-
3
-
-
61549106268
-
Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence
-
Bollback, J. P., and J. P. Huelsenbeck. 2009. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics 181:225-234.
-
(2009)
Genetics
, vol.181
, pp. 225-234
-
-
Bollback, J.P.1
Huelsenbeck, J.P.2
-
4
-
-
33746045633
-
Optimality models of phage life history and parallels in disease evolution
-
Bull, J. J. 2006. Optimality models of phage life history and parallels in disease evolution. J. Theor. Biol. 241:928-938.
-
(2006)
J. Theor. Biol.
, vol.241
, pp. 928-938
-
-
Bull, J.J.1
-
5
-
-
2342624623
-
Genome properties and the limits of adaptation in bacteriophages
-
Bull, J. J., M. R. Badgett, R. Springman, and I. J. Molineux. 2004. Genome properties and the limits of adaptation in bacteriophages. Evolution 58:692-701.
-
(2004)
Evolution
, vol.58
, pp. 692-701
-
-
Bull, J.J.1
Badgett, M.R.2
Springman, R.3
Molineux, I.J.4
-
6
-
-
0034035485
-
Big-benefit mutations in a bacteriophage inhibited with heat
-
Bull, J. J., M. R. Badgett, and H. A. Wichman. 2000. Big-benefit mutations in a bacteriophage inhibited with heat. Mol. Biol. Evol. 17:942-950.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 942-950
-
-
Bull, J.J.1
Badgett, M.R.2
Wichman, H.A.3
-
7
-
-
0030823001
-
Exceptional convergent evolution in a virus
-
Bull, J. J., M. R. Badgett, H. A. Wichman, J. P. Huelsenbeck, D. M. Hillis, A. Gulati, C. Ho, and I. J. Molineux. 1997. Exceptional convergent evolution in a virus. Genetics 147:1497-1507.
-
(1997)
Genetics
, vol.147
, pp. 1497-1507
-
-
Bull, J.J.1
Badgett, M.R.2
Wichman, H.A.3
Huelsenbeck, J.P.4
Hillis, D.M.5
Gulati, A.6
Ho, C.7
Molineux, I.J.8
-
8
-
-
33646166237
-
Evolutionary feedback mediated through population density, illustrated with viruses in chemostats
-
Bull, J. J., J. Millstein, J. Orcutt, and H. A. Wichman. 2006. Evolutionary feedback mediated through population density, illustrated with viruses in chemostats. Am. Nat. 167:E36-E51.
-
(2006)
Am. Nat.
, vol.167
-
-
Bull, J.J.1
Millstein, J.2
Orcutt, J.3
Wichman, H.A.4
-
9
-
-
42449101317
-
Predicting evolution from genomics: experimental evolution of bacteriophage T7
-
Bull, J. J., and I. J. Molineux. 2008. Predicting evolution from genomics: experimental evolution of bacteriophage T7. Heredity 100:453-463.
-
(2008)
Heredity
, vol.100
, pp. 453-463
-
-
Bull, J.J.1
Molineux, I.J.2
-
10
-
-
33847247125
-
Theory of lethal mutagenesis for viruses
-
Bull, J. J., R. Sanjuan, and C. O. Wilke. 2007a. Theory of lethal mutagenesis for viruses. J. Virol. 81:2930-2939.
-
(2007)
J. Virol.
, vol.81
, pp. 2930-2939
-
-
Bull, J.J.1
Sanjuan, R.2
Wilke, C.O.3
-
11
-
-
34047202740
-
Compensatory evolution in response to a novel RNA polymerase: orthologous replacement of a central network gene
-
Bull, J. J., R. Springman, and I. J. Molineux. 2007b. Compensatory evolution in response to a novel RNA polymerase: orthologous replacement of a central network gene. Mol. Biol. Evol. 24:900-908.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 900-908
-
-
Bull, J.J.1
Springman, R.2
Molineux, I.J.3
-
12
-
-
75849141082
-
Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell
-
Chang, C. Y., P. Kemp, and I. J. Molineux. 2010. Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology 398:176-786.
-
(2010)
Virology
, vol.398
, pp. 176-786
-
-
Chang, C.Y.1
Kemp, P.2
Molineux, I.J.3
-
15
-
-
0032518266
-
DNA shuffling of a family of genes from diverse species accelerates directed evolution
-
Crameri, A., S. A. Raillard, E. Bermudez, and W. P. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288-291.
-
(1998)
Nature
, vol.391
, pp. 288-291
-
-
Crameri, A.1
Raillard, S.A.2
Bermudez, E.3
Stemmer, W.P.4
-
16
-
-
0003834965
-
-
Harper & Row, Publishers, New York, Evanston, London
-
Crow, J. F., and M. Kimura. 1970. An introduction to population genetics theory. Harper & Row, Publishers, New York, Evanston, London.
