Searching journal content for articles similar to Gonzàlez-Porta et al. 22 (3): 528.

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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer Gabriela D.A. Guardia1,5, Carlos H. dos Anjos1,5, Aline Rangel-Pozzo2, Filipe F. dos Santos1,3, Alexander Birbrair4, Paula F. Asprino1, Anamaria A. Camargo1 and Pedro A.F. Galante1 1...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...FilterMismatchNmax 999 ‐‐outFilterMismatchNoverReadLmax 0.04 ‐‐alignIntronMax 1,000,000 ‐‐alignMatesGapMax 100,000). Differential alternative splicing events were called using replicate Multivariate Analysis of Transcript Splicing (rMATS) v4.1.2 (Shen et al. 2014) using the ‐‐variable-read-length flag to include trimmed...
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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
...expression and alternative splicing, thus impacting complex traits and phenotypes (Teng et al. 2024).Our comparative analysis across species revealed both conserved and species-specific aspects of APA regulation. In neuronal and germline cells, APA dynamics were remarkably conserved across evolution, from...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...owing to splice site gain/loss is observed for 42 variants, with 30 (71%) producing alternative transcripts owing to new or cryptic splice sites. These findings are used to update our aberration type predictor called SpliceAI-10k calculator, resulting in 94% specificity and 90% sensitivity for major...
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Method: Identifying cell state–associated alternative splicing events and their coregulation
- Carlos F. Buen Abad Najar,
- Prakruthi Burra,
- Nir Yosef,
- and Liana F. Lareau
Genome Res. July 2022 32: 1385-1397; Published in Advance July 20, 2022, doi:10.1101/gr.276109.121
...-to-cell variability of alternative splicing. Here, we present a method, Psix, to confidently identify splicing that changes across a landscape of single cells, using a probabilistic model that is robust against the data limitations of scRNA-seq. Its autocorrelation-inspired approach finds patterns of alternative...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...arising from highly similar sequences (e.g., resulting from in-gene duplication) or very short sequences. The alternative usage of orthologous exons may then be investigated using compact representations of transcript variability, such as splicing graphs (Heber et al. 2002), where the nodes represent...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five...
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Research: Allele-specific alternative splicing and its functional genetic variants in human tissues
- Kofi Amoah,
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yiwei Sun,
- Christina Burghard,
- Boon Xin Tan,
- Ei-Wen Yang,
- and Xinshu Xiao
Genome Res. March 2021 31: 359-371; Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
...variability are involved in heart or skeletal muscle function, supporting the particular importance of alternative splicing in the biophysical properties and functions of cells (Kelemen et al. 2013).Leveraging the GTEx genotype information and GMAS events, we developed a new method to pinpoint functional SNPs...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
...or the modulatory cleavage factor I (CFI) complex cause neurodevelopmental disorders (Gennarino et al. 2015; Grozdanov et al. 2020; de Prisco et al. 2023). Alternative polyadenylation (APA) alters the length of 3′ UTRs, whereas alternative splicing may lead to alternative last exons (ALEs) and intronic...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...RNA-producing site (Luo et al. 2023). Such dsRNA may be readily formed from sense and antisense transcripts of TEs (Luo et al. 2023).Alternative mechanisms that could trigger the host defense against an invading TE include failed splicing of TE transcripts (Yu et al. 2019), environmentally induced spontaneous...
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