{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T05:35:42Z","timestamp":1757309742769},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The use of high-throughput RNA sequencing to predict dynamic operon structures in prokaryotic genomes has recently gained popularity in bioinformatics. We provide the R implementation of a novel method that uses transcriptomic features extracted from RNA-seq transcriptome profiles to develop ensemble classifiers for condition-dependent operon predictions. The CONDOP package provides a deeper insight into RNA-seq data analysis and allows scientists to highlight the operon organization in the context of transcriptional regulation with a few lines of code.<\/jats:p>\n               <jats:p>Availability and Implementation: CONDOP is implemented in R and is freely available at CRAN.<\/jats:p>\n               <jats:p>Contact: \u00a0vittorio.fortino@helsinki.fi<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw330","type":"journal-article","created":{"date-parts":[[2016,6,14]],"date-time":"2016-06-14T02:00:59Z","timestamp":1465869659000},"page":"3199-3200","source":"Crossref","is-referenced-by-count":6,"title":["CONDOP: an R package for CONdition-Dependent Operon Predictions"],"prefix":"10.1093","volume":"32","author":[{"given":"Vittorio","family":"Fortino","sequence":"first","affiliation":[{"name":"1 Institute of Biotechnology, University of Helsinki, Helsinki, Finland"}]},{"given":"Roberto","family":"Tagliaferri","sequence":"additional","affiliation":[{"name":"2 NeuRoNe Lab, DISA-MIS, University of Salerno, Fisciano, Italy"}]},{"given":"Dario","family":"Greco","sequence":"additional","affiliation":[{"name":"1 Institute of Biotechnology, University of Helsinki, Helsinki, Finland"}]}],"member":"286","published-online":{"date-parts":[[2016,6,13]]},"reference":[{"key":"2023020113480091200_btw330-B1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/1471-2105-15-145","article-title":"Transcriptome dynamics-based operon prediction in prokaryotes","volume":"15","author":"Fortino","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020113480091200_btw330-B2","first-page":"1","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"25","author":"Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"2023020113480091200_btw330-B3","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020113480091200_btw330-B4","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1093\/nar\/gkn757","article-title":"DOOR: a database for prokaryotic operons","volume":"37","author":"Mao","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020113480091200_btw330-B5","doi-asserted-by":"crossref","first-page":"e140","DOI":"10.1093\/nar\/gkt444","article-title":"Computational analysis of bacterial RNA-Seq data","volume":"41","author":"McClure","year":"2013","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/20\/3199\/49022055\/bioinformatics_32_20_3199.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/20\/3199\/49022055\/bioinformatics_32_20_3199.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:52:08Z","timestamp":1675295528000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/20\/3199\/2196380"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6,13]]},"references-count":5,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2016,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw330","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,10,15]]},"published":{"date-parts":[[2016,6,13]]}}}