Searching journal content for articles similar to Rocha 14 (11): 2279.

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  1. Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
    • William Gao,
    • Carlos J. Gallardo-Dodd,
    • and Claudia Kutter
    Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
    ...information on chromatin accessibility as a proxy for quantification of anticodon usages, and investigate the interdependencies of matched codon and anticodon pools at the cell-type level. Finally, we calculate translation efficiency by correlating AA demand and supply from the mRNA and tRNA side...
  2. 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
    ...(Liu et al. 2013; Wu et al. 2019), codon usage (Radhakrishnan et al. 2016), and identification of novel translated open reading frames (ORFs) and micropeptides (fewer than 100 amino acids) encoded in a (Ji et al. 2015; Calviello et al. 2016; Chen et al. 2020).However, current ribosome profiling...
  3. Research: Variation in the fitness impact of translationally optimal codons among animals
    • Florian Bénitière,
    • Tristan Lefébure,
    • and Laurent Duret
    Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
    ...codons in the transcriptome (i.e., the codon demand) and (2) selection on the SCU of genes to match the pool of tRNAs, referred to as translational selection (TS).It is generally considered that there are two main benefits of using translationally optimal codons. First, this leads to faster translation...
  4. LETTER: Causes for the intriguing presence of tRNAs in phages
    • Marc Bailly-Bechet,
    • Massimo Vergassola,
    • and Eduardo Rocha
    Genome Res. October 2007 17: 1486-1495; Published in Advance September 4, 2007, doi:10.1101/gr.6649807
    ..., which, accordingly, contain more tRNAs than temperate ones. We observed higher codon usage bias in virulent phages. Why should that be? We speculate that it is because virulent phages replicate faster and need to translate very efficiently their mRNAs. Although we could not find data on latency times...
  5. LETTER: Similar compositional biases are caused by very different mutational effects
    • Eduardo P.C. Rocha,
    • Marie Touchon,
    • and Edward J. Feil
    Genome Res. December 2006 16: 1537-1547; Published in Advance October 26, 2006, doi:10.1101/gr.5525106
    ...( Rocha and Danchin 2003 ). Hence, we used the CAI index ( Sharp and Li 1987 ) to remove the top 10% genes with most biased codon usage, expected to be the most highly expressed. We checked that removing even more genes (15%) from the with the highest codon usage bias ( E. coli ) led to the same results...
  6. ERRATUM: Correction for Volume 14, p. 2279 Genome Res. December 2004 14: 2510
    ...genome;14/12/2510-c 1088-9051 Correction for Volume 14, p. 2279 Correction for Volume 14, p. 2279 Genome Research 14: 2279-2286 (2004) Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization Eduardo P.C. Rocha In the first...
  7. ERRATUM: Correction for Volume 14, p. 2221 Genome Res. December 2004 14: 2510
    .... The authors apologize for any inconvenience this error may have caused other investigators in the field. Genome Research 14: 2279–2286 (2004) Codon usage bias from tRNA’s point of view: Redundancy, specialization, and efficient decoding for translation optimization Eduardo P.C. Rocha In the first paragraph...
  8. ERRATUM: Correction for Volume 14, p. 1786 Genome Res. December 2004 14: 2510
    ...is reprinted below. The authors apologize for any inconvenience this error may have caused other investigators in the field. Genome Research 14: 2279–2286 (2004) Codon usage bias from tRNA’s point of view: Redundancy, specialization, and efficient decoding for translation optimization Eduardo P.C. Rocha...
  9. ERRATUM: Correction for Volume 13, p. 875 Genome Res. December 2004 14: 2510
    ...investigators in the field. Genome Research 14: 2279–2286 (2004) Codon usage bias from tRNA’s point of view: Redundancy, specialization, and efficient decoding for translation optimization Eduardo P.C. Rocha In the first paragraph of the first column on page 2281 and in Figure 1, there is a typo...
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