{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T17:59:22Z","timestamp":1772733562059,"version":"3.50.1"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,4,13]],"date-time":"2025-04-13T00:00:00Z","timestamp":1744502400000},"content-version":"vor","delay-in-days":43,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001509","name":"Royal Society of New Zealand Te Ap\u0101rangi","doi-asserted-by":"publisher","award":["MFP-UOO-2111"],"award-info":[{"award-number":["MFP-UOO-2111"]}],"id":[{"id":"10.13039\/501100001509","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Marsden Fund Fast-Start Grant","award":["MFP-UOO-2111"],"award-info":[{"award-number":["MFP-UOO-2111"]}]},{"name":"University of Otago Research"},{"name":"Otago School of Biomedical Sciences Dean\u2019s Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the specificity of detecting open reading frames (ORFs) that can be translated, such as small ORFs located upstream and downstream of the annotated ORFs. However, most genomes (e.g. bacterial genomes) lack the annotations for the transcription start and termination sites. This hinders the systematic discovery of novel ORFs in the \u2018untranslated\u2019 regions in ribosome profiling data. Here, we develop a new computational pipeline called RIBOSS to discover noncanonical ORFs and assess their translational potential against annotated ORFs. The RIBOSS Python modules are versatile, and we use them to analyse both prokaryotic and eukaryotic data. We present a resulting list of noncanonical ORFs with high translational potential in Homo sapiens, Arabidopsis thaliana, and Salmonella enterica. We further illustrate RIBOSS utility when studying organisms with incomplete transcriptome annotations. We leverage long-read and short-read data for reference-guided transcriptome assembly and highly phased ribosome profiling data for detecting novel translational events in the assembled transcriptome for S. enterica. In sum, RIBOSS is the first integrated computational pipeline for noncanonical ORF detection and translational potential assessment that incorporates long- and short-read sequencing technologies to investigate translation. RIBOSS is freely available at https:\/\/github.com\/lcscs12345\/riboss.<\/jats:p>","DOI":"10.1093\/bib\/bbaf164","type":"journal-article","created":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T14:19:26Z","timestamp":1743257966000},"source":"Crossref","is-referenced-by-count":2,"title":["RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling"],"prefix":"10.1093","volume":"26","author":[{"given":"Chun Shen","family":"Lim","sequence":"first","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]}]},{"given":"Alexandra K","family":"Gibbon","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]}]},{"given":"Anh Thu","family":"Tran Nguyen","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]}]},{"given":"Gabrielle S W","family":"Chieng","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]}]},{"given":"Chris M","family":"Brown","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , 710 Cumberland Street, Dunedin North, Dunedin 9016 ,","place":["New Zealand"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,13]]},"reference":[{"key":"2025041313265854100_ref1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a032698","article-title":"Ribosome profiling: Global views of translation","volume":"11","author":"Ingolia","year":"2019","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2025041313265854100_ref2","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome 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