Searching journal content for articles similar to Michel et al. 22 (11): 2219.

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  1. Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
    • Jack A.S. Tierney,
    • Michał Świrski,
    • Håkon Tjeldnes,
    • Jonathan M. Mudge,
    • Joanna Kufel,
    • Nicola Whiffin,
    • Eivind Valen,
    • and Pavel V. Baranov
    Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
    .... Observation of dually decoded regions of the human using ribosome profiling data. Genome Res 22: 2219–2229. doi:10.1101/gr.133249.111 ↵Michel AM, Andreev DE, Baranov PV. 2014. Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account...
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  2. Research: Ribosome profiling reveals an important role for translational control in circadian gene expression
    • Christopher Jang,
    • Nicholas F. Lahens,
    • John B. Hogenesch,
    • and Amita Sehgal
    Genome Res. December 2015 25: 1836-1847; Published in Advance September 3, 2015, doi:10.1101/gr.191296.115
    ...), as described at http://creativecommons.org/licenses/bync/4.0/. Research 1836 Genome Research 25:1836–1847 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org www..org experiments in human U2OS cells and compared these results with RNA-seq. Ribosome profiling is based on the protection...
  3. Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
    • Qianru Li,
    • Haiwang Yang,
    • Emily K. Stroup,
    • Hongbin Wang,
    • and Zhe Ji
    Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
    ...compared footprints in other genomic regions and observed major differences in small noncoding RNAs (Supplemental Fig. S3A); 11.5% of our RNase footprinting reads were mapped to small noncoding RNAs, which is 3.7-fold that of ribosome profiling (Supplemental Fig. S3A–C). These reads were found within...
  4. Research: Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context
    • Maria S. Benitez-Cantos,
    • Martina M. Yordanova,
    • Patrick B.F. O'Connor,
    • Alexander V. Zhdanov,
    • Sergey I. Kovalchuk,
    • Dmitri B. Papkovsky,
    • Dmitry E. Andreev,
    • and Pavel V. Baranov
    Genome Res. July 2020 30: 974-984; Published in Advance July 15, 2020, doi:10.1101/gr.257352.119
    ...), whereas for AASDHPPT, ribosome profiling data suggest that initiation at sAUG is greater than at fdAUG, contrary to our reporter assay (Fig. 4D). For intact GWIPS-viz screenshots of each of the 10 genomic loci, see Supplemental Figures S3–S12. A certain level of disagreement between the two approaches...
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  5. Perspective: Functional transcriptomics in the post-ENCODE era
    • Jonathan M. Mudge,
    • Adam Frankish,
    • and Jennifer Harrow
    Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
    ...are used (a situation confounded by the occurrence of AS) (Tanner et al. 2007; Brosch et al. 2011; Ezkurdia et al. 2012). Ribosome profiling (RP) is a newer technique designed to infer translated regions of RNA molecules (Ingolia et al. 2009). Essentially, the short portion of an RNA that is bound...
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  6. Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
    • Mayank Murali,
    • Jamie Saquing,
    • Senbao Lu,
    • Ziyang Gao,
    • Emily F. Watts,
    • Ben Jordan,
    • Zachary Peters Wakefield,
    • Ana Fiszbein,
    • David R. Cooper,
    • Peter J. Castaldi,
    • Dmitry Korkin,
    • and Gloria M. Sheynkman
    Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
    ...” in the other frame a new stop codon that is now decoded by the ribosome (i.e., frameshift-driven events) (Supplemental Table S9).In direct splice-driven events, the stop codon availability is dictated by the actively transcribed regions that contain the stop codon. We find this scenario for 72% (8877 of 12...
  7. Research: Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
    • Yuliya A. Sytnikova,
    • Reazur Rahman,
    • Gung-wei Chirn,
    • Josef P. Clark,
    • and Nelson C. Lau
    Genome Res. December 2014 24: 1977-1990; Published in Advance September 29, 2014, doi:10.1101/gr.178129.114
    ....114. 24:1977–1990 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/14; www..org Genome Research 1977 www..org Figure 1. Transcriptome profiling and CLIP-seq confirm that transposable elements (TEs) are the main direct targets of PIWI-mediated regulation. (A) Bioinformatic prediction...
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