-
1
-
-
33846820156
-
A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates
-
Zouridis H, Hatzimanikatis V, (2007) A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates. Biophysical Journal 92: 717-730.
-
(2007)
Biophysical Journal
, vol.92
, pp. 717-730
-
-
Zouridis, H.1
Hatzimanikatis, V.2
-
2
-
-
51049096159
-
Effects of codon distributions and tRNA competition on protein translation
-
Zouridis H, Hatzimanikatis V, (2008) Effects of codon distributions and tRNA competition on protein translation. Biophysical Journal 95: 1018-1033.
-
(2008)
Biophysical Journal
, vol.95
, pp. 1018-1033
-
-
Zouridis, H.1
Hatzimanikatis, V.2
-
3
-
-
33645775569
-
An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks
-
Mehra A, Hatzimanikatis V, (2006) An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks. Biophysical Journal 90: 1136-1146.
-
(2006)
Biophysical Journal
, vol.90
, pp. 1136-1146
-
-
Mehra, A.1
Hatzimanikatis, V.2
-
4
-
-
0347132484
-
Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations
-
Mehra A, Lee KH, Hatzimanikatis V, (2003) Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol Bioeng 84: 822-833.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 822-833
-
-
Mehra, A.1
Lee, K.H.2
Hatzimanikatis, V.3
-
5
-
-
84984085494
-
Concerning the Kinetics of Polypeptide Synthesis on Polyribosomes
-
MacDonald C, Gibbs J, (1969) Concerning the Kinetics of Polypeptide Synthesis on Polyribosomes. Biopolymers 7: 707-725.
-
(1969)
Biopolymers
, vol.7
, pp. 707-725
-
-
MacDonald, C.1
Gibbs, J.2
-
6
-
-
0019178883
-
Mathematical modelling of translation of mRNA in eucaryotes; steady state, time-dependent processes and application to reticulocytes
-
Heinrich R, Rapoport TA, (1980) Mathematical modelling of translation of mRNA in eucaryotes; steady state, time-dependent processes and application to reticulocytes. J Theor Biol 86: 279-313.
-
(1980)
J Theor Biol
, vol.86
, pp. 279-313
-
-
Heinrich, R.1
Rapoport, T.A.2
-
7
-
-
0037388094
-
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
-
Arava Y, Wang Y, Storey J, Liu C, Brown P, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. P Natl Acad Sci Usa 100: 3889-3894.
-
(2003)
P Natl Acad Sci Usa
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
Wang, Y.2
Storey, J.3
Liu, C.4
Brown, P.5
-
8
-
-
17844395239
-
Dissecting eukaryotic translation and its control by ribosome density mapping
-
Arava Y, Boas F, Brown P, Herschlag D, (2005) Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 33: 2421-2432.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2421-2432
-
-
Arava, Y.1
Boas, F.2
Brown, P.3
Herschlag, D.4
-
9
-
-
73149106617
-
Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis
-
Piques M, Schulze WX, Hoehne M, Usadel B, Gibon Y, et al. (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Molecular Systems Biology 5: 314.
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 314
-
-
Piques, M.1
Schulze, W.X.2
Hoehne, M.3
Usadel, B.4
Gibon, Y.5
-
10
-
-
79959727271
-
Polysome profiling of the malaria parasite Plasmodium falciparum
-
Lacsina JR, Lamonte G, Nicchitta CV, Chi J-T, (2011) Polysome profiling of the malaria parasite Plasmodium falciparum. Mol Biochem Parasitol 179: 42-46.
-
(2011)
Mol Biochem Parasitol
, vol.179
, pp. 42-46
-
-
Lacsina, J.R.1
Lamonte, G.2
Nicchitta, C.V.3
Chi, J.-T.4
-
11
-
-
84866931928
-
Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression
-
Picard F, Milhem H, Loubière P, Laurent B, Cocaign-Bousquet M, et al. (2012) Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression. BMC Genomics 13: 528.
-
(2012)
BMC Genomics
, vol.13
, pp. 528
-
-
Picard, F.1
Milhem, H.2
Loubière, P.3
Laurent, B.4
Cocaign-Bousquet, M.5
-
12
-
-
80052229054
-
Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information
-
Dressaire C, Redon E, Gitton C, Loubière P, Monnet V, et al. (2011) Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information. Microb Cell Fact 10 Suppl 1: S18.
-
(2011)
Microb Cell Fact
, vol.10
, Issue.SUPPL.
