{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T04:15:09Z","timestamp":1782015309944,"version":"3.54.5"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T00:00:00Z","timestamp":1737763200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["833522"],"award-info":[{"award-number":["833522"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R\/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>doubletrouble is available on Bioconductor (https:\/\/bioconductor.org\/packages\/doubletrouble), and the source code is available in a GitHub repository (https:\/\/github.com\/almeidasilvaf\/doubletrouble). doubletroubledb is available online at https:\/\/almeidasilvaf.github.io\/doubletroubledb\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf043","type":"journal-article","created":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T16:32:03Z","timestamp":1737822723000},"source":"Crossref","is-referenced-by-count":25,"title":["<i>doubletrouble<\/i>: an R\/Bioconductor package for the identification, classification, and analysis of gene and genome duplications"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5314-2964","authenticated-orcid":false,"given":"Fabricio","family":"Almeida-Silva","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052,","place":["Belgium"]},{"name":"VIB Center for Plant Systems Biology, VIB , Ghent 9052,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052,","place":["Belgium"]},{"name":"VIB Center for Plant Systems Biology, VIB , Ghent 9052,","place":["Belgium"]},{"name":"Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria , Pretoria 0028,","place":["South Africa"]},{"name":"College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing 210095, Nanjing,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,25]]},"reference":[{"key":"2025030422280687900_btaf043-B1","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1007\/s00425-020-03499-8","article-title":"Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks","volume":"252","author":"Almeida-Silva","year":"2020","journal-title":"Planta"},{"key":"2025030422280687900_btaf043-B2","doi-asserted-by":"crossref","first-page":"btac806","DOI":"10.1093\/bioinformatics\/btac806","article-title":"syntenet: an R\/Bioconductor package for the inference and analysis of synteny 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