Searching journal content for articles similar to Calvo-Roitberg et al. 34 (11): 1719.

Displaying results 1-10 of 128

For checked items

view abstracts
download to citation manager

Select this article
Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...also examined two ONT assemblies generated with Flye (Kolmogorov et al. 2019), with different read length cutoffs (1 kb and 45 kb; the coverages are 400× and 100×). Briefly, we checked for each mRNA, the proportion of its sequence that is present in the assemblies (Supplemental Methods). The rationale...
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
...↵Castells-Roca L, García-Martínez J, Moreno J, Herrero E, Bellí G, Pérez-Ortín JE. 2011. Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One 6: e17272. doi:10.1371/journal.pone.0017272 ↵Chen Y-C, Chen C-Y, Chiang T-W, Chan M-H, Hsiao M, Ke H-M, Tsai IJ...
OPEN ACCESS ARTICLE
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
...annotated Usher syndrome–associated transcripts were identified in the human retina by IsoQuant analysis. Additionally, it highlights frequently observed novel transcript isoforms and events identified by IsoQuant, and validated by Oxford Nanopore Technologies (ONT) long-read mRNA sequencing of independent...
Select this article
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
..., and therapeutic perspective. Med Oncol 40: 71. doi:10.1007/s12032-022-01943-1 ↵Calvo-Roitberg E, Daniels RF, Pai AA. 2024. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. Genome Res 34: 1719–1734. doi:10.1101/gr.279559...
Select this article
Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...; Murdock et al. 2021; Yépez et al. 2022). However, previous studies have relied on SRS, which has limited ability to reconstruct full-length mRNA transcripts, making it challenging to interpret the exact impact of splice-altering variants or fully resolve novel gene fusions. Long-read RNA-seq in contrast...
OPEN ACCESS ARTICLE
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
...detection without the need for an assembly step. As with any technology, lrRNA-seq is not without errors, and factors such as mRNA degradation, library preparation failures, and sequencing inaccuracies can result in bias in the data.A database tracking bioinformatic tools for LRS (Amarasinghe et al. 2021...
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
...-cell sequencing and long-read sequencing, have greatly expanded. Both have been used in transcriptomics to characterize the mRNA expression profiles of cells. Single-cell sequencing allows transcript molecules to be traced to individual cells, thus preserving cell-type-specific information about expression. Long-read...
OPEN ACCESS ARTICLE
Select this article
Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...Oxford Nanopore Technologies long-read s of 68 individuals from the undiagnosed disease network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read s, we detected 716 long-read rare (MAF < 0.01) SV...
OPEN ACCESS ARTICLE
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
...transcripts (Fig. 4A).View larger version: In this window In a new window Figure 4. SF3B1 mutation results in altered mRNAs potentially translated into modified proteins. (A) Coding potential of the known and novel isoforms identified divided by CDS similarity to annotated isoforms and NMD prediction. (B...
OPEN ACCESS ARTICLE
Select this article
Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
.... Cells were harvested by trypsin dissociation for long-read CAGE and nanoCAGE library preparation and by scraping for HLA-I pulldown experiment.Library preparation of LRCAGE, LRhex, and nanoCAGETo enrich our RNA samples for reverse transcription with full-length mRNA, we added two additional steps, poly...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Calvo-Roitberg et al. 34 (11): 1719.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: