-
1
-
-
84861843696
-
A mechanistic overview of translation initiation in eukaryotes
-
Aitken J.L.C. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 2012, 6:568-576. http://www.nature.com/nsmb/journal/v19/n6/full/nsmb.2303.html, 10.1038/nsmb.2303.
-
(2012)
Nat. Struct. Mol. Biol.
, vol.6
, pp. 568-576
-
-
Aitken, J.L.C.1
-
2
-
-
84879654928
-
Efficient translation initiation dictates codon usage at gene start.
-
Bentele K., Saffert P., Rauscher R., Ignatova Z., Bluthgen N. Efficient translation initiation dictates codon usage at gene start. Mol. Syst. Biol. 2013, 9:675. 10.1038/msb.2013.32.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 675
-
-
Bentele, K.1
Saffert, P.2
Rauscher, R.3
Ignatova, Z.4
Bluthgen, N.5
-
3
-
-
35648990568
-
Nonequilibrium steady states of matrix-product form: a solver's guide
-
Blythe R., Evans M. Nonequilibrium steady states of matrix-product form: a solver's guide. J. Phys. A: Math. Theor. 2007, 40(46):R333. http://stacks.iop.org/1751-8121/40/i=46/a=R01.
-
(2007)
J. Phys. A: Math. Theor.
, vol.40
, Issue.46
-
-
Blythe, R.1
Evans, M.2
-
4
-
-
84875465945
-
Positively charged residues are the major determinants of ribosomal velocity
-
Charneski C., Hurst L. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol. 2013, 11(3):e1001508. 10.1371/journal.pbio.1001508.
-
(2013)
PLoS Biol.
, vol.11
, Issue.3
-
-
Charneski, C.1
Hurst, L.2
-
5
-
-
84869074692
-
The architecture of eukaryotic translation
-
Chu D., von der Haar T. The architecture of eukaryotic translation. Nucleic Acids Res. 2012, 40(20):10098-10106. 10.1093/nar/gks825.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.20
, pp. 10098-10106
-
-
Chu, D.1
von der Haar, T.2
-
6
-
-
80055071250
-
The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae
-
Chu D., Barnes D., von der Haar T. The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Res. 2011, 39(15):6705-6714. http://nar.oxfordjournals.org/content/39/15/6705.abstract, 10.1093/nar/gkr300.
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.15
, pp. 6705-6714
-
-
Chu, D.1
Barnes, D.2
von der Haar, T.3
-
7
-
-
84856117068
-
A novel and versatile computational tool to model translation
-
Chu D., Zabet N., von der Haar T. A novel and versatile computational tool to model translation. Bioinformatics 2012, 28(2):292-293. http://bioinformatics.oxfordjournals.org/content/28/2/292.abstract, 10.1093/bioinformatics/btr650.
-
(2012)
Bioinformatics
, vol.28
, Issue.2
, pp. 292-293
-
-
Chu, D.1
Zabet, N.2
von der Haar, T.3
-
8
-
-
84894646451
-
Translation elongation can control translation initiation on eukaryotic mRNAs
-
Chu D., Kazana E., Bellanger N., Singh T., Tuite M., von der Haar T. Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J. 2013, 33(1):21-34. arXiv:http://emboj.embopress.org/content/33/1/21.full.pdf, http://emboj.embopress.org/content/33/1/21. 10.1002/embj.201385651.
-
(2013)
EMBO J.
, vol.33
, Issue.1
, pp. 21-34
-
-
Chu, D.1
Kazana, E.2
Bellanger, N.3
Singh, T.4
Tuite, M.5
von der Haar, T.6
-
9
-
-
77952020413
-
Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation
-
Ciandrini L., Stansfield I., Romano M. Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation. Phys. Rev. 2010, E81(5 Pt 1):051904.
-
(2010)
Phys. Rev.
, vol.E81
, Issue.5 PART 1
, pp. 051904
-
-
Ciandrini, L.1
Stansfield, I.2
Romano, M.3
-
10
-
-
0034666040
-
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
-
Coghlan A., Wolfe K.H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000, 16(12):1131-1145. http://dx.doi.org/3.0.CO;2-F.
-
(2000)
Yeast
, vol.16
, Issue.12
, pp. 1131-1145
-
-
Coghlan, A.1
Wolfe, K.H.2
-
11
-
-
0344237338
-
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
-
dos Reis M., Wernisch L., Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 2003, 31(23):6976-6985.
-
(2003)
Nucleic Acids Res.
, vol.31
, Issue.23
, pp. 6976-6985
-
-
dos Reis, M.1
Wernisch, L.2
Savva, R.3
-
12
-
-
34948856961
-
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis
-
Fluitt A., Pienaar E., Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput. Biol. Chem. 2007, 31(5-6):335-346. 10.1016/j.compbiolchem.2007.07.003.
-
(2007)
Comput. Biol. Chem.
