Searching journal content for articles similar to Agosto et al. 29 (12): 2046.

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  1. 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
    ...Table S2).View larger version: In this window In a new window Figure 1. KCl induces widespread changes in alternative splicing in mouse primary cortical neurons. (A) General experiment workflow for depolarization of mouse primary neurons using KCl. (B) Volcano plots of global differential splicing...
  2. 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
    ..., we addressed the problem of exon orthology detection in the context of AS. Our specific aims were to develop a novel and general method revisiting splicing graph representation to account for the whole transcript variability observed in a set of species and to apply this method at the protein...
  3. Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
    • Luis Ferrández-Peral,
    • Xiaoyu Zhan,
    • Marina Alvarez-Estape,
    • Cristina Chiva,
    • Paula Esteller-Cucala,
    • Raquel García-Pérez,
    • Eva Julià,
    • Esther Lizano,
    • Òscar Fornas,
    • Eduard Sabidó,
    • Qiye Li,
    • Tomàs Marquès-Bonet,
    • David Juan,
    • and Guojie Zhang
    Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
    ...out of 50,769) compared with the Universal Human Reference RNA (UHRR) Iso-Seq data set, which comprises full-length isoforms from 10 human cell lines derived from multiple tissues (Supplemental Fig. S4). The AS events newly disclosed by deep long-read sequencing (73% of all detected events, 31,544 out...
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  4. Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
    • Ulrich Omasits,
    • Adithi R. Varadarajan,
    • Michael Schmid,
    • Sandra Goetze,
    • Damianos Melidis,
    • Marc Bourqui,
    • Olga Nikolayeva,
    • Maxime Québatte,
    • Andrea Patrignani,
    • Christoph Dehio,
    • Juerg E. Frey,
    • Mark D. Robinson,
    • Bernd Wollscheid,
    • and Christian H. Ahrens
    Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
    ...annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential...
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