-
2
-
-
0031803072
-
Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview
-
Day D, Tuite M, (1998) Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview. J Endocrinol 157: 361-371.
-
(1998)
J Endocrinol
, vol.157
, pp. 361-371
-
-
Day, D.1
Tuite, M.2
-
3
-
-
0024405193
-
Codon usage determines translation rate in escherichia coli
-
Sørensen MA, Kurland CG, Pedersen S, (1989) Codon usage determines translation rate in escherichia coli. J Mol Biol 207: 365-377.
-
(1989)
J Mol Biol
, vol.207
, pp. 365-377
-
-
Sørensen, M.A.1
Kurland, C.G.2
Pedersen, S.3
-
4
-
-
0038179369
-
Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage
-
Elf J, Nilsson D, Tenson T, Ehrenberg M, (2003) Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage. Science 300: 1718-1722.
-
(2003)
Science
, vol.300
, pp. 1718-1722
-
-
Elf, J.1
Nilsson, D.2
Tenson, T.3
Ehrenberg, M.4
-
5
-
-
0003880161
-
-
Garland Pub. Inc, 5th edition
-
Alberts B, Johnson A, Walter P, Lewis J, (2008) Molecular Biology of the Cell Garland Pub. Inc, 5th edition.
-
(2008)
Molecular Biology of the Cell
-
-
Alberts, B.1
Johnson, A.2
Walter, P.3
Lewis, J.4
-
6
-
-
0021760637
-
Codon usage can affect efficiency of translation of genes in escherichia coli
-
Robinson M, Lilley R, Little S, Emtage J, Yarranton G, et al. (1984) Codon usage can affect efficiency of translation of genes in escherichia coli. Nucl Acids Res 12: 6663-6671.
-
(1984)
Nucl Acids Res
, vol.12
, pp. 6663-6671
-
-
Robinson, M.1
Lilley, R.2
Little, S.3
Emtage, J.4
Yarranton, G.5
-
7
-
-
70349913474
-
Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources
-
Cook LJ, Zia RKP, Schmittmann B, (2009) Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources. Phys Rev E 80: 031142.
-
(2009)
Phys Rev E
, vol.80
, pp. 031142
-
-
Cook, L.J.1
Zia, R.K.P.2
Schmittmann, B.3
-
8
-
-
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
-
9
-
-
0001366373
-
An exact solution of a one-dimensional asymmetric exclusion model with open boundaries
-
Derrida B, Domany E, Mukamel D, (1992) An exact solution of a one-dimensional asymmetric exclusion model with open boundaries. J Stat Phys 69: 667-687.
-
(1992)
J Stat Phys
, vol.69
, pp. 667-687
-
-
Derrida, B.1
Domany, E.2
Mukamel, D.3
-
10
-
-
0040629192
-
Phase transitions in an exactly soluble one-dimensional exclusion process
-
Schütz G, Domany E, (1993) Phase transitions in an exactly soluble one-dimensional exclusion process. J Stat Phys 72: 277-296.
-
(1993)
J Stat Phys
, vol.72
, pp. 277-296
-
-
Schütz, G.1
Domany, E.2
-
11
-
-
42749104044
-
Disordered asymmetric simple exclusion process: Mean-field treatment
-
Harris RJ, Stinchcombe RB, (2004) Disordered asymmetric simple exclusion process: Mean-field treatment. Phys Rev E 70: 016108.
-
(2004)
Phys Rev E
, vol.70
, pp. 016108
-
-
Harris, R.J.1
Stinchcombe, R.B.2
-
12
-
-
77955644296
-
Limited resources in a driven diffusion process
-
Brackley CA, Romano MC, Grebogi C, Thiel M, (2010) Limited resources in a driven diffusion process. Phys Rev Lett 105: 078102.
-
(2010)
Phys Rev Lett
, vol.105
, pp. 078102
-
-
Brackley, C.A.1
Romano, M.C.2
Grebogi, C.3
Thiel, M.4
-
13
-
-
42749107950
-
Mean-field approaches to the totally asymmetric exclusion process with quenched disorder and large particles
-
Shaw LB, Sethna JP, Lee KH, (2004) Mean-field approaches to the totally asymmetric exclusion process with quenched disorder and large particles. Phys Rev E 70: 021901.
-
(2004)
Phys Rev E
, vol.70
, pp. 021901
-
-
Shaw, L.B.1
Sethna, J.P.2
Lee, K.H.3
-
14
-
-
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. Biophys J 92: 717-730.
