-
1
-
-
0034082141
-
Analysis of a local fitness landscape with a mo del of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and ther-molysin
-
Aita, T., Uchiyama, H., Inaoka, T., Naka-jima, M., Kokubo, T., and Husimi, Y. (2000). Analysis of a local fitness landscape with a mo del of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and ther-molysin. Biopolymers 54, 64-79.
-
(2000)
Biopolymers
, vol.54
, pp. 64-79
-
-
Aita, T.1
Uchiyama, H.2
Inaoka, T.3
Naka-Jima, M.4
Kokubo, T.5
Husimi, Y.6
-
2
-
-
34247881991
-
Analysis of epistatic interactions and fitness landscapes using a new geometric approach
-
doi:10.1186/1471-2148-7-60
-
Beerenwinkel, N., Pachter, L., Sturmfels, B., Elena, S. F., and Lenski, R. E. (2007). Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol. Biol. 7, 60. doi:10.1186/1471-2148-7-60
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.60
-
-
Beerenwinkel, N.1
Pachter, L.2
Sturmfels, B.3
Elena, S.F.4
Lenski, R.E.5
-
3
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N., and Tawfik, D. S. (2006). Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444, 929-932.
-
(2006)
Nature
, vol.444
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
4
-
-
67749108208
-
Phy-logenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence
-
Besnard, G., Muasya, A. M., Russier, E, Roalson, E. H., Salamin, N., and Christin, P. A. (2009). Phy-logenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Mol. Biol. Evol. 26,1909-1919.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1909-1919
-
-
Besnard, G.1
Muasya, A.M.2
Russier, E.3
Roalson, E.H.4
Salamin, N.5
Christin, P.A.6
-
5
-
-
45849093668
-
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
-
Blount,Z. D., Borland, C. Z., and Lenski, R. E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105, 7899-7906.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 7899-7906
-
-
Blount, Z.D.1
Borland, C.Z.2
Lenski, R.E.3
-
6
-
-
0026570624
-
Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects
-
Boucher, C. A., O'Sullivan, E., Mulder, J. W., Ramautarsing, C., Kel-lam, P., Darby, G., et al. (1992). Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J. Infect. Dis. 165, 105-110.
-
(1992)
J. Infect. Dis.
, vol.165
, pp. 105-110
-
-
Boucher, C.A.1
O'Sullivan, E.2
Mulder, J.W.3
Ramautarsing, C.4
Kellam, P.5
Darby, G.6
-
7
-
-
78649365006
-
Compensatory mutations restore fitness during the evolution of dihydrofolate reductase
-
Brown, K. M., Costanzo, M. S., Xu, W., Roy, S., Lozovsky, E. R., and Hartl, D. L. (2010). Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. Mol. Biol. Evol. 27, 2682-2690.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 2682-2690
-
-
Brown, K.M.1
Costanzo, M.S.2
Xu, W.3
Roy, S.4
Lozovsky, E.R.5
Hartl, D.L.6
-
8
-
-
76549129324
-
Colloquium papers: adaptive landscapes and protein evolution
-
Carneiro, M., and Hartl, D. L. (2010). Colloquium papers: adaptive landscapes and protein evolution. Proc. Natl.Acad. Sci. U.S.A. 107(Suppl. 1), 1747-1751.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, Issue.SUPPL. 1
, pp. 1747-1751
-
-
Carneiro, M.1
Hartl, D.L.2
-
9
-
-
34447337260
-
C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes
-
Christin, P. A., Salamin, N., Savolainen, V., Duvall, M. R., and Besnard, G. (2007). C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr. Biol. 17, 1241-1247.
-
(2007)
Curr. Biol.
, vol.17
, pp. 1241-1247
-
-
Christin, P.A.1
Salamin, N.2
Savolainen, V.3
Duvall, M.R.4
Besnard, G.5
-
10
-
-
77649133888
-
Experimental evolution with E. coli in diverse resource environments, I. Fluctuating environments promote divergence of replicate populations
-
doi:10.1186/1471-2148-10-11
-
Cooper, T. F., and Lenski, R. E. (2010). Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol. Biol. 10, 11. doi:10.1186/1471-2148-10-11
-
(2010)
BMC Evol. Biol.
