-
1
-
-
14544277543
-
Variation in the strength of selected codon usage bias among bacteria
-
DOI 10.1093/nar/gki242
-
Sharp, P. M., Bailes, E., Grocock, R. J., Peden, J. F. & Sockett, R. E. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33, 1141-1153 (2005). (Pubitemid 41439907)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.4
, pp. 1141-1153
-
-
Sharp, P.M.1
Bailes, E.2
Grocock, R.J.3
Peden, J.F.4
Sockett, R.E.5
-
2
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255-258 (2009).
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
3
-
-
84873601673
-
Good codons, bad transcript: Large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme
-
Agashe, D., Martinez-Gomez, N. C., Drummond, D. A. & Marx, C. J. Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol. Biol. Evol. 30, 549-560 (2013).
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 549-560
-
-
Agashe, D.1
Martinez-Gomez, N.C.2
Drummond, D.A.3
Marx, C.J.4
-
4
-
-
78650304100
-
Synonymous but not the same: The causes and consequences of codon bias
-
Plotkin, J. B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 12, 32-42 (2011).
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
5
-
-
84876348105
-
Sounds of silence: Synonymous nucleotides as a key to biological regulation and complexity
-
Shabalina, S. A., Spiridonov, N. A. & Kashina, A. Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res. 41, 2073-2094 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 2073-2094
-
-
Shabalina, S.A.1
Spiridonov, N.A.2
Kashina, A.3
-
6
-
-
33846504706
-
A silent polymorphism in the MDR1 gene changes substrate specificity
-
DOI 10.1126/science.1135308
-
Kimchi-Sarfaty, C. et al. A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525-528 (2007). (Pubitemid 46175758)
-
(2007)
Science
, vol.315
, Issue.5811
, pp. 525-528
-
-
Kimchi-Sarfaty, C.1
Oh, J.M.2
Kim, I.-W.3
Sauna, Z.E.4
Calcagno, A.M.5
Ambudkar, S.V.6
Gottesman, M.M.7
-
7
-
-
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. Mol. Biol. 16, 274-280 (2009).
-
(2009)
Nat. Struct. Mol. Biol
, vol.16
, pp. 274-280
-
-
Zhang, G.1
Hubalewska, M.2
Ignatova, Z.3
-
8
-
-
3042742751
-
Experimental reduction of codon bias in the Drosophila alcohol dehydrogenase gene results in decreased ethanol tolerance of adult flies
-
DOI 10.1111/j.1420-9101.2004.00725.x
-
Carlini, D. B. Experimental reduction of codon bias in the Drosophila alcohol dehydrogenase gene results in decreased ethanol tolerance of adult flies. J. Evol. Biol. 17, 779-785 (2004). (Pubitemid 38871330)
-
(2004)
Journal of Evolutionary Biology
, vol.17
, Issue.4
, pp. 779-785
-
-
Carlini, D.B.1
-
9
-
-
78149293610
-
Mutational robustness of ribosomal protein genes
-
Lind, P. A., Berg, O. G. & Andersson, D. I. Mutational robustness of ribosomal protein genes. Science 330, 825-827 (2010).
-
(2010)
Science
, vol.330
, pp. 825-827
-
-
Lind, P.A.1
Berg, O.G.2
Andersson, D.I.3
-
10
-
-
84861312619
-
The fitness effects of synonymous mutations in DNA and RNA viruses
-
Cuevas, J. M., Domingo-Calap, P. & Sanjuan, R. The fitness effects of synonymous mutations in DNA and RNA viruses. Mol. Biol. Evol. 29, 17-20 (2012).
-
(2012)
Mol. Biol. Evol
, vol.29
, pp. 17-20
-
-
Cuevas, J.M.1
Domingo-Calap, P.2
Sanjuan, R.3
-
11
-
-
84864070833
-
Quantifying the adaptive potential of an antibiotic resistance enzyme
-
Schenk, M. F., Szendro, I. G., Krug, J. & de Visser, J. A. Quantifying the adaptive potential of an antibiotic resistance enzyme. PLoS Genet. 8, e1002783 (2012).
-
(2012)
PLoS Genet
, vol.8
-
-
Schenk, M.F.1
Szendro, I.G.2
Krug, J.3
De Visser, J.A.4
-
13
-
-
0029985179
-
Molecular evolution between Drosophila melanogaster and D. Simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. Melanogaster
-
Akashi, H. Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144, 1297-1307 (1996).
-
(1996)
Genetics
, vol.144
, pp. 1297-1307
-
-
Akashi, H.1
-
14
-
-
0035157374
-
Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
-
McVean, G. A. & Vieira, J. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157, 245-257 (2001). (Pubitemid 32066311)
-
(2001)
Genetics
, vol.157
, Issue.1
, pp. 245-257
-
-
McVean, G.A.T.1
Vieira, J.2
-
15
-
-
79955426758
-
Determinants of synonymous and nonsynonymous variability in three species of Drosophila
-
Haddrill, P. R., Zeng, K. & Charlesworth, B. Determinants of synonymous and nonsynonymous variability in three species of Drosophila. Mol. Biol. Evol. 28, 1731-1743 (2011).
-
(2011)
Mol. Biol. Evol
, vol.28
, pp. 1731-1743
-
-
Haddrill, P.R.1
Zeng, K.2
Charlesworth, B.3
-
16
-
-
84878486976
-
Strong purifying selection at synonymous sites in D. Melanogaster
-
Lawrie, D. S., Messer, P. W., Hershberg, R. & Petrov, D. A. Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet. 9, e1003527 (2013).
-
(2013)
PLoS Genet
, vol.9
-
-
Lawrie, D.S.1
Messer, P.W.2
Hershberg, R.3
Petrov, D.A.4
-
17
-
-
75349114758
-
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
-
Conrad, T. M. et al. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 10, R118 (2009).
-
(2009)
Genome Biol
, vol.10
-
-
Conrad, T.M.1
-
18
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1247 (2009).
-
(2009)
Nature
, vol.461
, pp. 1243-1247
-
-
Barrick, J.E.1
-
19
-
-
84883132678
-
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations
-
Lang, G. I. et al. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500, 571-574 (2013).
-
(2013)
Nature
, vol.500
, pp. 571-574
-
-
Lang, G.I.1
-
20
-
-
84863692451
-
Spatial structure of ecological opportunity drives adaptation in a bacterium
-
Bailey, S. F. & Kassen, R. Spatial structure of ecological opportunity drives adaptation in a bacterium. Am. Nat. 180, 270-283 (2012).
-
(2012)
Am. Nat
, vol.180
, pp. 270-283
-
-
Bailey, S.F.1
Kassen, R.2
-
21
-
-
0019190802
-
Protein D1: A glucose-inducible, pore-forming protein from the outer membrane of Pseudomonas aeruginosa
-
DOI 10.1016/0378-1097(80)90079-8
-
Hancock, R. E. & Carey, A. M. Protein D1 - a glucose-inducible, pore-forming protein from the outer membrane of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 8, 105-109 (1980). (Pubitemid 10062205)
-
(1980)
FEMS Microbiology Letters
, vol.8
, Issue.2
, pp. 105-109
-
-
Hancock, R.E.W.1
Carey, A.M.2
-
22
-
-
0027282263
-
Substrate specificity of the high-affinity glucose transport system of Pseudomonas aeruginosa
-
Wylie, J. L. & Worobec, E. A. Substrate specificity of the high-affinity glucose transport system of Pseudomonas aeruginosa. Can. J. Microbiol. 39, 722-725 (1993). (Pubitemid 23280640)
-
(1993)
Canadian Journal of Microbiology
, vol.39
, Issue.7
, pp. 722-725
-
-
Wylie, J.L.1
Worobec, E.A.2
-
23
-
-
34447522100
-
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: Genomic and flux analysis
-
DOI 10.1128/JB.00203-07
-
del Castillo, T. et al. Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J. Bacteriol. 189, 5142-5152 (2007). (Pubitemid 47076060)
-
(2007)
Journal of Bacteriology
, vol.189
, Issue.14
, pp. 5142-5152
-
-
Del Castillo, T.1
Ramos, J.L.2
Rodriguez-Herva, J.J.3
Fuhrer, T.4
Sauer, U.5
Duque, E.6
-
24
-
-
41549126717
-
A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate
-
DOI 10.1128/JB.01726-07
-
del Castillo, T., Duque, E. & Ramos, J. L. A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate. J. Bacteriol. 190, 2331-2339 (2008). (Pubitemid 351466328)
-
(2008)
Journal of Bacteriology
, vol.190
, Issue.7
, pp. 2331-2339
-
-
Del Castillo, T.1
Duque, E.2
Ramos, J.L.3
-
25
-
-
77955132055
-
Carbon catabolite repression in Pseudomonas: Optimizing metabolic versatility and interactions with the environment
-
Rojo, F. Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol. Rev. 34, 658-684 (2010).
-
(2010)
FEMS Microbiol. Rev
, vol.34
, pp. 658-684
-
-
Rojo, F.1
-
26
-
-
78649333094
-
Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria
-
Browne, P., Barret, M., O'Gara, F. & Morrissey, J. P. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria. BMC Microbiol. 10, 300 (2010).
-
(2010)
BMC Microbiol
, vol.10
, pp. 300
-
-
Browne, P.1
Barret, M.2
O'Gara, F.3
Morrissey, J.P.4
-
27
-
-
84863924309
-
Bacterial small RNA regulators: Versatile roles and rapidly evolving variations
-
Gottesman, S. & Storz, G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect. Biol. 3, a003798 (2011).
-
(2011)
Cold Spring Harb. Perspect. Biol
, vol.3
-
-
Gottesman, S.1
Storz, G.2
-
28
-
-
84875457350
-
Bacterial small RNA-based negative regulation: Hfq and its accomplices
-
De Lay, N., Schu, D. J. & Gottesman, S. Bacterial small RNA-based negative regulation: Hfq and its accomplices. J. Biol. Chem. 288, 7996-8003 (2013).
-
(2013)
J. Biol. Chem
, vol.288
, pp. 7996-8003
-
-
De Lay, N.1
Schu, D.J.2
Gottesman, S.3
-
29
-
-
32244448730
-
A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: Application for DNA fragment transfer between chromosomes and plasmid transformation
-
DOI 10.1016/j.mimet.2005.06.001, PII S0167701205001582
-
Choi, K. H., Kumar, A. & Schweizer, H. P. A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J. Microbiol. Methods 64, 391-397 (2006). (Pubitemid 43212814)
-
(2006)
Journal of Microbiological Methods
, vol.64
, Issue.3
, pp. 391-397
-
-
Choi, K.-H.1
Kumar, A.2
Schweizer, H.P.3
-
31
-
-
84860663163
-
Evolutionary insight from whole-genome sequencing of experimentally evolved microbes
-
Dettman, J. R. et al. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 21, 2058-2077 (2012).
-
(2012)
Mol. Ecol
, vol.21
, pp. 2058-2077
-
-
Dettman, J.R.1
-
32
-
-
33745402876
-
Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype
-
DOI 10.1534/genetics.106.055863
-
Goymer, P. et al. Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype. Genetics 173, 515-526 (2006). (Pubitemid 43945875)
-
(2006)
Genetics
, vol.173
, Issue.2
, pp. 515-526
-
-
Goymer, P.1
Kahn, S.G.2
Malone, J.G.3
Gehrig, S.M.4
Spiers, A.J.5
Rainey, P.B.6
-
33
-
-
0033140434
-
Adaptation of Pseudomonas fluorescens to the plant rhizosphere
-
Rainey, P. B. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1, 243-257 (1999). (Pubitemid 129640046)
-
(1999)
Environmental Microbiology
, vol.1
, Issue.3
, pp. 243-257
-
-
Rainey, P.B.1
-
34
-
-
0032575051
-
A broad-host-range F1p-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: Application for isolation of unmarked Pseudomonas aeruginosa mutants
-
DOI 10.1016/S0378-1119(98)00130-9, PII S0378111998001309
-
Hoang, T. T., Karkhoff-Schweizer, R. R., Kutchma, A. J. & Schweizer, H. P. A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212, 77-86 (1998). (Pubitemid 28269135)
-
(1998)
Gene
, vol.212
, Issue.1
, pp. 77-86
-
-
Hoang, T.T.1
Karkhoff-Schweizer, R.R.2
Kutchma, A.J.3
Schweizer, H.P.4
-
35
-
-
21444457864
-
A Tn7-based broad-range bacterial cloning and expression system
-
Choi, K. H. et al. A Tn7-based broad-range bacterial cloning and expression system. Nat. Methods 2, 443-448 (2005).
-
(2005)
Nat. Methods 2
, pp. 443-448
-
-
Choi, K.H.1
-
36
-
-
33749531431
-
Mini-Tn7 insertion in bacteria with single attTn7 sites: Example Pseudomonas aeruginosa
-
Choi, K. H. & Schweizer, H. P. mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat. Protoc. 1, 153-161 (2006).
-
(2006)
Nat. Protoc
, vol.1
, pp. 153-161
-
-
Choi, K.H.1
Schweizer, H.P.2
-
37
-
-
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. 15, 1281-1295 (1987).
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
38
-
-
41149089793
-
-
(eds Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M.) Springer Verlag
-
Charif, D. & Lobry, J. R. in Structural Approaches to Sequence Evolution: Molecules, Networks, Populations (eds Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M.) 207-232 (Springer Verlag, 2007).
-
(2007)
Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
, pp. 207-232
-
-
Charif, D.1
Lobry, J.R.2
-
39
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
DOI 10.1093/nar/gkg595
-
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003). (Pubitemid 37442169)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3406-3415
-
-
Zuker, M.1
-
40
-
-
0035010435
-
ABC transporters catalyzing carbohydrate uptake
-
DOI 10.1016/S0923-2508(01)01201-3, PII S0923250801012013
-
Schneider, E. ABC transporters catalyzing carbohydrate uptake. Res. Microbiol. 152, 303-310 (2001). (Pubitemid 32436488)
-
(2001)
Research in Microbiology
, vol.152
, Issue.3-4
, pp. 303-310
-
-
Schneider, E.1
|