H. Zouridis and V. Hatzimanikatis, A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates, Biophysical Journal, vol.92, pp.717-730, 2007.

H. Zouridis and V. Hatzimanikatis, Effects of codon distributions and tRNA competition on protein translation, Biophysical Journal, vol.95, pp.1018-1033, 2008.

A. Mehra and V. Hatzimanikatis, An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks, Biophysical Journal, vol.90, pp.1136-1146, 2006.

A. Mehra, K. H. Lee, and V. Hatzimanikatis, Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations, Biotechnol Bioeng, vol.84, pp.822-833, 2003.

C. Macdonald and J. Gibbs, Concerning the Kinetics of Polypeptide Synthesis on Polyribosomes, Biopolymers, vol.7, pp.707-725, 1969.

R. Heinrich and T. A. Rapoport, Mathematical modelling of translation of mRNA in eucaryotes; steady state, time-dependent processes and application to reticulocytes, J Theor Biol, vol.86, pp.279-313, 1980.

Y. Arava, Y. Wang, J. Storey, C. Liu, and P. Brown, Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, P Natl Acad Sci, vol.100, pp.3889-3894, 2003.

Y. Arava, F. Boas, P. Brown, and D. Herschlag, Dissecting eukaryotic translation and its control by ribosome density mapping, Nucleic Acids Res, vol.33, pp.2421-2432, 2005.

M. Piques, W. X. Schulze, M. Hoehne, B. Usadel, and Y. Gibon, Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis, Molecular Systems Biology, vol.5, p.314, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02666439

J. R. Lacsina, G. Lamonte, C. V. Nicchitta, and J. Chi, Polysome profiling of the malaria parasite Plasmodium falciparum, Mol Biochem Parasitol, vol.179, pp.42-46, 2011.

F. Picard, H. Milhem, P. Loubière, B. Laurent, and M. Cocaign-bousquet, Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression, BMC Genomics, vol.13, p.528, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01268281

C. Dressaire, E. Redon, C. Gitton, P. Loubière, and V. Monnet, Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information, Microb Cell Fact, vol.10, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02645800

E. Redon, P. Loubiere, and M. Cocaign-bousquet, Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation, J Biol Chem, vol.280, pp.36380-36385, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682214

B. S. Laursen, H. P. Sorensen, K. K. Mortensen, . Sperling-petersen, and . Hu, Initiation of protein synthesis in bacteria, Microbiol Mol Biol Rev, vol.69, pp.101-123, 2005.

J. Racle, J. Overney, and V. Hatzimanikatis, A computational framework for the design of optimal protein synthesis, Biotechnol Bioeng, vol.109, pp.2127-2133, 2012.

N. T. Ingolia, S. Ghaemmaghami, J. Newman, and J. S. Weissman, Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling, Science, vol.324, pp.218-223, 2009.

C. Dressaire, C. Gitton, P. Loubiere, V. Monnet, and I. Queinnec, Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis, PLoS Comput Biol, vol.5, p.1000606, 2009.

A. Raj and A. Van-oudenaarden, Single-Molecule Approaches to Stochastic Gene Expression, Annu Rev Biophys, vol.38, pp.255-270, 2009.

K. D. Passalacqua, A. Varadarajan, B. D. Ondov, D. T. Okou, and M. E. Zwick, Structure and complexity of a bacterial transcriptome, Journal of Bacteriology, vol.191, pp.3203-3211, 2009.

O. Miller, B. Hamkalo, and C. Thomas, Visualization of bacterial genes in action, Science, vol.169, pp.392-395, 1970.

W. Hu, T. J. Sweet, S. Chamnongpol, K. E. Baker, and J. Coller, Co-translational mRNA decay in Saccharomyces cerevisiae, Nature, vol.461, pp.225-229, 2009.

S. Bakshi, A. Siryaporn, M. Goulian, and J. C. Weisshaar, Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells, Molecular Microbiology, vol.85, pp.21-38, 2012.

V. R. Kaberdin and U. Blasi, Translation initiation and the fate of bacterial mRNAs, FEMS Microbiol Rev, vol.30, pp.967-979, 2006.

Y. Tsai, D. Du, L. Domínguez-malfavón, D. Dimastrogiovanni, and J. Cross, Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli, Nucleic Acids Research, vol.40, pp.10417-10431, 2012.

A. J. Carpousis, The RNA degradosome of Escherichia coli: an mRNAdegrading machine assembled on RNase E, Annu Rev Microbiol, vol.61, pp.71-87, 2007.

M. Lehnik-habrink, J. Newman, F. M. Rothe, A. S. Solovyova, and C. Rodrigues, RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli, Journal of Bacteriology, vol.193, pp.5431-5441, 2011.

A. Bolotin, S. Mauger, K. Malarme, S. Ehrlich, and A. Sorokin, Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome, Anton Leeuw Int J G, vol.76, pp.27-76, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02694223

A. Bolotin, P. Wincker, S. Mauger, O. Jaillon, and K. Malarme, The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403, Genome Res, vol.11, pp.731-753, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02681585

C. Dressaire, B. Laurent, P. Loubiere, P. Besse, and M. Cocaign-bousquet, Linear covariance models to examine the determinants of protein levels in Lactococcus lactis, Mol BioSyst, vol.6, pp.1255-1264, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00960013

H. Bremer and P. Dennis, Modulation of chemical composition and other parameters of the cell by growth rate, Escherichia coli and Salmonella: cellular and molecular biology, vol.2, pp.1553-1569, 1996.

L. Nie, G. Wu, and W. Zhang, Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations, Biochem Biophys Res Commun, vol.339, pp.603-610, 2006.

T. Tuller, A. Carmi, K. Vestsigian, S. Navon, and Y. Dorfan, An evolutionarily conserved mechanism for controlling the efficiency of protein translation, Cell, vol.141, pp.344-354, 2010.

T. Tuller, Y. Y. Waldman, M. Kupiec, and E. Ruppin, Translation efficiency is determined by both codon bias and folding energy, Proc Natl Acad Sci U S A, vol.107, pp.3645-3650, 2010.

H. Gingold and Y. Pilpel, Determinants of translation efficiency and accuracy, Mol Syst Biol, vol.7, p.481, 2011.

F. Picard, P. Loubière, L. Girbal, and M. Cocaign-bousquet, The significance of translation regulation in the stress response, BMC Genomics, vol.14, p.588, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268301

A. K. Sharma and D. Chowdhury, Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript, Journal of Theoretical Biology, vol.289, pp.36-46, 2011.

M. Siwiak and P. Zielenkiewicz, A Comprehensive, Quantitative, and Genome-Wide Model of Translation, Plos Comput Biol, vol.6, p.1000865, 2010.

E. Oh, A. H. Becker, A. Sandikci, D. Huber, and R. Chaba, Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo, Cell, vol.147, pp.1295-1308, 2011.

G. Li, E. Oh, and J. S. Weissman, The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria, Nature, vol.484, pp.538-541, 2012.