, vol.10
, Issue.11
-
-
Cooper, T.F.1
Lenski, R.E.2
-
11
-
-
79956356758
-
Fitnesstrade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falci-parum
-
doi:10.1371/journal.pone.0019636
-
Costanzo, M. S., Brown, K. M., and Hartl, D. L. (2011). Fitnesstrade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falci-parum. PLoS ONE 6, e19636. doi:10.1371/journal.pone.0019636
-
(2011)
PLoS ONE
, vol.6
-
-
Costanzo, M.S.1
Brown, K.M.2
Hartl, D.L.3
-
12
-
-
80053133668
-
The evolutionary landscape of antifolate resistance in Plasmodium falciparum
-
Costanzo, M. S., and Hartl, D. L. (2011). The evolutionary landscape of antifolate resistance in Plasmodium falciparum. J. Genet. 90, 187-190.
-
(2011)
J. Genet.
, vol.90
, pp. 187-190
-
-
Costanzo, M.S.1
Hartl, D.L.2
-
13
-
-
48249115639
-
The ascent of the abundant: how muta-tional networks constrain evolution
-
doi:10.1371/journal.pcbi.1000110
-
Cowperthwaite, M. C., Economo, E. P., Harcombe, W. R., Miller, E. L., and Meyers, L. A. (2008). The ascent of the abundant: how muta-tional networks constrain evolution. PLoS Comput. Biol. 4, e1000110. doi:10.1371/journal.pcbi.1000110
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Cowperthwaite, M.C.1
Economo, E.P.2
Harcombe, W.R.3
Miller, E.L.4
Meyers, L.A.5
-
14
-
-
77955933105
-
Parallel genetic and phenotypic evolution of DNA super-helicity in experimental populations of Escherichia coli. Mol
-
Crozat, E., Winkworth, C., Gaffe, J., Hallin, P. F., Riley, M. A., Lenski, R. E., et al. (2010). Parallel genetic and phenotypic evolution of DNA super-helicity in experimental populations of Escherichia coli. Mol. Biol. Evol. 27,2113-2128.
-
(2010)
Biol. Evol.
, vol.27
, pp. 2113-2128
-
-
Crozat, E.1
Winkworth, C.2
Gaffe, J.3
Hallin, P.F.4
Riley, M.A.5
Lenski, R.E.6
-
15
-
-
77956641491
-
Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region
-
da Silva, J., Coetzer, M., Nedel-lec, R., Pastore, C., and Mosier, D. E. (2010). Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185, 293-303.
-
(2010)
Genetics
, vol.185
, pp. 293-303
-
-
da Silva, J.1
Coetzer, M.2
Nedel-lec, R.3
Pastore, C.4
Mosier, D.E.5
-
16
-
-
66149185556
-
Compensatory mutations are repeatable and clustered within proteins
-
Davis, B. H., Poon, A. F., and Whit-lock, M. C. (2009). Compensatory mutations are repeatable and clustered within proteins. Proc. Biol. Sci. 276, 1823-1827.
-
(2009)
Proc. Biol. Sci.
, vol.276
, pp. 1823-1827
-
-
Davis, B.H.1
Poon, A.F.2
Whit-lock, M.C.3
-
17
-
-
77954499525
-
Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape
-
Dawid, A., Kiviet, D. J., Kogenaru, M., de Vos, M., and Tans, S. J. (2010). Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape. Chaos 20, 026105.
-
(2010)
Chaos
, vol.20
, pp. 026105
-
-
Dawid, A.1
Kiviet, D.J.2
Kogenaru, M.3
De Vos, M.4
Tans, S.J.5
-
18
-
-
68549127130
-
Exploring the effect of sex on empirical fitness landscapes
-
de Visser, J. A., Park, S. C., and Krug, J. (2009). Exploring the effect of sex on empirical fitness landscapes. Am. Nat. 174(Suppl. 1), 15-30.
-
(2009)
Am. Nat.
, vol.174
, Issue.SUPPL. 1
, pp. 15-30
-
-
De Visser, J.A.1
Park, S.C.2
Krug, J.3
-
19
-
-
77956469635
-
High-resolution mapping of evolutionary trajectories in a phage
-
Dickins, B., and Nekrutenko, A. (2009). High-resolution mapping of evolutionary trajectories in a phage. Genome Biol. Evol. 1,294-307.
-
(2009)
Genome Biol. Evol.
, vol.1
, pp. 294-307
-
-
Dickins, B.1
Nekrutenko, A.2
-
20
-
-
0038441327
-
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
-
Elena, S. F., and Lenski, R. E. (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4,457-469.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
21
-
-
61849168524
-
Clonal interference, multiple mutations and adaptation in large asexual populations
-
Fogle, C. A., Nagle, J. L., and Desai, M. M. (2008). Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics 180,2163-2173.
