R. Grantham, C. Gautier, M. Gouy, R. Mercier, and A. Pavé, Codon catalog usage and the genome hypothesis, Nucleic Acids Research, vol.8, issue.1, pp.49-62, 1980.
DOI : 10.1093/nar/8.1.197-c

URL : https://hal.archives-ouvertes.fr/hal-00697923

M. Gouy and C. Gautier, Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Research, vol.10, issue.22, pp.7055-74, 1982.
DOI : 10.1093/nar/10.22.7055

URL : https://hal.archives-ouvertes.fr/hal-00697906

J. B. Plotkin and G. Kudla, Synonymous but not the same: the causes and consequences of codon bias, Nature Reviews Genetics, vol.7, issue.103, pp.32-42, 2011.
DOI : 10.1007/s002390010155

T. E. Quax, N. J. Claassens, D. Sö-ll, and J. Van-der-oost, Codon Bias as a Means to Fine-Tune Gene Expression, Molecular Cell, vol.59, issue.2, pp.149-61, 2015.
DOI : 10.1016/j.molcel.2015.05.035

URL : http://doi.org/10.1016/j.molcel.2015.05.035

S. Pechmann and J. Frydman, Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding, Nature Structural & Molecular Biology, vol.39, issue.2, pp.237-280, 2013.
DOI : 10.1093/nar/gkq1105

C. Yu, Y. Dang, and Z. Zhou, Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding, Molecular Cell, vol.59, issue.5, pp.744-54, 2015.
DOI : 10.1016/j.molcel.2015.07.018

P. M. Sharp, T. M. Tuohy, and K. R. Mosurski, Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes, Nucleic Acids Research, vol.14, issue.13, pp.5125-5168, 1986.
DOI : 10.1093/nar/14.13.5125

URL : https://academic.oup.com/nar/article-pdf/14/13/5125/3945191/14-13-5125.pdf

N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, and J. S. Weissman, Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling, Science, vol.71, issue.1, pp.218-241, 2009.
DOI : 10.1016/0092-8674(92)90269-I

B. Guo, T. Zeng, and H. Wu, Recent advances of DNA sequencing via nanopore-based technologies, Science Bulletin, vol.60, issue.3, pp.287-95, 2014.
DOI : 10.1007/s11434-014-0707-6

J. G. Dunn, C. K. Foo, N. G. Belletier, E. R. Gavis, and J. S. Weissman, Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster, p.1179, 2013.
DOI : 10.7554/elife.01179

URL : http://doi.org/10.7554/elife.01179

A. Zupanic, C. Meplan, and S. N. Grellscheid, Detecting translational regulation by change point analysis of ribosome profiling data sets, RNA, vol.20, issue.10, pp.1507-1525, 2014.
DOI : 10.1261/rna.045286.114

X. Gao, J. Wan, B. Liu, M. Ma, B. Shen et al., Quantitative profiling of initiating ribosomes in vivo, Nature Methods, vol.12, issue.2, pp.147-53, 2015.
DOI : 10.1016/j.molcel.2012.12.001

D. E. Weinberg, P. Shah, S. W. Eichhorn, J. A. Hussmann, J. B. Plotkin et al., Improved ribosome-footprint and mrna measurements provide insights into dynamics and regulation of yeast translation , Cell Rep, pp.1787-99, 2016.

P. M. Sharp and K. R. Bradnam, Appendix 3 Codon Usage in C. elegans, C Elegans II. 2nd Ed, 1997.

N. Philippe, M. Salson, T. Commes, and E. Rivals, CRAC: an integrated approach to the analysis of RNA-seq reads, Genome Biology, vol.14, issue.3, p.30, 2013.
DOI : 10.1371/journal.pone.0012271

URL : https://hal.archives-ouvertes.fr/inserm-00850972

M. Stadler and A. Fire, Wobble base-pairing slows in vivo translation elongation in metazoans, RNA, vol.17, issue.12, pp.2063-73, 2011.
DOI : 10.1261/rna.02890211

URL : http://rnajournal.cshlp.org/content/17/12/2063.full.pdf

M. Lynch, The Origins of Genome Architecture, 2007.

L. Duret, tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, vol.16, issue.7, pp.287-296, 2000.
DOI : 10.1016/S0168-9525(00)02041-2

URL : https://hal.archives-ouvertes.fr/hal-00427076

P. P. Chan and T. M. Lowe, GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes, Nucleic Acids Research, vol.44, issue.D1, pp.184-193, 2016.
DOI : 10.1093/nar/gkv1309

F. H. Crick, Codon???anticodon pairing: The wobble hypothesis, Journal of Molecular Biology, vol.19, issue.2, pp.548-55, 1966.
DOI : 10.1016/S0022-2836(66)80022-0

B. Schwanh?-ausser, D. Busse, and N. Li, Global quantification of mammalian gene expression control, Nature, pp.473-337, 2011.

T. Ikemura, Codon usage and tRNA content in unicellular and multicellular organisms, Mol. Biol. Evol, vol.2, pp.13-34, 1985.

Z. Zhou, Y. Dang, and M. Zhou, Codon usage is an important determinant of gene expression levels largely through its effects on transcription, Proc. Natl. Acad. Sci, pp.6117-6125, 2016.
DOI : 10.1073/pnas.1315133110

C. E. Gamble, C. E. Brule, K. M. Dean, S. Fields, and E. J. Grayhack, Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast, Cell, vol.166, issue.3, pp.679-90, 2016.
DOI : 10.1016/j.cell.2016.05.070