-
(2007)
Biophys J
, vol.92
, pp. 717-730
-
-
Zouridis, H.1
Hatzimanikatis, V.2
-
15
-
-
66049160486
-
Queueing phase transition: Theory of translation
-
Romano MC, Thiel M, Stansfield I, Grebogi C, (2009) Queueing phase transition: Theory of translation. Phys Rev Lett 102: 198104.
-
(2009)
Phys Rev Lett
, vol.102
, pp. 198104
-
-
Romano, M.C.1
Thiel, M.2
Stansfield, I.3
Grebogi, C.4
-
16
-
-
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. Proceedings of the National Academy of Sciences 107: 3645-3650.
-
(2010)
Proceedings of the National Academy of Sciences
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.Y.2
Kupiec, M.3
Ruppin, E.4
-
17
-
-
0037388094
-
Genome-wide analysis of mrna translation profiles in saccharomyces cerevisiae
-
Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mrna translation profiles in saccharomyces cerevisiae. Proc Natl Acad Sci USA 100: 3889-3894.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
Wang, Y.2
Storey, J.D.3
Liu, C.L.4
Brown, P.O.5
-
20
-
-
78651370036
-
Slow sites in an exclusion process with limited resources
-
Brackley CA, Romano MC, Thiel M, (2010) Slow sites in an exclusion process with limited resources. Phys Rev E 82: 051920.
-
(2010)
Phys Rev E
, vol.82
, pp. 051920
-
-
Brackley, C.A.1
Romano, M.C.2
Thiel, M.3
-
21
-
-
0037470280
-
Totally asymmetric exclusion processes with particles of arbitrary size
-
Lakatos G, Chou T, (2003) Totally asymmetric exclusion processes with particles of arbitrary size. J Phys A 36: 2027.
-
(2003)
J Phys A
, vol.36
, pp. 2027
-
-
Lakatos, G.1
Chou, T.2
-
22
-
-
42749107428
-
Totally asymmetric exclusion process with extended objects: A model for protein synthesis
-
Shaw LB, Zia RKP, Lee KH, (2003) Totally asymmetric exclusion process with extended objects: A model for protein synthesis. Phys Rev E 68: 021910.
-
(2003)
Phys Rev E
, vol.68
, pp. 021910
-
-
Shaw, L.B.1
Zia, R.K.P.2
Lee, K.H.3
-
23
-
-
1342347334
-
Local inhomogeneity in asymmetric simple exclusion processes with extended objects
-
Shaw LB, Kolomeisky AB, Lee KH, (2004) Local inhomogeneity in asymmetric simple exclusion processes with extended objects. J Phys A 37: 2105.
-
(2004)
J Phys A
, vol.37
, pp. 2105
-
-
Shaw, L.B.1
Kolomeisky, A.B.2
Lee, K.H.3
-
24
-
-
0032579110
-
Asymmetric simple exclusion model with local inhomogeneity
-
Kolomeisky AB, (1998) Asymmetric simple exclusion model with local inhomogeneity. J Phys A 31: 1153.
-
(1998)
J Phys A
, vol.31
, pp. 1153
-
-
Kolomeisky, A.B.1
-
25
-
-
0942289341
-
Queuing transitions in the asymmetric simple exclusion process
-
Ha M, Timonen J, den Nijs M, (2003) Queuing transitions in the asymmetric simple exclusion process. Phys Rev E 68: 056122.
-
(2003)
Phys Rev E
, vol.68
, pp. 056122
-
-
Ha, M.1
Timonen, J.2
den Nijs, M.3
-
26
-
-
4243740606
-
Driven lattice gases with quenched disorder: Exact results and different macroscopic regimes
-
Tripathy G, Barma M, (1998) Driven lattice gases with quenched disorder: Exact results and different macroscopic regimes. Phys Rev E 58: 1911-1926.
-
(1998)
Phys Rev E
, vol.58
, pp. 1911-1926
-
-
Tripathy, G.1
Barma, M.2
-
27
-
-
36148962461
-
Inhomogeneous exclusion processes with extended objects: The effect of defect locations
-
Dong JJ, Schmittmann B, Zia RKP, (2007) Inhomogeneous exclusion processes with extended objects: The effect of defect locations. Phys Rev E 76: 051113.
-
(2007)
Phys Rev E
, vol.76
, pp. 051113
-
-
Dong, J.J.1
Schmittmann, B.2
Zia, R.K.P.3
-
28
-
-
0002296942
-
A new algorithm for monte carlo simulation of ising spin systems
-
Bortz AB, Kalos MH, Lebowitz JL, (1975) A new algorithm for monte carlo simulation of ising spin systems. J of Comput Phys 17: 10-18.
