Searching journal content for articles similar to Uapinyoying et al. 30 (6): 885.

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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...Evaluation of strategies for evidence-driven annotation using long-read RNA-seq Alejandro Paniagua1,2,6, Cristina Agustín-García1,6, Francisco J. Pardo-Palacios1, Thomas Brown3,4, Maite De Maria5, Nancy D. Denslow5, Camila J. Mazzoni3,4 and Ana Conesa1 1Institute for Integrative Systems Biology...
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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
...nested PCR or high-throughput sequencing (HTS), which may introduce bias and is restricted to detecting junctions between HBV and host s. Recently, the advancement of long-read sequencing has improved our understanding of HBV integration and its role in HCC development. HBV can integrate into the human...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...variants in the transcriptome (Glinos et al. 2022). Furthermore, long-read sequencing enables comprehensive analysis of splicing (Tilgner et al. 2015, 2018; Joglekar et al. 2021) which has fundamental importance for determining mRNA modifications due to their dependence on splicing patterns and transcript...
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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
.... (2024) combined long-read sequencing with transcript analysis to identify a novel intragenic duplication in the PALB2 gene in a patient with triple-negative breast cancer. This PALB2 duplication was reclassified as pathogenic, suggesting a potential causal link between this genetic alteration...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
..., expanding the applicability of long-read sequencing across diverse genomic studies (Wenger et al. 2019; Koren et al. 2024). Both platforms are capable of DNA and cDNA sequencing and detecting DNA methylation. At the same time, ONT offers additional functionalities such as adaptive sampling and direct RNA-seq...
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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
...-quality 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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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...isoform detection. Future studies should consider employing long-read snRNA-seq technologies such as Oxford Nanopore Technologies (ONT) or Pacific Biosciences (PacBio) to overcome these limitations and provide more comprehensive insights. Second, our reliance on the CISBP-RNA database for RBP motifs...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated s, while developing new algorithms and experimental approaches to handle the noisy data. The Long-read RNA-seq Genome Annotation Assessment Project community effort benchmarked LRS...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
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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
...of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories...

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