of Edinburgh , Edinburgh EH9 3BF, UK"}]},{"given":"Junchen","family":"Liu","sequence":"additional","affiliation":[{"name":"EPCC, The University of Edinburgh , Edinburgh EH8 9BT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0096-200X","authenticated-orcid":false,"given":"Emma","family":"MacKenzie","sequence":"additional","affiliation":[{"name":"Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh , Edinburgh EH9 3BF, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1424-3711","authenticated-orcid":false,"given":"Vikram","family":"Shivakumar","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1238-6468","authenticated-orcid":false,"given":"Peter","family":"Tilton","sequence":"additional","affiliation":[{"name":"Department of Genetics, Rutgers University , Piscataway, NJ 08854-8082, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9109-285X","authenticated-orcid":false,"given":"Sophie M","family":"Winterbourne","sequence":"additional","affiliation":[{"name":"Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh , Edinburgh EH9 3BF, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8101-564X","authenticated-orcid":false,"given":"Siyin","family":"Xue","sequence":"additional","affiliation":[{"name":"Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh , Edinburgh EH9 3BF, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9167-7145","authenticated-orcid":false,"given":"Kostas","family":"Kavoussanakis","sequence":"additional","affiliation":[{"name":"EPCC, The University of Edinburgh , Edinburgh EH8 9BT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3223-3426","authenticated-orcid":false,"given":"Liana 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