Gene of interest
Analysis and Visualization of Ribosome Profiling Data
A Github wiki of the methods can be found
Currently available datasets
References for the currently available datasets are:
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S. & Weissman, J. S. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science 324, 218–223 (2009).
Brar, G. A. et al. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335, 552–557 (2012).
Zinshteyn, B. & Gilbert, W. V. Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet 9, e1003675 (2013).
Guydosh, N. R. & Green, R. Dom34 rescues ribosomes in 3' untranslated regions. Cell 156, 950–962 (2014).
McManus, C. J., Coolon, J. D., Eipper-Mains, J., Wittkopp, P. J. & Graveley, B. R. Evolution of splicing regulatory networks in Drosophila. Genome Res 24, 786–796 (2014).
Artieri, C. G. & Fraser, H. B. Evolution at two levels of gene expression in yeast. Genome Res 24, 411–421 (2014).
Gerashchenko, M. V., & Gladyshev, V. N. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic acids research, 42(17), e134-e134 (2014).
Pop, C. et al. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol 10, 770–770 (2014).
Gardin, J. et al. Measurement of average decoding rates of the 61 sense codons in vivo. eLife 3, (2014).
Lareau, L. F., Hite, D. H., Hogan, G. J. & Brown, P. O. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. eLife 3, e01257 (2014).
Jan, C. H., Williams, C. C. & Weissman, J. S. Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science 346, 1257521–1257521 (2014).
Williams, C. C., Jan, C. H. & Weissman, J. S. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science 346, 748–751 (2014).
Nedialkova, D. D. & Leidel, S. A. Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. Cell 161, 1606–1618 (2015).
Sen, N. D., Zhou, F., Ingolia, N. T. & Hinnebusch, A. G. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Res 25, 1196–1205 (2015).
Weinberg, D. E. et al. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. Cell Rep 14, 1787–1799 (2016).
© 2017 Oana Carja and Premal Shah