-
-
Dressaire, C.1
Redon, E.2
Gitton, C.3
Loubière, P.4
Monnet, V.5
-
13
-
-
27744606973
-
Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation
-
Redon E, Loubiere P, Cocaign-Bousquet M, (2005) Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280: 36380-36385.
-
(2005)
J Biol Chem
, vol.280
, pp. 36380-36385
-
-
Redon, E.1
Loubiere, P.2
Cocaign-Bousquet, M.3
-
14
-
-
14844340954
-
Initiation of protein synthesis in bacteria
-
Laursen BS, Sorensen HP, Mortensen KK, Sperling-Petersen HU, (2005) Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 69: 101-123.
-
(2005)
Microbiol Mol Biol Rev
, vol.69
, pp. 101-123
-
-
Laursen, B.S.1
Sorensen, H.P.2
Mortensen, K.K.3
Sperling-Petersen, H.U.4
-
15
-
-
84862666301
-
A computational framework for the design of optimal protein synthesis
-
Racle J, Overney J, Hatzimanikatis V, (2012) A computational framework for the design of optimal protein synthesis. Biotechnol Bioeng 109: 2127-2133.
-
(2012)
Biotechnol Bioeng
, vol.109
, pp. 2127-2133
-
-
Racle, J.1
Overney, J.2
Hatzimanikatis, V.3
-
16
-
-
62549134121
-
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
-
Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS, (2009) Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science 324: 218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.S.3
Weissman, J.S.4
-
17
-
-
74549124254
-
Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis
-
Dressaire C, Gitton C, Loubiere P, Monnet V, Queinnec I, et al. (2009) Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol 5: e1000606.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Dressaire, C.1
Gitton, C.2
Loubiere, P.3
Monnet, V.4
Queinnec, I.5
-
18
-
-
67650319009
-
Single-Molecule Approaches to Stochastic Gene Expression
-
Raj A, Van Oudenaarden A, (2009) Single-Molecule Approaches to Stochastic Gene Expression. Annu Rev Biophys 38: 255-270.
-
(2009)
Annu Rev Biophys
, vol.38
, pp. 255-270
-
-
Raj, A.1
Van Oudenaarden, A.2
-
19
-
-
65549099632
-
Structure and complexity of a bacterial transcriptome
-
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, et al. (2009) Structure and complexity of a bacterial transcriptome. Journal of Bacteriology 191: 3203-3211.
-
(2009)
Journal of Bacteriology
, vol.191
, pp. 3203-3211
-
-
Passalacqua, K.D.1
Varadarajan, A.2
Ondov, B.D.3
Okou, D.T.4
Zwick, M.E.5
-
20
-
-
0014960630
-
Visualization of bacterial genes in action
-
Miller O, Hamkalo B, Thomas C, (1970) Visualization of bacterial genes in action. Science 169: 392-395.
-
(1970)
Science
, vol.169
, pp. 392-395
-
-
Miller, O.1
Hamkalo, B.2
Thomas, C.3
-
21
-
-
70249141564
-
Co-translational mRNA decay in Saccharomyces cerevisiae
-
Hu W, Sweet TJ, Chamnongpol S, Baker KE, Coller J, (2009) Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461: 225-229.
-
(2009)
Nature
, vol.461
, pp. 225-229
-
-
Hu, W.1
Sweet, T.J.2
Chamnongpol, S.3
Baker, K.E.4
Coller, J.5
-
22
-
-
84862765893
-
Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells
-
Bakshi S, Siryaporn A, Goulian M, Weisshaar JC, (2012) Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Molecular Microbiology 85: 21-38.
-
(2012)
Molecular Microbiology
, vol.85
, pp. 21-38
-
-
Bakshi, S.1
Siryaporn, A.2
Goulian, M.3
Weisshaar, J.C.4
-
23
-
-
33750043437
-
Translation initiation and the fate of bacterial mRNAs
-
Kaberdin VR, Blasi U, (2006) Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol Rev 30: 967-979.
-
(2006)
FEMS Microbiol Rev
, vol.30
, pp. 967-979
-
-
Kaberdin, V.R.1
Blasi, U.2
-
24
-
-
84869021523
-
Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli
-
Tsai Y-C, Du D, Domínguez-Malfavón L, Dimastrogiovanni D, Cross J, et al. (2012) Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli. Nucleic Acids Research 40: 10417-10431.
-
(2012)
Nucleic Acids Research
, vol.40
, pp. 10417-10431
-
-
Tsai, Y.-C.1
Du, D.2
Domínguez-Malfavón, L.3
Dimastrogiovanni, D.4
Cross, J.5
-
25
-
-
35548995356
-
The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E
-
Carpousis AJ, (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61: 71-87.