-
(1975)
J of Comput Phys
, vol.17
, pp. 10-18
-
-
Bortz, A.B.1
Kalos, M.H.2
Lebowitz, J.L.3
-
29
-
-
10944232800
-
Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale
-
Beyer A, Hollunder J, Nasheuer HP, Wilhelm T, (2004) Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale. Mol Cell Proteomics 3: 1083-1092.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1083-1092
-
-
Beyer, A.1
Hollunder, J.2
Nasheuer, H.P.3
Wilhelm, T.4
-
30
-
-
0016730809
-
Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast
-
Waldron C, Lacroute F, (1975) Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol 122: 855-865.
-
(1975)
J Bacteriol
, vol.122
, pp. 855-865
-
-
Waldron, C.1
Lacroute, F.2
-
31
-
-
17444449538
-
Transfer rna gene redundancy and translational selection in saccharomyces cerevisiae
-
Percudani R, Pavesi A, Ottonello S, (1997) Transfer rna gene redundancy and translational selection in saccharomyces cerevisiae. J Mol Biol 268: 322-330.
-
(1997)
J Mol Biol
, vol.268
, pp. 322-330
-
-
Percudani, R.1
Pavesi, A.2
Ottonello, S.3
-
32
-
-
0028148904
-
Seryl-trna synthetase from escherichia col: implication of its n-termspecificity
-
Borel F, Vincent C, Leberman R, Hartlein M, (1994) Seryl-trna synthetase from escherichia col: implication of its n-termspecificity. Nucl Acids Res 22.
-
(1994)
Nucl Acids Res
, vol.22
-
-
Borel, F.1
Vincent, C.2
Leberman, R.3
Hartlein, M.4
-
33
-
-
0028985111
-
Molecular recognition of trnapro by Escherichia coli proline trna synthetase in vitro
-
Liu H, Peterson R, Kessler J, Musier-Forsyth K, (1995) Molecular recognition of trnapro by Escherichia coli proline trna synthetase in vitro. Nucl Acids Res 23: 165-169.
-
(1995)
Nucl Acids Res
, vol.23
, pp. 165-169
-
-
Liu, H.1
Peterson, R.2
Kessler, J.3
Musier-Forsyth, K.4
-
34
-
-
0031030184
-
Defining the active site of yeast seryl-trna synthetase
-
Lenhard B, Filipić S, Landeka I, Škrtić I, Söll D, et al. (1997) Defining the active site of yeast seryl-trna synthetase. J Biol Chem 272: 1136-1141.
-
(1997)
J Biol Chem
, vol.272
, pp. 1136-1141
-
-
Lenhard, B.1
Filipić, S.2
Landeka, I.3
Škrtić, I.4
Söll, D.5
-
35
-
-
0032584780
-
Catalytic defect in mutants of class ii histidyl-trna synthetase from salmonella typhimurium previously linked to decreased control of histidine biosynthesis regulation
-
Francklyn C, Adamd J, Augustine J, (1998) Catalytic defect in mutants of class ii histidyl-trna synthetase from salmonella typhimurium previously linked to decreased control of histidine biosynthesis regulation. J Mol Biol 280: 847-858.
-
(1998)
J Mol Biol
, vol.280
, pp. 847-858
-
-
Francklyn, C.1
Adamd, J.2
Augustine, J.3
-
36
-
-
0032497422
-
The role of tryptophan residues in escherichia coli arginyl-trna synthetase
-
Zhang Qs, Wang Ed, Wang Yl, (1998) The role of tryptophan residues in escherichia coli arginyl-trna synthetase. Biochimica et Biophysica Acta 1387: 136-142.
-
(1998)
Biochimica Et Biophysica Acta
, vol.1387
, pp. 136-142
-
-
Zhang, Q.1
Wang, E.2
Wang, Y.3
-
37
-
-
57149143976
-
A quantitative estimation of the global translational activity in logarithmically growing yeast cells
-
von der Haar T, (2008) A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Sys Biol 2: 87.
-
(2008)
BMC Sys Biol
, vol.2
, pp. 87
-
-
von der Haar, T.1
-
38
-
-
0024117032
-
Ribosome pausing and stacking during translation of a eukaryotic mrna
-
Wolin SL, Walter P, (1988) Ribosome pausing and stacking during translation of a eukaryotic mrna. EMBO J 7: 3559-3569.
-
(1988)
EMBO J
, vol.7
, pp. 3559-3569
-
-
Wolin, S.L.1
Walter, P.2
-
39
-
-
18144385852
-
Clustered bottlenecks in mrna translation and protein synthesis
-
Chou T, Lakatos G, (2004) Clustered bottlenecks in mrna translation and protein synthesis. Phys Rev Lett 93: 198101.