, vol.31
, Issue.5-6
, pp. 335-346
-
-
Fluitt, A.1
Pienaar, E.2
Viljoen, H.3
-
13
-
-
79954456859
-
Determinants of translation efficiency and accuracy
-
Gingold H., Pilpel Y. Determinants of translation efficiency and accuracy. Mol. Syst. Biol. 2011, 7:481. 10.1038/msb.2011.14.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 481
-
-
Gingold, H.1
Pilpel, Y.2
-
14
-
-
84856631926
-
Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles
-
Greulich P., Ciandrini L.L., Allen R., Romano M. Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles. Phys. Rev. 2012, E85:011142. 10.1103/PhysRevE.85.011142.
-
(2012)
Phys. Rev.
, vol.E85
, pp. 011142
-
-
Greulich, P.1
Ciandrini, L.L.2
Allen, R.3
Romano, M.4
-
15
-
-
0842267211
-
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
-
Gromadski K., Rodnina M. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 2004, 13(2):191-200. 10.1016/S1097-2765(04)00005-X.
-
(2004)
Mol. Cell
, vol.13
, Issue.2
, pp. 191-200
-
-
Gromadski, K.1
Rodnina, M.2
-
16
-
-
3042782585
-
Codon bias and heterologous protein expression
-
Gustafsson C., Govindarajan S., Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol. 2004, 22(7):346-353. 10.1016/j.tibtech.2004.04.006.
-
(2004)
Trends Biotechnol.
, vol.22
, Issue.7
, pp. 346-353
-
-
Gustafsson, C.1
Govindarajan, S.2
Minshull, J.3
-
17
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
-
Ingolia N., Ghaemmaghami S., Newman J., Weissman J. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324(5924):218-223. 10.1126/science.1168978.
-
(2009)
Science
, vol.324
, Issue.5924
, pp. 218-223
-
-
Ingolia, N.1
Ghaemmaghami, S.2
Newman, J.3
Weissman, J.4
-
18
-
-
0035220937
-
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
-
Knight R.D., Freeland S.J., Landweber L.F. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2001, 2(4).
-
(2001)
Genome Biol.
, vol.2
, Issue.4
-
-
Knight, R.D.1
Freeland, S.J.2
Landweber, L.F.3
-
19
-
-
43349102982
-
Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA.
-
Kopeina G., Afonina Z., Gromova K., Shirokov V., Vasiliev V., Spirin A. Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA. Nucleic Acids Res. 2008, 36(8):2476-2488. 10.1093/nar/gkm1177.
-
(2008)
Nucleic Acids Res.
, vol.36
, Issue.8
, pp. 2476-2488
-
-
Kopeina, G.1
Afonina, Z.2
Gromova, K.3
Shirokov, V.4
Vasiliev, V.5
Spirin, A.6
-
20
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G., Murray A., Tollervey D., Plotkin J. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324(5924):255-258. 10.1126/science.1170160.
-
(2009)
Science
, vol.324
, Issue.5924
, pp. 255-258
-
-
Kudla, G.1
Murray, A.2
Tollervey, D.3
Plotkin, J.4
-
21
-
-
0032126484
-
Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli
-
Moriyama E.N., Powell J.R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 1998, 26(13):3188-3193.
-
(1998)
Nucleic Acids Res.
, vol.26
, Issue.13
, pp. 3188-3193
-
-
Moriyama, E.N.1
Powell, J.R.2
-
22
-
-
34548709778
-
Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of gc3 rich genes towards protein stability
-
Mukhopadhyay P., Basak S., Ghosh T. Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of gc3 rich genes towards protein stability. J. Biosci. 2007, 32(5):947-963.
-
(2007)
J. Biosci.
, vol.32
, Issue.5
, pp. 947-963
-
-
Mukhopadhyay, P.1
Basak, S.2
Ghosh, T.3
-
23
-
-
79952308837
-
The role of codon selection in regulation of translation efficiency deduced from synthetic libraries
-
Navon S., Pilpel Y. The role of codon selection in regulation of translation efficiency deduced from synthetic libraries. Genome Biol. 2011, 12(2):R12. 10.1186/gb-2011-12-2-r12.
-
(2011)
Genome Biol.
, vol.12
, Issue.2
-
-
Navon, S.1
Pilpel, Y.2
-
24
-
-
84867732569
-
Speeding with control: codon usage, trnas, and ribosomes
-
Novoa E., Pouplana L. Speeding with control: codon usage, trnas, and ribosomes. Trends Genet. 2012, 28(11):574-581. 10.1016/j.tig.2012.07.006.
-
(2012)
Trends Genet.
, vol.28
, Issue.11
, pp. 574-581
-
-
Novoa, E.1
Pouplana, L.2
-
25
-
-
84859219968
-
Balanced codon usage optimizes eukaryotic translational efficiency
-
Qian W., Yang J., Pearson N., Maclean C., Zhang J. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet. 2012, 8(3):e1002603. 10.1371/journal.pgen.1002603.
-
(2012)
PLoS Genet.
