{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T22:47:15Z","timestamp":1779144435525,"version":"3.51.4"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T00:00:00Z","timestamp":1764720000000},"content-version":"vor","delay-in-days":57,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Transcriptome analysis is one of the bases of modern biology, yet it is typically performed at the gene level, ignoring the complexity of alternative splicing and differential transcription initiation\/termination events. Over 95% of mammalian genes produce multiple transcripts, yet most RNA-seq analyses rely on short-read data, for which transcript-level interpretation remains challenging. Current tools suffer from low accuracy, inconsistency with annotations, and lack quick solutions for downstream biological interpretation. Here, we present Isoformic, a customizable R pipeline for transcript-level analysis of short-read RNA-seq data, available on GitHub. Isoformic processes differential expression results to detect genes with transcript-level changes, visualize exon-intron structures, and perform functional enrichment stratified by transcript type. Validated on diverse datasets, including preeclampsia, SARS-CoV-2 infection, and murine anxiety models, Isoformic reveals biologically relevant transcript variants and their possible phenotypic associations. Compatible with GENCODE reference transcriptome, Isoformic enhances the resolution of RNA-seq studies, enabling researchers to uncover the regulatory roles of alternative transcription events.<\/jats:p>","DOI":"10.1093\/nargab\/lqaf176","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:56:45Z","timestamp":1762865805000},"source":"Crossref","is-referenced-by-count":3,"title":["Isoformic: a workflow for transcript-level RNA-seq interpretation"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0707-5588","authenticated-orcid":false,"given":"Izabela","family":"Mamede","sequence":"first","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]},{"name":"D\u2019Or Institute for Research and Education , S\u00e3o Paulo, SP, 01401-002 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucio R","family":"Queiroz","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]},{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Mata-Machado","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00falia Teixeira","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Laboratory for Macromolecular Biophysics, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3161-8888","authenticated-orcid":false,"given":"Thomaz","family":"Luscher-Dias","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nayara E","family":"de\u00a0Toledo","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paulo P","family":"Amaral","sequence":"additional","affiliation":[{"name":"Instituto de Ensino e Pesquisa INSPER , S\u00e3o Paulo, SP 04546-042 ,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7336-8071","authenticated-orcid":false,"given":"Luigi","family":"Marchionni","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gloria R","family":"Franco","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics Biochemistry, Departamento de Bioqu\u00edmica e Imunologia, Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais 31270-901 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