-
(1970)
An introduction to population genetics theory
-
-
Crow, J.F.1
Kimura, M.2
-
17
-
-
0037649306
-
Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation
-
de Visser, J. A., and R. E. Lenski. 2002. Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation. BMC Evol. Biol. 2:19.
-
(2002)
BMC Evol. Biol.
, vol.2
, pp. 19
-
-
de Visser, J.A.1
Lenski, R.E.2
-
18
-
-
0346449046
-
Complete genomic sequence of the virulent Salmonella bacteriophage SP6
-
Dobbins, A. T., M. George, Jr., D. A. Basham, M. E. Ford, J. M. Houtz, M. L. Pedulla, J. G. Lawrence, G. F. Hatfull, and R. W. Hendrix. 2004. Complete genomic sequence of the virulent Salmonella bacteriophage SP6. J. Bacteriol. 186:1933-1944.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 1933-1944
-
-
Dobbins, A.T.1
George Jr., M.2
Basham, D.A.3
Ford, M.E.4
Houtz, J.M.5
Pedulla, M.L.6
Lawrence, J.G.7
Hatfull, G.F.8
Hendrix, R.W.9
-
19
-
-
34250749323
-
High frequency of mutations that expand the host range of an RNA virus
-
Ferris, M. T., P. Joyce, and C. L. Burch. 2007. High frequency of mutations that expand the host range of an RNA virus. Genetics 176:1013-1022.
-
(2007)
Genetics
, vol.176
, pp. 1013-1022
-
-
Ferris, M.T.1
Joyce, P.2
Burch, C.L.3
-
20
-
-
10544233778
-
Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli
-
Garcia, L. R., and I. J. Molineux. 1996. Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli. J. Bacteriol. 178:6921-6929.
-
(1996)
J. Bacteriol.
, vol.178
, pp. 6921-6929
-
-
Garcia, L.R.1
Molineux, I.J.2
-
21
-
-
67649536027
-
Compensatory evolution for a gene deletion is not limited to its immediate functional network
-
Harcombe, W. R., R. Springman, and J. J. Bull. 2009. Compensatory evolution for a gene deletion is not limited to its immediate functional network. BMC Evol. Biol. 9:106.
-
(2009)
BMC Evol. Biol.
, vol.9
, pp. 106
-
-
Harcombe, W.R.1
Springman, R.2
Bull, J.J.3
-
22
-
-
34347354221
-
Testing optimality with experimental evolution: lysis time in a bacteriophage
-
Heineman, R. H., and J. J. Bull. 2007. Testing optimality with experimental evolution: lysis time in a bacteriophage. Evolution Int. J. Org. Evolution 61:1695-1709.
-
(2007)
Evolution Int. J. Org. Evolution
, vol.61
, pp. 1695-1709
-
-
Heineman, R.H.1
Bull, J.J.2
-
23
-
-
24744451431
-
Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene
-
Heineman, R. H., I. J. Molineux, and J. J. Bull. 2005. Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene. J. Mol. Evol. 61:181-191.
-
(2005)
J. Mol. Evol.
, vol.61
, pp. 181-191
-
-
Heineman, R.H.1
Molineux, I.J.2
Bull, J.J.3
-
24
-
-
78149369899
-
Estimation, effectiveness and opportunities of long term genetic improvement in animals and maize
-
Hill, W. G. 2008. Estimation, effectiveness and opportunities of long term genetic improvement in animals and maize. Lohmann Information 43:3-20.
-
(2008)
Lohmann Information
, vol.43
, pp. 3-20
-
-
Hill, W.G.1
-
25
-
-
2342449750
-
Inferences on the genetics of quantitative traits from long-term selection in laboratory and domestic animals
-
Hill, W. G., and L. Bunger. 2003. Inferences on the genetics of quantitative traits from long-term selection in laboratory and domestic animals. Plant Breeding Reviews 24:169-210.
-
(2003)
Plant Breeding Reviews
, vol.24
, pp. 169-210
-
-
Hill, W.G.1
Bunger, L.2
-
26
-
-
44649112395
-
Estimating the optimal bottleneck ratio for experimental evolution: the burst-death model
-
Hubbarde, J. E., and L. M. Wahl. 2008. Estimating the optimal bottleneck ratio for experimental evolution: the burst-death model. Math Biosci. 213:113-118.
-
(2008)
Math Biosci.
, vol.213
, pp. 113-118
-
-
Hubbarde, J.E.1
Wahl, L.M.2
-
27
-
-
24944579983
-
Changes in bacteriophage T7 virion structure at the initiation of infection
-
Kemp, P., L. R. Garcia, and I. J. Molineux. 2005. Changes in bacteriophage T7 virion structure at the initiation of infection. Virology 340:307-317.
-
(2005)
Virology
, vol.340
, pp. 307-317
-
-
Kemp, P.1
Garcia, L.R.2
Molineux, I.J.3
-
28
-
-
4344657166
-
Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism
-
Kemp, P., M. Gupta, and I. J. Molineux. 2004. Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism. Mol. Microbiol. 53:1251-1265.
-
(2004)
Mol. Microbiol.
, vol.53
, pp. 1251-1265
-
-
Kemp, P.1
Gupta, M.2
Molineux, I.J.3
-
29
-
-
47749097091
-
No evidence of selection for mutational robustness during lethal mutagenesis of lymphocytic choriomeningitis virus
-
Martin, V., A. Grande-Perez, and E. Domingo. 2008. No evidence of selection for mutational robustness during lethal mutagenesis of lymphocytic choriomeningitis virus. Virology 378:185-192.
-
(2008)
Virology
, vol.378
, pp. 185-192
-
-
Martin, V.1
Grande-Perez, A.2
Domingo, E.3
-
30
-
-
0003918633
-
-
Cambridge Univ. Press, Cambridge, England, New York
-
Maynard Smith, J. 1978. The evolution of sex. Cambridge Univ. Press, Cambridge, England, New York.
-
(1978)
The evolution of sex
-
-
Maynard Smith, J.1
-
31
-
-
21844441735
-
-
The T7 group. Calendar, ed. Oxford Univ. Press, New York, NY
-
Molineux, I. 2006. The T7 group. Pp. 277-301 in Calendar, ed. The bacteriophages. Oxford Univ. Press, New York, NY.
-
(2006)
The bacteriophages
, pp. 277-301
-
-
Molineux, I.1
-
32
-
-
0025662627
-
Optimality theory in evolutionary biology
-
Parker, G. A., and J. Maynard Smith. 1990. Optimality theory in evolutionary biology. Nature 348:27-33.
-
(1990)
Nature
, vol.348
, pp. 27-33
-
-
Parker, G.A.1
Maynard Smith, J.2
-
33
-
-
0035989644
-
Genome shuffling of Lactobacillus for improved acid tolerance
-
Patnaik, R., S. Louie, V. Gavrilovic, K. Perry, W. P. Stemmer, C. M. Ryan, and S. del Cardayre. 2002. Genome shuffling of Lactobacillus for improved acid tolerance. Nat. Biotechnol. 20:707-712.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 707-712
-
-
Patnaik, R.1
Louie, S.2
Gavrilovic, V.3
Perry, K.4
Stemmer, W.P.5
Ryan, C.M.6
del Cardayre, S.7
-
34
-
-
0030722164
-
Applications of DNA shuffling to pharmaceuticals and vaccines
-
Patten, P. A., R. J. Howard, and W. P. Stemmer. 1997. Applications of DNA shuffling to pharmaceuticals and vaccines. Curr. Opin. Biotechnol. 8:724-733.
-
(1997)
Curr. Opin. Biotechnol.
, vol.8
, pp. 724-733
-
-
Patten, P.A.1
Howard, R.J.2
Stemmer, W.P.3
-
35
-
-
33747849237
-
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli
-
Pelosi, L., L. Kuhn, D. Guetta, J. Garin, J. Geiselmann, R. E. Lenski, and D. Schneider. 2006. Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics 173:1851-1869.
-
(2006)
Genetics
, vol.173
, pp. 1851-1869
-
-
Pelosi, L.1
Kuhn, L.2
Guetta, D.3
Garin, J.4
Geiselmann, J.5
Lenski, R.E.6
Schneider, D.7
-
36
-
-
54349092997
-
Beneficial fitness effects are not exponential for two viruses
-
Rokyta, D. R., C. J. Beisel, P. Joyce, M. T. Ferris, C. L. Burch, and H. A. Wichman. 2008. Beneficial fitness effects are not exponential for two viruses. J. Mol. Evol. 67:368-376.
-
(2008)
J. Mol. Evol.
, vol.67
, pp. 368-376
-
-
Rokyta, D.R.1
Beisel, C.J.2
Joyce, P.3
Ferris, M.T.4
Burch, C.L.5
Wichman, H.A.6
-
37
-
-
0041324888
-
A comparison of directed evolution approaches using the beta-glucuronidase model system
-
Rowe, L. A., M. L. Geddie, O. B. Alexander, and I. Matsumura. 2003. A comparison of directed evolution approaches using the beta-glucuronidase model system. J. Mol. Biol. 332:851-860.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 851-860
-
-
Rowe, L.A.1
Geddie, M.L.2
Alexander, O.B.3
Matsumura, I.4
-
38
-
-
0347914560
-
Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup
-
Scholl, D., J. Kieleczawa, P. Kemp, J. Rush, C. C. Richardson, C. Merril, S. Adhya, and I. J. Molineux. 2004. Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J. Mol. Biol. 335:1151-1171.
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 1151-1171
-
-
Scholl, D.1
Kieleczawa, J.2
Kemp, P.3
Rush, J.4
Richardson, C.C.5
Merril, C.6
Adhya, S.7
Molineux, I.J.8
-
39
-
-
0000870489
-
The optimal balance between size and number of offspring
-
Smith, C. C., and S. D. Fretwell. 1974. The optimal balance between size and number of offspring. Am. Nat. 108:499-506.
-
(1974)
Am. Nat.
, vol.108
, pp. 499-506
-
-
Smith, C.C.1
Fretwell, S.D.2
-
40
-
-
25144479277
-
Gene order constrains adaptation in bacteriophage T7
-
Springman, R., M. R. Badgett, I. J. Molineux, and J. J. Bull. 2005. Gene order constrains adaptation in bacteriophage T7. Virology 341:141-152.
-
(2005)
Virology
, vol.341
, pp. 141-152
-
-
Springman, R.1
Badgett, M.R.2
Molineux, I.J.3
Bull, J.J.4
-
41
-
-
74249123371
-
Evolution at a high imposed mutation rate: adaptation obscures the load in phage T7
-
Springman, R., T. Keller, I. J. Molineux, and J. J. Bull. 2010. Evolution at a high imposed mutation rate: adaptation obscures the load in phage T7. Genetics 184:221-232.
-
(2010)
Genetics
, vol.184
, pp. 221-232
-
-
Springman, R.1
Keller, T.2
Molineux, I.J.3
Bull, J.J.4
-
42
-
-
0014603893
-
The genetics and physiology of bacteriophage T7
-
Studier, F. W. 1969. The genetics and physiology of bacteriophage T7. Virology 39:562-574.
-
(1969)
Virology
, vol.39
, pp. 562-574
-
-
Studier, F.W.1
-
43
-
-
31144465690
-
Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population
-
Vignuzzi, M., J. K. Stone, J. J. Arnold, C. E. Cameron, and R. Andino. 2006. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439:344-348.
-
(2006)
Nature
, vol.439
, pp. 344-348
-
-
Vignuzzi, M.1
Stone, J.K.2
Arnold, J.J.3
Cameron, C.E.4
Andino, R.5
-
44
-
-
0033770580
-
Rational evolutionary design: the theory of in vitro protein evolution
-
Voigt, C. A., S. Kauffman, and Z. G. Wang. 2000. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 55:79-160.
-
(2000)
Adv. Protein Chem.
, vol.55
, pp. 79-160
-
-
Voigt, C.A.1
Kauffman, S.2
Wang, Z.G.3
-
45
-
-
0033756453
-
Models of experimental evolution: the role of genetic chance and selective necessity
-
Wahl, L. M., and D. C. Krakauer. 2000. Models of experimental evolution: the role of genetic chance and selective necessity. Genetics 156:1437-1448.
-
(2000)
Genetics
, vol.156
, pp. 1437-1448
-
-
Wahl, L.M.1
Krakauer, D.C.2
-
46
-
-
20444382446
-
Adaptive molecular evolution for 13,000 phage generations: a possible arms race
-
Wichman, H. A., J. Millstein, and J. J. Bull. 2005. Adaptive molecular evolution for 13, 000 phage generations: a possible arms race. Genetics 170:19-31.
-
(2005)
Genetics
, vol.170
, pp. 19-31
-
-
Wichman, H.A.1
Millstein, J.2
Bull, J.J.3
-
47
-
-
0034731035
-
Experimental evolution recapitulates natural evolution
-
Wichman, H. A., L. A. Scott, C. D. Yarber, and J. J. Bull. 2000. Experimental evolution recapitulates natural evolution. Philos. Trans. R Soc. Lond. B Biol. Sci. 355:1677-1684.
-
(2000)
Philos. Trans. R Soc. Lond. B Biol. Sci.
, vol.355
, pp. 1677-1684
-
-
Wichman, H.A.1
Scott, L.A.2
Yarber, C.D.3
Bull, J.J.4
-
49
-
-
0003898977
-
-
Princeton Univ. Press, Princeton, NJ
-
Williams, G. C. 1975. Sex and evolution. Princeton Univ. Press, Princeton, NJ.
-
(1975)
Sex and evolution
-
-
Williams, G.C.1
-
50
-
-
33745166593
-
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli
-
Woods, R., D. Schneider, C. L. Winkworth, M. A. Riley, and R. E. Lenski. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. USA 103:9107-9112.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 9107-9112
-
-
Woods, R.1
Schneider, D.2
Winkworth, C.L.3
Riley, M.A.4
Lenski, R.E.5
|