{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T15:41:04Z","timestamp":1776786064905,"version":"3.51.2"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,27]],"date-time":"2020-07-27T00:00:00Z","timestamp":1595808000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2012\/24731-1"],"award-info":[{"award-number":["2012\/24731-1"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2018\/15579-8"],"award-info":[{"award-number":["2018\/15579-8"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Instituto Serrapilheira. FORR","award":["2015\/25020-0"],"award-info":[{"award-number":["2015\/25020-0"]}]},{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity and genomic context and classifying them as somatic or polymorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them, in addition to finding polymorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of bona fide retroCNVs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>sideRETRO is available at https:\/\/github.com\/galantelab\/sideRETRO<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa689","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T15:15:12Z","timestamp":1595517312000},"page":"419-421","source":"Crossref","is-referenced-by-count":9,"title":["sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies"],"prefix":"10.1093","volume":"37","author":[{"given":"Thiago L A","family":"Miller","sequence":"first","affiliation":[{"name":"Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060 ,","place":["Brazil"]},{"name":"Departmento de Bioqu\u00edmica, Universidade de S\u00e3o Paulo , S\u00e3o Paulo 05508-000,","place":["Brazil"]}]},{"given":"Fernanda","family":"Orpinelli Rego","sequence":"additional","affiliation":[{"name":"Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060 ,","place":["Brazil"]}]},{"given":"Jos\u00e9 Leonel L","family":"Buzzo","sequence":"additional","affiliation":[{"name":"Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060 ,","place":["Brazil"]},{"name":"Departmento de Bioqu\u00edmica, Universidade de S\u00e3o Paulo , S\u00e3o Paulo 05508-000,","place":["Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4820-4155","authenticated-orcid":false,"given":"Pedro A F","family":"Galante","sequence":"additional","affiliation":[{"name":"Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060 ,","place":["Brazil"]}]}],"member":"286","published-online":{"date-parts":[[2020,7,27]]},"reference":[{"key":"2026041420022227400_btaa689-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2026041420022227400_btaa689-B2","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1101\/gr.154625.113","article-title":"Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division","volume":"23","author":"Abyzov","year":"2013","journal-title":"Genome Res"},{"key":"2026041420022227400_btaa689-B3","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrc.2017.35","article-title":"Transposable elements in cancer","volume":"17","author":"Burns","year":"2017","journal-title":"Nat. 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