, vol.8
, Issue.3
-
-
Qian, W.1
Yang, J.2
Pearson, N.3
Maclean, C.4
Zhang, J.5
-
26
-
-
0034949816
-
Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency.
-
Sato T., Terabe M., Watanabe H., Gojobori T., Hori-Takemoto C., Miura K. Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency. J. Biochem. 2001, 129(6):851-860.
-
(2001)
J. Biochem.
, vol.129
, Issue.6
, pp. 851-860
-
-
Sato, T.1
Terabe, M.2
Watanabe, H.3
Gojobori, T.4
Hori-Takemoto, C.5
Miura, K.6
-
27
-
-
78049445381
-
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias
-
Shah P., Gilchrist M. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. PLoS Genet. 2010, 6(9). 10.1371/journal.pgen.1001128.
-
(2010)
PLoS Genet.
, vol.6
, Issue.9
-
-
Shah, P.1
Gilchrist, M.2
-
28
-
-
79959982593
-
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift
-
Shah P., Gilchrist M. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc. Natl. Acad. Sci. U.S.A. 2011, 108(25):10231-10236. 10.1073/pnas.1016719108.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, Issue.25
, pp. 10231-10236
-
-
Shah, P.1
Gilchrist, M.2
-
29
-
-
84879345901
-
Rate-limiting steps in yeast protein translation
-
Shah P., Ding Y., Niemczyk M., Kudla G., Plotkin J. Rate-limiting steps in yeast protein translation. Cell 2013, 153(7):1589-1601. 10.1016/j.cell.2013.05.049.
-
(2013)
Cell
, vol.153
, Issue.7
, pp. 1589-1601
-
-
Shah, P.1
Ding, Y.2
Niemczyk, M.3
Kudla, G.4
Plotkin, J.5
-
30
-
-
0023650543
-
The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp P.M., Li W.H. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987, 15(3):1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, Issue.3
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
31
-
-
78049245511
-
A comprehensive, quantitative, and genome-wide model of translation.
-
Siwiak M., Zielenkiewicz P. A comprehensive, quantitative, and genome-wide model of translation. PLoS Comput. Biol. 2010, 6(7):e1000865. 10.1371/journal.pcbi.1000865.
-
(2010)
PLoS Comput. Biol.
, vol.6
, Issue.7
-
-
Siwiak, M.1
Zielenkiewicz, P.2
-
32
-
-
33846786904
-
Synonymous codon usage in Escherichia coli: selection for translational accuracy
-
Stoletzki N., Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol. Biol. Evol. 2007, 24(2):374-381. 10.1093/molbev/msl166.
-
(2007)
Mol. Biol. Evol.
, vol.24
, Issue.2
, pp. 374-381
-
-
Stoletzki, N.1
Eyre-Walker, A.2
-
33
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller T., Waldman Y., Kupiec M., Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl. Acad. Sci. U.S.A. 2010, 107(8):3645-3650. 10.1073/pnas.0909910107.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, Issue.8
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.2
Kupiec, M.3
Ruppin, E.4
-
34
-
-
80155213999
-
Composite effects of gene determinants on the translation speed and density of ribosomes
-
Tuller T., Veksler-Lublinsky I., Gazit N., Kupiec M., Ruppin E., Ziv-Ukelson M. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol. 2011, 12(11):R110. 10.1186/gb-2011-12-11-r110.
-
(2011)
Genome Biol.
, vol.12
, Issue.11
-
-
Tuller, T.1
Veksler-Lublinsky, I.2
Gazit, N.3
Kupiec, M.4
Ruppin, E.5
Ziv-Ukelson, M.6
-
35
-
-
0032112017
-
Circularization of mRNA by eukaryotic translation initiation factors
-
Wells S., Hillner P., Vale R., Sachs A. Circularization of mRNA by eukaryotic translation initiation factors. Mol. Cell 1998, 2(1):135-140.
-
(1998)
Mol. Cell
, vol.2
, Issue.1
, pp. 135-140
-
-
Wells, S.1
Hillner, P.2
Vale, R.3
Sachs, A.4
-
36
-
-
0031697801
-
The relationship between synonymous codon usage and protein structure.
-
Xie T., Ding D., Tao X., Dafu D. The relationship between synonymous codon usage and protein structure. FEBS Lett. 1998, 434(1-2):93-96.
-
(1998)
FEBS Lett.
, vol.434
, Issue.1-2
, pp. 93-96
-
-
Xie, T.1
Ding, D.2
Tao, X.3
Dafu, D.4
-
37
-
-
62049083910
-
Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
-
Zhang G., Hubalewska M., Ignatova Z. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat. Struct. Biol. 2009, 16(3):274-280. 10.1038/nsmb.1554.
-
(2009)
Nat. Struct. Biol.
, vol.16
, Issue.3
, pp. 274-280
-
-
Zhang, G.1
Hubalewska, M.2
Ignatova, Z.3
|