{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T06:09:11Z","timestamp":1776492551935,"version":"3.51.2"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T00:00:00Z","timestamp":1772409600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-CoG 101170846"],"award-info":[{"award-number":["ERC-CoG 101170846"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["PID2021-124757NB-I00"],"award-info":[{"award-number":["PID2021-124757NB-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Ministry of Science and Innovation to the EMBL partnership"},{"name":"Centro de Excelencia Severo Ochoa and the CERCA Programme"},{"name":"INPhINIT PhD fellowship from LaCaixa Foundation","award":["LCF\/BQ\/DI21\/11860036"],"award-info":[{"award-number":["LCF\/BQ\/DI21\/11860036"]}]},{"DOI":"10.13039\/100010434","name":"\u201cla Caixa\u201d Foundation","doi-asserted-by":"crossref","award":["LCF\/BQ\/PR24\/12050023"],"award-info":[{"award-number":["LCF\/BQ\/PR24\/12050023"]}],"id":[{"id":"10.13039\/100010434","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often gene 3\u02b9 ends are inaccurately annotated, while most scRNA-seq methods only capture the 3\u02b9 transcript region. This results in many genes being incorrectly quantified or not detected.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>GeneExt leverages scRNA-seq data to refine gene annotations. We exemplify GeneExt usage and its impact on the gene expression quantification of eight non-model organism single-cell atlases. By extending and homogenizing gene annotations, our tool will help improve biological interpretation and cross-species comparisons of cell type expression atlases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>GeneExt is available at https:\/\/github.com\/sebepedroslab\/GeneExt (DOI: https:\/\/doi.org\/10.5281\/zenodo.18712940) under a GNU General Public license, together with test data and usage instructions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag094","type":"journal-article","created":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T12:51:38Z","timestamp":1772283098000},"source":"Crossref","is-referenced-by-count":1,"title":["GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3971-3070","authenticated-orcid":false,"given":"Grygoriy","family":"Zolotarov","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Barcelona,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1978-5824","authenticated-orcid":false,"given":"Xavier","family":"Grau-Bov\u00e9","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Barcelona,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9896-9746","authenticated-orcid":false,"given":"Arnau","family":"Seb\u00e9-Pedr\u00f3s","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Barcelona,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona,","place":["Spain"]},{"name":"ICREA , Barcelona,","place":["Spain"]},{"name":"Tree of Life Program, Wellcome Sanger Institute , Hinxton,","place":["UK"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,2]]},"reference":[{"key":"2026030914140992000_btag094-B1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41586-023-06490-x","article-title":"The status of the human gene catalogue","volume":"622","author":"Amaral","year":"2023","journal-title":"Nature"},{"key":"2026030914140992000_btag094-B2","doi-asserted-by":"crossref","first-page":"jkad220","DOI":"10.1093\/g3journal\/jkad220","article-title":"A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). 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