-
(2007)
Annu Rev Microbiol
, vol.61
, pp. 71-87
-
-
Carpousis, A.J.1
-
26
-
-
80053594659
-
RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli
-
Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, et al. (2011) RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. Journal of Bacteriology 193: 5431-5441.
-
(2011)
Journal of Bacteriology
, vol.193
, pp. 5431-5441
-
-
Lehnik-Habrink, M.1
Newman, J.2
Rothe, F.M.3
Solovyova, A.S.4
Rodrigues, C.5
-
27
-
-
0032872644
-
Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome
-
Bolotin A, Mauger S, Malarme K, Ehrlich S, Sorokin A, (1999) Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Anton Leeuw Int J G 76: 27-76.
-
(1999)
Anton Leeuw Int J G
, vol.76
, pp. 27-76
-
-
Bolotin, A.1
Mauger, S.2
Malarme, K.3
Ehrlich, S.4
Sorokin, A.5
-
28
-
-
0035021812
-
The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403
-
Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, et al. (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11: 731-753.
-
(2001)
Genome Res
, vol.11
, pp. 731-753
-
-
Bolotin, A.1
Wincker, P.2
Mauger, S.3
Jaillon, O.4
Malarme, K.5
-
29
-
-
77953577608
-
Linear covariance models to examine the determinants of protein levels in Lactococcus lactis
-
Dressaire C, Laurent B, Loubiere P, Besse P, Cocaign-Bousquet M, (2010) Linear covariance models to examine the determinants of protein levels in Lactococcus lactis. Mol BioSyst 6: 1255-1264.
-
(2010)
Mol BioSyst
, vol.6
, pp. 1255-1264
-
-
Dressaire, C.1
Laurent, B.2
Loubiere, P.3
Besse, P.4
Cocaign-Bousquet, M.5
-
31
-
-
28444475607
-
Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations
-
Nie L, Wu G, Zhang W, (2006) Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations. Biochem Biophys Res Commun 339: 603-610.
-
(2006)
Biochem Biophys Res Commun
, vol.339
, pp. 603-610
-
-
Nie, L.1
Wu, G.2
Zhang, W.3
-
32
-
-
77951715627
-
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
-
Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, et al. (2010) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141: 344-354.
-
(2010)
Cell
, vol.141
, pp. 344-354
-
-
Tuller, T.1
Carmi, A.2
Vestsigian, K.3
Navon, S.4
Dorfan, Y.5
-
33
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller T, Waldman YY, Kupiec M, Ruppin E, (2010) Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A 107: 3645-3650.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.Y.2
Kupiec, M.3
Ruppin, E.4
-
34
-
-
79954456859
-
Determinants of translation efficiency and accuracy
-
Gingold H, Pilpel Y, (2011) Determinants of translation efficiency and accuracy. Mol Syst Biol 7: 481.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 481
-
-
Gingold, H.1
Pilpel, Y.2
-
35
-
-
84883129155
-
The significance of translation regulation in the stress response
-
Picard F, Loubière P, Girbal L, Cocaign-Bousquet M, (2013) The significance of translation regulation in the stress response. BMC Genomics 14: 588.
-
(2013)
BMC Genomics
, vol.14
, pp. 588
-
-
Picard, F.1
Loubière, P.2
Girbal, L.3
Cocaign-Bousquet, M.4
-
36
-
-
80052524231
-
Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript
-
Sharma AK, Chowdhury D, (2011) Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript. Journal of Theoretical Biology 289: 36-46.
-
(2011)
Journal of Theoretical Biology
, vol.289
, pp. 36-46
-
-
Sharma, A.K.1
Chowdhury, D.2
-
37
-
-
78049245511
-
A Comprehensive, Quantitative, and Genome-Wide Model of Translation
-
Siwiak M, Zielenkiewicz P, (2010) A Comprehensive, Quantitative, and Genome-Wide Model of Translation. Plos Comput Biol 6: e1000865.
-
(2010)
Plos Comput Biol
, vol.6
-
-
Siwiak, M.1
Zielenkiewicz, P.2
-
38
-
-
83255164895
-
Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo
-
Oh E, Becker AH, Sandikci A, Huber D, Chaba R, et al. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147: 1295-1308.
-
(2011)
Cell
, vol.147
, pp. 1295-1308
-
-
Oh, E.1
Becker, A.H.2
Sandikci, A.3
Huber, D.4
Chaba, R.5
-
39
-
-
84860231100
-
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li G, Oh E, Weissman JS, (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538-541.
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.1
Oh, E.2
Weissman, J.S.3
|