-
1
-
-
14844348002
-
Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein
-
doi: 10.1093/nar/gki292
-
Baril, M. and Brakier-Gingras, L. 2005. Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res. 33: 1474-1486. doi: 10.1093/nar/gki292.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1474-1486
-
-
Baril, M.1
Brakier-Gingras, L.2
-
2
-
-
0242542705
-
Patterns of epistasis in RNA viruses: A review of the evidence from vaccine design
-
Burch, C.L., Turner, P.E., and Hanley, K.A. 2003. Patterns of epistasis in RNA viruses: A review of the evidence from vaccine design. J. Evol. Biol. 16: 1223-1235.
-
(2003)
J. Evol. Biol
, vol.16
, pp. 1223-1235
-
-
Burch, C.L.1
Turner, P.E.2
Hanley, K.A.3
-
3
-
-
0142088791
-
Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
-
Chare, E.R., Gould, E.A., and Holmes, E.C. 2003. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 84: 2691-2703.
-
(2003)
J. Gen. Virol
, vol.84
, pp. 2691-2703
-
-
Chare, E.R.1
Gould, E.A.2
Holmes, E.C.3
-
4
-
-
33846018059
-
The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens
-
doi: 10.1371/journal.ppat.0020136
-
Codoñer, F.M., Daròs, J.A., Solé, R.V., and Elena, S.F. 2006. The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog. 2: e136. doi: 10.1371/journal.ppat.0020136.
-
(2006)
PLoS Pathog
, vol.2
-
-
Codoñer, F.M.1
Daròs, J.A.2
Solé, R.V.3
Elena, S.F.4
-
5
-
-
11444257029
-
Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution
-
Cristina, J., Lopez, F., Moratorio, G., Lopez, L., Vasquez, S., Garcia-Aguirre, L., and Chunga, A. 2005. Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution. J. Gen. Virol. 86: 115-120.
-
(2005)
J. Gen. Virol
, vol.86
, pp. 115-120
-
-
Cristina, J.1
Lopez, F.2
Moratorio, G.3
Lopez, L.4
Vasquez, S.5
Garcia-Aguirre, L.6
Chunga, A.7
-
6
-
-
0035811016
-
RNA virus error catastrophe: Direct molecular test by using ribavirin
-
Crotty, S., Cameron, C.E., and Andino, R. 2001. RNA virus error catastrophe: Direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. 98: 6895-6900.
-
(2001)
Proc. Natl. Acad. Sci
, vol.98
, pp. 6895-6900
-
-
Crotty, S.1
Cameron, C.E.2
Andino, R.3
-
7
-
-
0033598717
-
Mutation rates among RNA viruses
-
Drake, J.W. and Holland, J.J. 1999. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. 96: 13910-13913.
-
(1999)
Proc. Natl. Acad. Sci
, vol.96
, pp. 13910-13913
-
-
Drake, J.W.1
Holland, J.J.2
-
8
-
-
0031916242
-
Rates of spontaneous mutation
-
Drake, J.W., Charlesworth, B., Charlesworth, D., and Crow, J.F. 1998. Rates of spontaneous mutation. Genetics 148: 1667-1686.
-
(1998)
Genetics
, vol.148
, pp. 1667-1686
-
-
Drake, J.W.1
Charlesworth, B.2
Charlesworth, D.3
Crow, J.F.4
-
9
-
-
0015133749
-
Selforganization of matter and the evolution of biological macromolecules
-
Eigen, M. 1971. Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
-
(1971)
Naturwissenschaften
, vol.58
, pp. 465-523
-
-
Eigen, M.1
-
10
-
-
0031458777
-
Test of synergistic interactions among deleterious mutations in bacteria
-
Elena, S.F. and Lenski, R.E. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390: 395-398.
-
(1997)
Nature
, vol.390
, pp. 395-398
-
-
Elena, S.F.1
Lenski, R.E.2
-
11
-
-
33645800999
-
Mechanisms of genetic robustness in RNA viruses
-
Elena, S.F., Carrasco, P., Daros, J.A., and Sanjuan, R. 2006. Mechanisms of genetic robustness in RNA viruses. EMBO Rep. 7: 168-173.
-
(2006)
EMBO Rep
, vol.7
, pp. 168-173
-
-
Elena, S.F.1
Carrasco, P.2
Daros, J.A.3
Sanjuan, R.4
-
12
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125: 1-15.
-
(1985)
Am. Nat
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
13
-
-
13844294363
-
Detecting overlapping coding sequences with pairwise alignments
-
Firth, A.E. and Brown, C.M. 2005. Detecting overlapping coding sequences with pairwise alignments. Bioinformatics 21: 282-292.
-
(2005)
Bioinformatics
, vol.21
, pp. 282-292
-
-
Firth, A.E.1
Brown, C.M.2
-
14
-
-
0033561022
-
Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae
-
Fukuda, Y., Washio, T., and Tomita, M. 1999. Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res. 27: 1847-1853.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1847-1853
-
-
Fukuda, Y.1
Washio, T.2
Tomita, M.3
-
15
-
-
33746099256
-
Recombination and the evolution of mutational robustness
-
Gardner, A. and Kalinka, A.T. 2006. Recombination and the evolution of mutational robustness. J. Theor. Biol. 241: 707-715.
-
(2006)
J. Theor. Biol
, vol.241
, pp. 707-715
-
-
Gardner, A.1
Kalinka, A.T.2
-
16
-
-
0001400708
-
The effect of variation on fitness
-
Haldane, J.B.S. 1937. The effect of variation on fitness. Am. Nat. 71: 337-349.
-
(1937)
Am. Nat
, vol.71
, pp. 337-349
-
-
Haldane, J.B.S.1
-
17
-
-
0032987974
-
The versatility of paramyxovirus RNA polymerase stuttering
-
Hausmann, S., Garcin, D., Delenda, C., and Kolakofsky, D. 1999. The versatility of paramyxovirus RNA polymerase stuttering. J. Virol. 73: 5568-5576.
-
(1999)
J. Virol
, vol.73
, pp. 5568-5576
-
-
Hausmann, S.1
Garcin, D.2
Delenda, C.3
Kolakofsky, D.4
-
18
-
-
0345059165
-
Error thresholds and the constraints to RNA virus evolution
-
Holmes, E.C. 2003. Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11: 543-546.
-
(2003)
Trends Microbiol
, vol.11
, pp. 543-546
-
-
Holmes, E.C.1
-
19
-
-
0036147047
-
Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
-
Jenkins, G.M., Rambaut, A., Pybus, O.G., and Holmes, E.C. 2002. Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis. J. Mol. Evol. 54: 156-165.
-
(2002)
J. Mol. Evol
, vol.54
, pp. 156-165
-
-
Jenkins, G.M.1
Rambaut, A.2
Pybus, O.G.3
Holmes, E.C.4
-
20
-
-
8744308029
-
Properties of overlapping genes are conserved across microbial genomes
-
Johnson, Z.I. and Chisholm, S.W. 2004. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 14: 2268-2272.
-
(2004)
Genome Res
, vol.14
, pp. 2268-2272
-
-
Johnson, Z.I.1
Chisholm, S.W.2
-
21
-
-
0029992175
-
On the prevalence of certain codons ("RNY") in genes for proteins
-
Jukes, T.H. 1996. On the prevalence of certain codons ("RNY") in genes for proteins. J. Mol. Evol. 42: 377-381.
-
(1996)
J. Mol. Evol
, vol.42
, pp. 377-381
-
-
Jukes, T.H.1
-
22
-
-
0026722407
-
Origins of genes: "Big bang" or continuous creation
-
Keese, P.K. and Gibbs, A. 1992. Origins of genes: "Big bang" or continuous creation. Proc. Natl. Acad. Sci. 89: 9489-9493.
-
(1992)
Proc. Natl. Acad. Sci
, vol.89
, pp. 9489-9493
-
-
Keese, P.K.1
Gibbs, A.2
-
23
-
-
0000977985
-
The mutational load with epistatic gene interactions in fitness
-
Kimura, M. and Maruyama, T. 1966. The mutational load with epistatic gene interactions in fitness. Genetics 54: 1337-1351.
-
(1966)
Genetics
, vol.54
, pp. 1337-1351
-
-
Kimura, M.1
Maruyama, T.2
-
24
-
-
0033926304
-
Stability and evolution of overlapping genes
-
Krakauer, D.C. 2000. Stability and evolution of overlapping genes. Evolution 54: 731-739.
-
(2000)
Evolution
, vol.54
, pp. 731-739
-
-
Krakauer, D.C.1
-
25
-
-
0037022396
-
Redundancy, antiredundancy, and the robustness of genomes
-
Krakauer, D.C. and Plotkin, J.B. 2002. Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. 99: 1405-1409.
-
(2002)
Proc. Natl. Acad. Sci
, vol.99
, pp. 1405-1409
-
-
Krakauer, D.C.1
Plotkin, J.B.2
-
26
-
-
0028988480
-
Identification of a Rev-related protein by analysis of spliced transcripts of the human endogenous retroviruses HTDV/HERV-K
-
Lower, R., Tonjes, R.R., Korbmacher, C., Kurth, R., and Lower, J. 1995. Identification of a Rev-related protein by analysis of spliced transcripts of the human endogenous retroviruses HTDV/HERV-K. J. Virol. 69: 141-149.
-
(1995)
J. Virol
, vol.69
, pp. 141-149
-
-
Lower, R.1
Tonjes, R.R.2
Korbmacher, C.3
Kurth, R.4
Lower, J.5
-
27
-
-
0033809519
-
In vivo analysis of human T-cell leukemia virus type 1 reverse transcription accuracy
-
Mansky, L.M. 2000. In vivo analysis of human T-cell leukemia virus type 1 reverse transcription accuracy. J. Virol. 74: 9525-9531.
-
(2000)
J. Virol
, vol.74
, pp. 9525-9531
-
-
Mansky, L.M.1
-
28
-
-
0031030479
-
Constrained evolution with respect to gene overlap of hepatitis B virus
-
Mizokami, M., Orito, E., Ohba, K., Ikeo, K., Lau, J.Y., and Gojobori, T. 1997. Constrained evolution with respect to gene overlap of hepatitis B virus. J. Mol. Evol. 44: S83-S90.
-
(1997)
J. Mol. Evol
, vol.44
-
-
Mizokami, M.1
Orito, E.2
Ohba, K.3
Ikeo, K.4
Lau, J.Y.5
Gojobori, T.6
-
29
-
-
27844567907
-
Evolution of mutational robustness in an RNA virus
-
doi: 10.1371/journal.pbio.0030381
-
Montville, R., Froissart, R., Remold, S.K., Tenaillon, O., and Turner, P.E. 2005. Evolution of mutational robustness in an RNA virus. PLoS Biol. 3: e381. doi: 10.1371/journal.pbio.0030381.
-
(2005)
PLoS Biol
, vol.3
-
-
Montville, R.1
Froissart, R.2
Remold, S.K.3
Tenaillon, O.4
Turner, P.E.5
-
30
-
-
0021007202
-
Overlapping genes
-
Normark, S., Bergstrom, S., Edlund, T., Grundstrom, T., Jaurin, B., Lindberg, F.P., and Olsson, O. 1983. Overlapping genes. Annu. Rev. Genet. 17: 499-525.
-
(1983)
Annu. Rev. Genet
, vol.17
, pp. 499-525
-
-
Normark, S.1
Bergstrom, S.2
Edlund, T.3
Grundstrom, T.4
Jaurin, B.5
Lindberg, F.P.6
Olsson, O.7
-
31
-
-
0027071241
-
What is a quasispecies?
-
Nowak, M.A. 1992. What is a quasispecies? Trends Ecol. Evol. 7: 118-121.
-
(1992)
Trends Ecol. Evol
, vol.7
, pp. 118-121
-
-
Nowak, M.A.1
-
32
-
-
0030976687
-
On the informational content of overlapping genes in prokaryotic and eukaryotic viruses
-
Pavesi, A., DeIaco, B., Granero, M.I., and Porati, A. 1997. On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J. Mol. Evol. 44: 625-631.
-
(1997)
J. Mol. Evol
, vol.44
, pp. 625-631
-
-
Pavesi, A.1
DeIaco, B.2
Granero, M.I.3
Porati, A.4
-
33
-
-
4644313330
-
Overlapping messages and survivability
-
Peleg, O., Kirzhner, V., Trifonov, E., and Bolshoy, A. 2004. Overlapping messages and survivability. J. Mol. Evol. 59: 520-527.
-
(2004)
J. Mol. Evol
, vol.59
, pp. 520-527
-
-
Peleg, O.1
Kirzhner, V.2
Trifonov, E.3
Bolshoy, A.4
-
34
-
-
0036575455
-
Purifying and directional selection in overlapping prokaryotic genes
-
Rogozin, I.B., Spiridonov, A.N., Sorokin, A.V., Wolf, Y.I., Jordan, I.K., Tatusov, R.L., and Koonin, E.V. 2002. Purifying and directional selection in overlapping prokaryotic genes. Trends Genet. 18: 228-232.
-
(2002)
Trends Genet
, vol.18
, pp. 228-232
-
-
Rogozin, I.B.1
Spiridonov, A.N.2
Sorokin, A.V.3
Wolf, Y.I.4
Jordan, I.K.5
Tatusov, R.L.6
Koonin, E.V.7
-
35
-
-
33749242962
-
Epistasis correlates to genomic complexity
-
Sanjuan, R. and Elena, S.F. 2006. Epistasis correlates to genomic complexity. Proc. Natl. Acad. Sci. 103: 14402-14405.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 14402-14405
-
-
Sanjuan, R.1
Elena, S.F.2
-
36
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuan, R., Moya, A., and Elena, S.F. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. 101: 8396-8401.
-
(2004)
Proc. Natl. Acad. Sci
, vol.101
, pp. 8396-8401
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
37
-
-
34347327212
-
Selection for robustness in mutagenized RNA viruses
-
doi: 10.1371/journal.pgen.0030093
-
Sanjuan, R., Cuevas, J.M., Furió, V., Holmes, E.C., and Moya, A. 2007. Selection for robustness in mutagenized RNA viruses. PLoS Genet. 3: e93. doi: 10.1371/journal.pgen.0030093.
-
(2007)
PLoS Genet
, vol.3
-
-
Sanjuan, R.1
Cuevas, J.M.2
Furió, V.3
Holmes, E.C.4
Moya, A.5
-
38
-
-
8144223724
-
The ambush hypothesis: Hidden stop codons prevent off-frame gene reading
-
Seligmann, H. and Pollock, D.D. 2004. The ambush hypothesis: Hidden stop codons prevent off-frame gene reading. DNA Cell Biol. 23: 701-705.
-
(2004)
DNA Cell Biol
, vol.23
, pp. 701-705
-
-
Seligmann, H.1
Pollock, D.D.2
-
39
-
-
12244297403
-
High rate of viral evolution associated with the emergence of carnivore parvovirus
-
Shackelton, L.A., Parrish, C.R., Truyen, U., and Holmes, E.C. 2005. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc. Natl. Acad. Sci. 102: 379-384.
-
(2005)
Proc. Natl. Acad. Sci
, vol.102
, pp. 379-384
-
-
Shackelton, L.A.1
Parrish, C.R.2
Truyen, U.3
Holmes, E.C.4
-
40
-
-
0019453879
-
Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code
-
Shepherd, J.C.W. 1981. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17: 94-102.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 94-102
-
-
Shepherd, J.C.W.1
-
41
-
-
0027064537
-
Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase
-
Steinhauer, D.A., Domingo, E., and Holland, J.J. 1992. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 122: 281-288.
-
(1992)
Gene
, vol.122
, pp. 281-288
-
-
Steinhauer, D.A.1
Domingo, E.2
Holland, J.J.3
-
42
-
-
0011754335
-
Transduction of a cellular oncogene - the genesis of Rous sarcoma virus
-
Swanstrom, R., Parker, R.C., Varmus, H.E., and Bishop, J.M. 1983. Transduction of a cellular oncogene - the genesis of Rous sarcoma virus. Proc. Natl. Acad. Sci. 80: 2519-2523.
-
(1983)
Proc. Natl. Acad. Sci
, vol.80
, pp. 2519-2523
-
-
Swanstrom, R.1
Parker, R.C.2
Varmus, H.E.3
Bishop, J.M.4
-
43
-
-
0003412658
-
-
Academic Press, San Diego
-
van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S.M., Maniloff, J., Mayo, M.A., McGeoch, D.J., Pringle, C.R., et al. 2000. Virus taxonomy: Classification and nomenclature of viruses. Academic Press, San Diego.
-
(2000)
Virus taxonomy: Classification and nomenclature of viruses
-
-
van Regenmortel, M.H.V.1
Fauquet, C.M.2
Bishop, D.H.L.3
Carstens, E.B.4
Estes, M.K.5
Lemon, S.M.6
Maniloff, J.7
Mayo, M.A.8
McGeoch, D.J.9
Pringle, C.R.10
-
44
-
-
0035452110
-
Alternative definitions of epistasis: Dependence and interaction
-
Wade, M.J., Winther, R.G., Agrawal, A.F., and Goodnight, C.J. 2001. Alternative definitions of epistasis: Dependence and interaction. Trends Ecol. Evol. 16: 498-504.
-
(2001)
Trends Ecol. Evol
, vol.16
, pp. 498-504
-
-
Wade, M.J.1
Winther, R.G.2
Agrawal, A.F.3
Goodnight, C.J.4
-
45
-
-
0037469371
-
Evolution of mutational robustness
-
Wilke, C.O. and Adami, C. 2003. Evolution of mutational robustness. Mutat. Res. 522: 3-11.
-
(2003)
Mutat. Res
, vol.522
, pp. 3-11
-
-
Wilke, C.O.1
Adami, C.2
-
46
-
-
0035913336
-
Evolution of digital organisms at high mutation rates leads to survival of the flattest
-
Wilke, C.O., Wang, J.L., Ofria, C., Lenski, R.E., and Adami, C. 2001. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331-333.
-
(2001)
Nature
, vol.412
, pp. 331-333
-
-
Wilke, C.O.1
Wang, J.L.2
Ofria, C.3
Lenski, R.E.4
Adami, C.5
-
47
-
-
0029840630
-
A reevaluation of the higher taxonomy of viruses based on RNA polymerases
-
Zanotto, P.M.D., Gibbs, M.J., Gould, E.A., and Holmes, E.C. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70: 6083-6096.
-
(1996)
J. Virol
, vol.70
, pp. 6083-6096
-
-
Zanotto, P.M.D.1
Gibbs, M.J.2
Gould, E.A.3
Holmes, E.C.4
|