{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T13:44:09Z","timestamp":1785937449727,"version":"3.56.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T00:00:00Z","timestamp":1785715200000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Department of Genetics, McDonnell Genome Institute"},{"name":"Institute for Informatics, Data Science and Biostatistics (I2DB) at Washington University School of Medicine"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Long-read RNA sequencing technologies, including Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enable direct characterization of full-length transcripts and transcriptome complexity. However, analysis of long-read RNA-seq data remains fragmented across multiple tools, limiting the ability to obtain a unified view of transcript structure, expression, and regulatory variation in long-read transcriptomes. We present NextLongIso, a scalable and reproducible Nextflow pipeline that enables coordinated analysis of multiple layers of transcript regulation. Rather than focusing solely on transcript reconstruction, NextLongIso integrates transcript discovery with downstream regulatory analyses to jointly characterize alternative splicing, isoform switching, transcript boundary dynamics (including alternative promoters and polyadenylation), and transposable element-associated transcription from both PacBio and ONT datasets. By eliminating complex cross-tool data harmonization, this unified framework facilitates the transition from transcript identification to functional interpretation of transcriptomic variation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>NextLongIso is implemented in Nextflow and is freely available at github: https:\/\/github.com\/YidanSunResearchLab\/nf-LongIso.git and Zenodo: https:\/\/doi.org\/10.5281\/zenodo.21049837.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag518","type":"journal-article","created":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T12:02:05Z","timestamp":1785585725000},"source":"Crossref","is-referenced-by-count":0,"title":["NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Jiang","family":"Tan","sequence":"first","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqing","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4019-8077","authenticated-orcid":false,"given":"Yidan","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","place":["United States"]},{"name":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","place":["United 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