Searching journal content for articles similar to Tardaguila et al. 28 (3): 396.

Displaying results 1-10 of 24

For checked items

view abstracts
download to citation manager

Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...inaccessible AG′ within the RNA secondary structure (Kesarwani et al. 2017). Despite these hypotheses, the exact mechanism of the effect of mutations in SF3B1 is still not resolved.Here, we aimed to comprehensively characterize the effects of SF3B1 mutations in cancer using long-read transcriptome sequencing...
OPEN ACCESS ARTICLE
Select this article
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
...prediction algorithms to enhance their efficacy. Aware of the limitations of long-read transcriptome sequencing, our study aimed to assess how lrRNA-seq data can be best used to support annotation efforts. Our results indicate that processing lrRNA-seq data into transcript models followed by SQANTI3 curation...
OPEN ACCESS ARTICLE
Select this article
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
...evaluating library preparation, sequencing platforms, and analysis tools for the identification and quantification of transcripts using LRS technologies (Pardo-Palacios et al. 2024b).LRGASP included sequencing from PacBio, ONT, and Illumina short reads, four library preparation methods, and the use of SQANTI...
OPEN ACCESS ARTICLE
Select this article
Corrigendum: Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. July 2018 28: 1096; doi:10.1101/gr.239137.118
OPEN ACCESS ARTICLE
Select this article
Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...only be considered possibly novel at best. In recent years, the SQANTI categories have become a popular approach to classifying distinct types of novelty (Tardaguila et al. 2018). The approach also relies on a comparison to a reference annotation. If a sequenced transcript has a novel intron chain...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Tardaguila et al. 28 (3): 396.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: