-
1
-
-
0033828846
-
Codon usage in nucleopolyhedro-viruses
-
Levin DB, Whiteome B. Codon usage in nucleopolyhedro-viruses. J Gen Virol. 2000;81:2313-25.
-
(2000)
J Gen Virol
, vol.81
, pp. 2313-2325
-
-
Levin, D.B.1
Whiteome, B.2
-
2
-
-
0035036803
-
-
Jenkins GM, Pagel M, Gould EA, de A Zanotto PM, Holmes EC. Evolution of base composition and codon usage bias in the genus Flavivirus. J Mol Evol. 2001;52:383-90.
-
Jenkins GM, Pagel M, Gould EA, de A Zanotto PM, Holmes EC. Evolution of base composition and codon usage bias in the genus Flavivirus. J Mol Evol. 2001;52:383-90.
-
-
-
-
3
-
-
0037372775
-
The extent of codon usage bias in human RNA viruses and its evolutionary origin
-
Jenkins GM, Holmes EC. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 2003;92:1-7.
-
(2003)
Virus Res
, vol.92
, pp. 1-7
-
-
Jenkins, G.M.1
Holmes, E.C.2
-
4
-
-
0019519371
-
Codon catalog usage is a genome strategy modulated for gene expressivity
-
Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 1981;9:r43-74.
-
(1981)
Nucleic Acids Res
, vol.9
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Jacobzone, M.4
Mercier, R.5
-
5
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985;2:13-34.
-
(1985)
Mol Biol Evol
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
6
-
-
0025988205
-
Synonymous codon usage in Saccharomyces cerevisiae
-
Sharp PM, Cowe E. Synonymous codon usage in Saccharomyces cerevisiae. Yeast. 1991;7:657-78.
-
(1991)
Yeast
, vol.7
, pp. 657-678
-
-
Sharp, P.M.1
Cowe, E.2
-
7
-
-
0034695438
-
Ribosome traffic in E. coli and regulation of gene expression
-
Lesnik T, Solomovici J, Deana A, Ehrlich R, Reiss C. Ribosome traffic in E. coli and regulation of gene expression. J Theor Biol. 2000, 202:175-85.
-
(2000)
J Theor Biol
, vol.202
, pp. 175-185
-
-
Lesnik, T.1
Solomovici, J.2
Deana, A.3
Ehrlich, R.4
Reiss, C.5
-
9
-
-
0035948585
-
Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa
-
Gupta SK, Ghosh TC. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene. 2001;273:63-70.
-
(2001)
Gene
, vol.273
, pp. 63-70
-
-
Gupta, S.K.1
Ghosh, T.C.2
-
10
-
-
0032493780
-
Specific correlations between relative synonymous codon usage and protein secondary structure
-
Oresic M, Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol. 1998;281:31-48.
-
(1998)
J Mol Biol
, vol.281
, pp. 31-48
-
-
Oresic, M.1
Shalloway, D.2
-
11
-
-
0031697801
-
The relationship between synonymous codon usage and protein structure
-
Xie T, Ding D. The relationship between synonymous codon usage and protein structure. FEBS Lett. 1998;434:93-6.
-
(1998)
FEBS Lett
, vol.434
, pp. 93-96
-
-
Xie, T.1
Ding, D.2
-
12
-
-
0034736516
-
Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code
-
Chiusano ML, Alvarez-valin F, Di Giulio M, D'Onofrio G, Ammirato G, Colonna G, et al. Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene. 2000; 261:63-9.
-
(2000)
Gene
, vol.261
, pp. 63-69
-
-
Chiusano, M.L.1
Alvarez-valin, F.2
Di Giulio, M.3
D'Onofrio, G.4
Ammirato, G.5
Colonna, G.6
-
13
-
-
0034708361
-
Studies on the relationships between the synonymous codon usage and protein secondary structural units
-
Gupta SK, Majumdar S, Bhattacharya TK, Ghosh TC. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem Biophys Res Commun. 2000;269:692-6.
-
(2000)
Biochem Biophys Res Commun
, vol.269
, pp. 692-696
-
-
Gupta, S.K.1
Majumdar, S.2
Bhattacharya, T.K.3
Ghosh, T.C.4
-
14
-
-
0037201997
-
The base composition of the genes is correlated with the secondary structures of the encoded proteins
-
D'Onofrio G, Ghosh TC, Bernardi G. The base composition of the genes is correlated with the secondary structures of the encoded proteins. Gene. 2002;300:179-87.
-
(2002)
Gene
, vol.300
, pp. 179-187
-
-
D'Onofrio, G.1
Ghosh, T.C.2
Bernardi, G.3
-
15
-
-
4444307575
-
Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis
-
Basak S, Banerjee T, Gupta SK, Ghosh TC. Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis. J Biomol Struct Dyn. 2004;22:205-14.
-
(2004)
J Biomol Struct Dyn
, vol.22
, pp. 205-214
-
-
Basak, S.1
Banerjee, T.2
Gupta, S.K.3
Ghosh, T.C.4
-
16
-
-
0028088517
-
Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
-
Lobry JR, Gautier C. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 1994;22:3174-80.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3174-3180
-
-
Lobry, J.R.1
Gautier, C.2
-
17
-
-
0034731415
-
Trends of amino acid usage in the proteins from the unicellular parasite Giardia lamblia
-
Garat B, Musto H. Trends of amino acid usage in the proteins from the unicellular parasite Giardia lamblia. Biochem Biophys Res Commun. 2000;279:996-1000.
-
(2000)
Biochem Biophys Res Commun
, vol.279
, pp. 996-1000
-
-
Garat, B.1
Musto, H.2
-
18
-
-
0036216144
-
Trends in codon and amino acid usage in Thermotoga maritima
-
Zavala A, Naya H, Romero H, Musto H. Trends in codon and amino acid usage in Thermotoga maritima. J Mol Evol. 2002; 54:563-8.
-
(2002)
J Mol Evol
, vol.54
, pp. 563-568
-
-
Zavala, A.1
Naya, H.2
Romero, H.3
Musto, H.4
-
19
-
-
4143154090
-
Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus
-
Baneriee T, Basak S, Gupta SK, Ghosh TC. Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus. J Biomol Struct Dyn. 2004;22:13-23.
-
(2004)
J Biomol Struct Dyn
, vol.22
, pp. 13-23
-
-
Baneriee, T.1
Basak, S.2
Gupta, S.K.3
Ghosh, T.C.4
-
20
-
-
8844280220
-
Correspondence analysis of amino acid usage within the family Bacillaceae
-
Naya H, Zavala A, Romero H, Rodriguez-Maseda H, Musto H. Correspondence analysis of amino acid usage within the family Bacillaceae. Biochem Biophys Res Commun. 2004; 325:1252-7.
-
(2004)
Biochem Biophys Res Commun
, vol.325
, pp. 1252-1257
-
-
Naya, H.1
Zavala, A.2
Romero, H.3
Rodriguez-Maseda, H.4
Musto, H.5
-
22
-
-
0021679725
-
Selection pressures on codon usage in the complete genome of bacteriophage T7
-
Sharp PM, Rogers MS, McConnell DJ. Selection pressures on codon usage in the complete genome of bacteriophage T7. J Mol Evol. 1984-85;21:150-60.
-
(1984)
J Mol Evol
, vol.21
, pp. 150-160
-
-
Sharp, P.M.1
Rogers, M.S.2
McConnell, D.J.3
-
23
-
-
0023372221
-
Codon contexts in enterobacterial and coliphage genes
-
Gouy M. Codon contexts in enterobacterial and coliphage genes. Mol Biol Evol. 1987;4:426-44.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 426-444
-
-
Gouy, M.1
-
24
-
-
0022589865
-
Codon usage and gene expression
-
Holm L. Codon usage and gene expression. Nucleic Acids Res. 1986;14:3075-87.
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 3075-3087
-
-
Holm, L.1
-
25
-
-
0027056781
-
Synonymous codon preferences in bacteriophage T4: A distinctive use of transfer RNAs from T4 and from its host Escherichia coli
-
Kunisawa T. Synonymous codon preferences in bacteriophage T4: a distinctive use of transfer RNAs from T4 and from its host Escherichia coli. J Theor Biol. 1992;159:287-98.
-
(1992)
J Theor Biol
, vol.159
, pp. 287-298
-
-
Kunisawa, T.1
-
26
-
-
0032585328
-
Comparison of synonymous codon distribution patterns of bacteriophage and host genomes
-
Kunisawa T, Kanaya S, Kutter E. Comparison of synonymous codon distribution patterns of bacteriophage and host genomes. DNA Res. 1998;5:319-26.
-
(1998)
DNA Res
, vol.5
, pp. 319-326
-
-
Kunisawa, T.1
Kanaya, S.2
Kutter, E.3
-
27
-
-
0034616968
-
Functional role of mycobacteriophage transfer RNAs
-
Kunisawa T. Functional role of mycobacteriophage transfer RNAs. J Theor Biol. 2000;205:167-70.
-
(2000)
J Theor Biol
, vol.205
, pp. 167-170
-
-
Kunisawa, T.1
-
28
-
-
4444239271
-
Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M. smegmatis: Identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species
-
Sahu K, Gupta SK, Ghosh TC, Sau S. Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M. smegmatis: Identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species. J Biochem Mol Biol. 2004;37:487-92.
-
(2004)
J Biochem Mol Biol
, vol.37
, pp. 487-492
-
-
Sahu, K.1
Gupta, S.K.2
Ghosh, T.C.3
Sau, S.4
-
29
-
-
20944451749
-
Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes
-
Sahu K, Gupta SK, Sau S, Ghosh TC. Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes. J Biomol Struct Dyn. 2005;23: 63-71.
-
(2005)
J Biomol Struct Dyn
, vol.23
, pp. 63-71
-
-
Sahu, K.1
Gupta, S.K.2
Sau, S.3
Ghosh, T.C.4
-
30
-
-
24944467406
-
Synonymous codon usage bias in 16 Staphylococcus aureus phages: Implication in phage therapy
-
Sau K, Gupta SK, Sau S, Ghosh TC. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Res. 2005;113:123-31.
-
(2005)
Virus Res
, vol.113
, pp. 123-131
-
-
Sau, K.1
Gupta, S.K.2
Sau, S.3
Ghosh, T.C.4
-
31
-
-
17444380108
-
Potential of the polyvalent anti-Staphylococcus bacteriophage K for control of antibiotic-resistant staphylococci from hospitals
-
O'Flaherty S, Ross RP, Meaney W, Fitzgerald GF, Elbreki MF, Coffey A. Potential of the polyvalent anti-Staphylococcus bacteriophage K for control of antibiotic-resistant staphylococci from hospitals. Appl Environ Microbiol. 2005;71: 1836-42.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 1836-1842
-
-
O'Flaherty, S.1
Ross, R.P.2
Meaney, W.3
Fitzgerald, G.F.4
Elbreki, M.F.5
Coffey, A.6
-
32
-
-
26944484468
-
Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ
-
Sau K, Sau S, Mandal SC, Ghosh TC. Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ. Acta Biochim Biophys Sin (Shanghai). 2005;37:625-33.
-
(2005)
Acta Biochim Biophys Sin (Shanghai)
, vol.37
, pp. 625-633
-
-
Sau, K.1
Sau, S.2
Mandal, S.C.3
Ghosh, T.C.4
-
33
-
-
0025323108
-
Isolation and characterization of bacteriophage PM3 from Aeromonas hydrophila the bacterial receptor for which is the monopolar flagellum
-
Merino S, Camprubi S, Tomas JM. Isolation and characterization of bacteriophage PM3 from Aeromonas hydrophila the bacterial receptor for which is the monopolar flagellum. FEMS Microbiol Lett. 1990;57:277-82.
-
(1990)
FEMS Microbiol Lett
, vol.57
, pp. 277-282
-
-
Merino, S.1
Camprubi, S.2
Tomas, J.M.3
-
34
-
-
0025707548
-
Isolation and characterization of bacteriophage PM2 from Aeromonas hydrophila
-
Merino S, Camprubi S, Tomas JM. Isolation and characterization of bacteriophage PM2 from Aeromonas hydrophila. FEMS Microbiol Lett. 1990;56:239-44.
-
(1990)
FEMS Microbiol Lett
, vol.56
, pp. 239-244
-
-
Merino, S.1
Camprubi, S.2
Tomas, J.M.3
-
35
-
-
0025253784
-
Identification of the cell surface receptor for bacteriophage 18 from Aeromonas hydrophila
-
Merino S, Camprubi S, Tomas JM. Identification of the cell surface receptor for bacteriophage 18 from Aeromonas hydrophila. Res Microbiol. 1990;141:173-80.
-
(1990)
Res Microbiol
, vol.141
, pp. 173-180
-
-
Merino, S.1
Camprubi, S.2
Tomas, J.M.3
-
36
-
-
0020571270
-
Isolation and partial characterization of two Aeromonas hydrophila bacteriophages
-
Chow MS, Rouf MA. Isolation and partial characterization of two Aeromonas hydrophila bacteriophages. Appl Environ Microbiol. 1983;45:1670-6.
-
(1983)
Appl Environ Microbiol
, vol.45
, pp. 1670-1676
-
-
Chow, M.S.1
Rouf, M.A.2
-
37
-
-
0035180718
-
Phytogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages
-
Tetart F, Desplats C, Kutateladze M, Monod C, Ackermann HW, Krisch HM. Phytogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J Bacteriol. 2001; 183:358-66.
-
(2001)
J Bacteriol
, vol.183
, pp. 358-366
-
-
Tetart, F.1
Desplats, C.2
Kutateladze, M.3
Monod, C.4
Ackermann, H.W.5
Krisch, H.M.6
-
38
-
-
0023650543
-
The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987;15:1281-95.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
39
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright F. The 'effective number of codons' used in a gene. Gene. 1990;87:23-9.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
40
-
-
1642412614
-
Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
-
Gu W, Zhou T, Ma J, Sun X, Lu Z. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res. 2004;101:155-61.
-
(2004)
Virus Res
, vol.101
, pp. 155-161
-
-
Gu, W.1
Zhou, T.2
Ma, J.3
Sun, X.4
Lu, Z.5
-
41
-
-
0008585246
-
Correlation between codon usage and tRNA content in microorganisms
-
Hatfield DL, Lee BJ, Pirtle RM, eds, Boca Raton, Ann Arbor, London, Tokyo: CRC Press;
-
Ikemura T. Correlation between codon usage and tRNA content in microorganisms. In: Hatfield DL, Lee BJ, Pirtle RM, eds. Transfer RNA in protein synthesis. Boca Raton, Ann Arbor, London, Tokyo: CRC Press; 1992.
-
(1992)
Transfer RNA in protein synthesis
-
-
Ikemura, T.1
-
42
-
-
0345188623
-
Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability
-
Zhou J, Liu WJ, Peng SW, Sun XY, Frazer I. Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J Virol. 1999;73: 4972-82.
-
(1999)
J Virol
, vol.73
, pp. 4972-4982
-
-
Zhou, J.1
Liu, W.J.2
Peng, S.W.3
Sun, X.Y.4
Frazer, I.5
-
43
-
-
0034821884
-
Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis
-
Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol. 2001; 53:290-8.
-
(2001)
J Mol Evol
, vol.53
, pp. 290-298
-
-
Kanaya, S.1
Yamada, Y.2
Kinouchi, M.3
Kudo, Y.4
Ikemura, T.5
-
44
-
-
0032882170
-
Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
-
Kanaya S, Yamada Y, Kudo Y, Ikemura T. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene. 1999;238:143-55.
-
(1999)
Gene
, vol.238
, pp. 143-155
-
-
Kanaya, S.1
Yamada, Y.2
Kudo, Y.3
Ikemura, T.4
-
45
-
-
0142075218
-
Fatal bacteremic pneumonia caused by Aeromonas hydrophila in a previously healthy child
-
Kao HT, Huang YC, Lin TY. Fatal bacteremic pneumonia caused by Aeromonas hydrophila in a previously healthy child. J Microbiol Immunol Infect. 2003;36:209-11.
-
(2003)
J Microbiol Immunol Infect
, vol.36
, pp. 209-211
-
-
Kao, H.T.1
Huang, Y.C.2
Lin, T.Y.3
-
47
-
-
0036156073
-
Bacteriophage therapy of infectious diseases in aquaculture
-
Nakai T, Park SC. Bacteriophage therapy of infectious diseases in aquaculture. Res Microbiol. 2002;153:13-8.
-
(2002)
Res Microbiol
, vol.153
, pp. 13-18
-
-
Nakai, T.1
Park, S.C.2
-
48
-
-
27644460427
-
Bacteriophage therapy: A revitalized therapy against bacterial infectious diseases
-
Matsuzaki S, Rashel M, Uchiyama J, Sakurai S, Ujihara T, Kuroda M, et al. Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother. 2005; 11:211-9.
-
(2005)
J Infect Chemother
, vol.11
, pp. 211-219
-
-
Matsuzaki, S.1
Rashel, M.2
Uchiyama, J.3
Sakurai, S.4
Ujihara, T.5
Kuroda, M.6
-
49
-
-
21444458163
-
Human volunteers receiving Escherichia coli phage T4 orally: A safety test of phage therapy
-
Bruttin A, Brüssow, H. Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy. Antimicrob Agents Chemother. 2005;49:2874-8.
-
(2005)
Antimicrob Agents Chemother
, vol.49
, pp. 2874-2878
-
-
Bruttin, A.1
Brüssow, H.2
-
50
-
-
2942554124
-
In vitro and in vivo bacteriolytic activities of Escherichia coli phages: Implications for phage therapy
-
Chibani-Chennoufi S, Sidoti J, Bruttin A, Kutter E, Sarker S, Brüssow H. In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy. Antimicrob Agents Chemother. 2004;48:2558-69.
-
(2004)
Antimicrob Agents Chemother
, vol.48
, pp. 2558-2569
-
-
Chibani-Chennoufi, S.1
Sidoti, J.2
Bruttin, A.3
Kutter, E.4
Sarker, S.5
Brüssow, H.6
-
51
-
-
2942526906
-
Evaluation of a cocktail of three bacteriophages for biocontrol of Escherichia coli O157:H7
-
O'Flynn G, Ross RP, Fitzgerald GF, Coffey A. Evaluation of a cocktail of three bacteriophages for biocontrol of Escherichia coli O157:H7. Appl Environ Microbiol. 2004;70:3417-24.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 3417-3424
-
-
O'Flynn, G.1
Ross, R.P.2
Fitzgerald, G.F.3
Coffey, A.4
-
52
-
-
0036139176
-
Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium
-
Biswas B, Adhya S, Washart P, Paul B, Trostel AN, Powell B, et al. Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun. 2002;70:204-10.
-
(2002)
Infect Immun
, vol.70
, pp. 204-210
-
-
Biswas, B.1
Adhya, S.2
Washart, P.3
Paul, B.4
Trostel, A.N.5
Powell, B.6
-
53
-
-
0343674508
-
Isolation of bacteriophages specific to a fish pathogen, Pseudomonas plecoglossicida, as a candidate for disease control
-
Park SC, Shimamura I, Fukunaga M, Mori KI, Nakai T. Isolation of bacteriophages specific to a fish pathogen, Pseudomonas plecoglossicida, as a candidate for disease control. Appl Environ Microbiol. 2000;66:1416-22.
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 1416-1422
-
-
Park, S.C.1
Shimamura, I.2
Fukunaga, M.3
Mori, K.I.4
Nakai, T.5
|