Searching journal content for articles similar to Tardaguila et al. 28 (7): 1096.

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Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
- Netanya Keil,
- Carolina Monzó,
- Lauren McIntyre,
- and Ana Conesa
Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
...-reads, an extension of SQANTI3 (Pardo-Palacios et al. 2024a), a tool originally designed for transcript model quality control, to jointly provide quality control metrics for long-read data and to analyze multiple samples for consistency and bias. We demonstrate that SQANTI3's structural categories and other quality...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...distinct structural categories using SQANTI3 (Fig. 4A; Tardaguila et al. 2018): (i) full splice match (FSM); (ii) incomplete splice match (ISM); (iii) novel in category (NIC); (iv) novel not in category (NNC); (v) fusion (F); (vi) genic (G); (vii) antisense (A); and (viii) intergenic (I). The statistics...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...associated with distinct subcellular fractions. All long-read libraries were pooled for de novo transcriptome assembly using Mandalorion (Volden et al. 2023). Mandalorion assembled a transcriptome consisting of transcripts with long-read support of five or more. We then used SQANTI3 to quality control...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...; however, its oncogenic mechanisms remain incompletely understood because of limitations in detection methods and sample availability. In this study, we employ Oxford Nanopore Technologies (ONT) whole- sequencing and full-length transcriptome sequencing to characterize HBV integration events at the genomic...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...to have the lowest rate of false positive isoforms compared to alternatives like SQANTI3 and TALON (Prjibelski et al. 2023; Pardo-Palacios et al. 2024). However, integrating the long transcript workflow data set into a combined IsoQuant analysis with the standard workflow data sets posed challenges...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...evidence-guided gene annotationsWe aimed to improve on current fungal gene annotations by incorporating extensive long-read cDNA sequencing data sets (Pardo-Palacios et al. 2024). We generated a detailed time course of ONT direct cDNA data sets for Pst104E gene annotation. The transcripts were sampled from...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...55421, USA Corresponding author: jshaw@ds.dfci.harvard.eduAbstractReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...characterization of individual exons toward studying alternative RNA processing events in the isoform context. Therefore, LRS provides an attractive approach for studying full-length RNA molecules.Challenges of terminal end identification with long-read RNA sequencingShort-read sequencing (SRS) technologies...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the , transcriptome, and epi, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long-read...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...are necessary to better understand this phenomenon.In conclusion, the long-read scRNA-seq approach was proved to be highly effective in identifying both known and novel isoforms. Our study stands as the first unbiased characterization of full-length transcription isoforms in single cells within the mouse retina...

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