-
(2004)
Phys Rev Lett
, vol.93
, pp. 198101
-
-
Chou, T.1
Lakatos, G.2
-
40
-
-
51849102802
-
Nonequilibrium processes: Driven lattice gases, interface dynamics, and quenched-disorder effects on density profiles and currents
-
de Queiroz SLA, Stinchcombe RB, (2008) Nonequilibrium processes: Driven lattice gases, interface dynamics, and quenched-disorder effects on density profiles and currents. Phys Rev E 78: 031106.
-
(2008)
Phys Rev E
, vol.78
, pp. 031106
-
-
de Queiroz, S.L.A.1
Stinchcombe, R.B.2
-
42
-
-
0023650543
-
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp P, Li W, (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-95.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.1
Li, W.2
-
43
-
-
27144515901
-
Movement of Eukaryotic mRNAs Between Polysomes and Cytoplasmic Processing Bodies
-
Brengues M, Teixeira D, Parker R, (2005) Movement of Eukaryotic mRNAs Between Polysomes and Cytoplasmic Processing Bodies. Science 310: 486-489.
-
(2005)
Science
, vol.310
, pp. 486-489
-
-
Brengues, M.1
Teixeira, D.2
Parker, R.3
-
44
-
-
69949167078
-
Genome-wide analysis of trna charging and activation of the eif2 kinase gcn2p
-
M109.000877
-
Zaborske JM, Narasimhan J, Jiang L, Wek SA, Dittmar KA, et al. (2009) Genome-wide analysis of trna charging and activation of the eif2 kinase gcn2p. J Biol Chem pp. M109.000877.
-
(2009)
J Biol Chem
-
-
Zaborske, J.M.1
Narasimhan, J.2
Jiang, L.3
Wek, S.A.4
Dittmar, K.A.5
-
45
-
-
0023722029
-
Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer rna binding to ribosomes in vitro
-
Thomas LK, Dix DB, Thompson RC, (1988) Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer rna binding to ribosomes in vitro. Proc Natl Acad Sci USA 85: 4242-4246.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 4242-4246
-
-
Thomas, L.K.1
Dix, D.B.2
Thompson, R.C.3
-
46
-
-
33645399045
-
A model of protein translation including codon bias, nonsense errors, and ribosome recycling
-
Gilchrist MA, Wagner A, (2006) A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 239: 417-434.
-
(2006)
J Theor Biol
, vol.239
, pp. 417-434
-
-
Gilchrist, M.A.1
Wagner, A.2
-
47
-
-
77952020413
-
Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mrna translation
-
Ciandrini L, Stansfield I, Romano MC, (2010) Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mrna translation. Phys Rev E 81: 051904.
-
(2010)
Phys Rev E
, vol.81
, pp. 051904
-
-
Ciandrini, L.1
Stansfield, I.2
Romano, M.C.3
-
48
-
-
11244258180
-
Near-critical behavior of aminoacyl-trna pools in e. coli at rate-limiting supply of amino acids
-
Elf J, Ehrenberg M, (2005) Near-critical behavior of aminoacyl-trna pools in e. coli at rate-limiting supply of amino acids. Biophys J 88: 132.
-
(2005)
Biophys J
, vol.88
, pp. 132
-
-
Elf, J.1
Ehrenberg, M.2
-
49
-
-
27344446707
-
Over expression of a trnaleu isoacceptor changes charging pattern of leucine trnas and reveals new codon reading
-
Sørensen MA, Elf J, Bouakaz E, Tenson T, Sanyal S, et al. (2005) Over expression of a trnaleu isoacceptor changes charging pattern of leucine trnas and reveals new codon reading. J Mol Biol 354: 16-24.
-
(2005)
J Mol Biol
, vol.354
, pp. 16-24
-
-
Sørensen, M.A.1
Elf, J.2
Bouakaz, E.3
Tenson, T.4
Sanyal, S.5
-
50
-
-
33645277360
-
Endonucleolytic cleavage of eukaryotic mrnas with stalls in translation elongation
-
Doma MK, Parker R, (2006) Endonucleolytic cleavage of eukaryotic mrnas with stalls in translation elongation. Nature 440: 561-564.
-
(2006)
Nature
, vol.440
, pp. 561-564
-
-
Doma, M.K.1
Parker, R.2
-
51
-
-
34548446795
-
Halting a cellular production line: responses to ribosomal pausing during translation
-
Buchan JR, Stansfield I, (2007) Halting a cellular production line: responses to ribosomal pausing during translation. Biology of the Cell 099: 475-487.
-
(2007)
Biology of the Cell
, vol.99
, pp. 475-487
-
-
Buchan, J.R.1
Stansfield, I.2
|