Searching journal content for articles similar to Kan et al. 11 (5): 889.

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  1. 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
    .... 2007; Turpin et al. 2016). Thus, a deeper understanding of these resistance mechanisms remains a critical challenge in overcoming and managing breast cancer tumors expressing HER2.Alternative splicing, a fundamental post-transcriptional process in eukaryotic gene expression, allows a single gene locus...
  2. Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
    • Chencheng Xu,
    • Suying Bao,
    • Ye Wang,
    • Wenxing Li,
    • Hao Chen,
    • Yufeng Shen,
    • Tao Jiang,
    • and Chaolin Zhang
    Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
    ...in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets...
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  3. 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
    ...across species. We show a clear link between the functional relevance, tissue regulation, and conservation of alternative transcripts on a set of 50 genes. By scaling up to the whole human protein-coding , we identify a few thousand genes where alternative splicing modulates the number and composition...
  4. Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
    • Fu-Yuan Zhu,
    • Xin Chen,
    • Yu-Chen Song,
    • Lydia Pui Ying Lam,
    • Yuki Tobimatsu,
    • Bei Gao,
    • Mo-Xian Chen,
    • and Fu-Liang Cao
    Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
    ...available at the proteomic level and apply it to assess the currently available genomic information of organisms, including identifying novel genes and spliced isoforms, assigning correct start sites and validating predicted exons and genes. Second, the use of SWATH-MS-based quantitative proteomics...
  5. 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
    ...transcripts. Novel genes did not match any annotated gene in Ensembl. We also aligned the Iso-Seq transcriptome to the most recent assembly (Supplemental Table S4; Nath et al. 2021). Of the 26,432 isoforms, only 6410 exactly matched the Ensembl predicted splicing (FSM; 25%) (Fig. 1; Table 1). The remainder...
  6. Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
    • Bina Koterniak,
    • Pallavi P. Pilaka,
    • Xicotencatl Gracida,
    • Lisa-Marie Schneider,
    • Iva Pritišanac,
    • Yun Zhang,
    • and John A. Calarco
    Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
    ...are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C...
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  7. Research: Transposon accumulation at xenobiotic gene family loci in aphids
    • Tobias Baril,
    • Adam Pym,
    • Chris Bass,
    • and Alex Hayward
    Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
    ...al. 2011), allelic succession leading to increases in resistance gene copy number (Schmidt et al. 2010), and alternative splicing and production of truncated proteins that prevent interactions with xenobiotics (Gahan et al. 2001; Darboux et al. 2007; Yang et al. 2007; Zhao et al. 2010).Studies...
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  8. Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
    • Yamile Marquez,
    • Markus Höpfler,
    • Zahra Ayatollahi,
    • Andrea Barta,
    • and Maria Kalyna
    Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
    ..., Austria Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also...
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  9. ENSEMBL Special: ESTGenes: Alternative Splicing From ESTs in Ensembl
    • Eduardo Eyras,
    • Mario Caccamo,
    • Val Curwen,
    • and Michele Clamp
    Genome Res. May 2004 14: 976-987; doi:10.1101/gr.1862204
    ...) for the prediction accuracy for cases of alternative splicing. Our case is special as there is abundant alternative splicing in both the annotations and the ESTGene predictions. We have tried to adapt some of the standard measures to our case. A gene was considered as found if its genomic extent had an overlap...
  10. Resource: Genome-wide dynamics of alternative polyadenylation in rice
    • Haihui Fu,
    • Dewei Yang,
    • Wenyue Su,
    • Liuyin Ma,
    • Yingjia Shen,
    • Guoli Ji,
    • Xinfu Ye,
    • Xiaohui Wu,
    • and Qingshun Q. Li
    Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
    .... This is termed alternative polyadenylation, or APA. For example, studies showed that ∼50% and 82% of genes in rice had more than one poly(A) site using the expressed sequence tags (EST) database, restriction enzyme digestion–mediated massively parallel signature sequencing (MPSS), or Illumina sequencing...
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