-
(2008)
Genetics
, vol.180
, pp. 2163-2173
-
-
Fogle, C.A.1
Nagle, J.L.2
Desai, M.M.3
-
22
-
-
80052329913
-
Evolutionary accessibility of mutational pathways
-
doi:10.1371/journal.pcbi.1002134
-
Franke, J., Klozer, A., de Visser, J. A., and Krug, J. (2011). Evolutionary accessibility of mutational pathways. PLoS Comput. Biol. 7, e1002134. doi:10.1371/journal.pcbi.1002134
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Franke, J.1
Klozer, A.2
De Visser, J.A.3
Krug, J.4
-
23
-
-
84876074625
-
Fitness Landscapes and the Origin of Species. Princeton
-
Princeton University Press.Gillespie, J. H. (1985). The interaction of genetic drift and mutation with selection in a fluctuating environment
-
Gavrilets, S. (2004). Fitness Landscapes and the Origin of Species. Princeton: Princeton University Press.Gillespie, J. H. (1985). The interaction of genetic drift and mutation with selection in a fluctuating environment. Theor. Popul. Biol. 27, 222-237.
-
(2004)
Theor. Popul. Biol.
, vol.27
, pp. 222-237
-
-
Gavrilets, S.1
-
25
-
-
58149166731
-
The reper toire and dynamics of evolu tionary adaptations to controlled nutrient-limited environments in yeast
-
doi:10.1371/journal.pgen.1000303
-
M., Tucker, C.M., Jenq, H. T., Pai, D. A., Ward, A., et al. (2008). The reper toire and dynamics of evolu tionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4, e1000303. doi:10.1371/journal.pgen.1000303
-
(2008)
PLoS Genet
, vol.4
-
-
Gresham, D.1
Desai, M.M.2
Tucker, C.M.3
Jenq, H.T.4
Pai, D.A.5
Ward, A.6
-
26
-
-
34247603929
-
Experimental rugged fitness landscape in protein sequence space
-
doi:10.1371/journal.pone.0000096
-
Hayashi, Y., Aita, T., Toyota, H., Husimi, Y., Urabe, I., and Yomo, T. (2006). Experimental rugged fitness landscape in protein sequence space. PLoS ONE 1, e96. doi:10.1371/journal.pone.0000096
-
(2006)
PLoS ONE
, vol.1
-
-
Hayashi, Y.1
Aita, T.2
Toyota, H.3
Husimi, Y.4
Urabe, I.5
Yomo, T.6
-
27
-
-
33751544539
-
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
-
Herring, C. D., Raghunathan, A., Honisch, C., Patel, T., Applebee, M. K., Joyce, A. R., et al. (2006). Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 38, 1406-1412.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1406-1412
-
-
Herring, C.D.1
Raghunathan, A.2
Honisch, C.3
Patel, T.4
Applebee, M.K.5
Joyce, A.R.6
-
28
-
-
56749107039
-
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Sac-charomyces cerevisiae
-
Kao, K. C., and Sherlock, G. (2008). Molecular characterization of clonal interference during adaptive evolution in asexual populations of Sac-charomyces cerevisiae. Nat. Genet. 40, 1499-1504.
-
(2008)
Nat. Genet.
, vol.40
, pp. 1499-1504
-
-
Kao, K.C.1
Sherlock, G.2
-
29
-
-
0023647382
-
Towards a general theory of adaptive walks on rugged landscapes
-
Kauffman, S., and Levin, S. (1987). Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 128, 11-45.
-
(1987)
J. Theor. Biol.
, vol.128
, pp. 11-45
-
-
Kauffman, S.1
Levin, S.2
-
30
-
-
0024803111
-
The NK model of rugged fitness landscapes and its application to maturation of the immune-response
-
Kauffman, S. A., and Weinberger, E. D. (1989). The NK model of rugged fitness landscapes and its application to maturation of the immune-response. J. Theor. Biol. 141,211-245.
-
(1989)
J. Theor. Biol.
, vol.141
, pp. 211-245
-
-
Kauffman, S.A.1
Weinberger, E.D.2
-
31
-
-
0027954914
-
Zidovudine treatment results in the selection of human immunodeficiency virus type 1 variants whose genotypes confer increasing levels of drug resistance
-
Kellam, P., Boucher, C. A., Tijnagel, J. M., and Larder, B. A. (1994). Zidovudine treatment results in the selection of human immunodeficiency virus type 1 variants whose genotypes confer increasing levels of drug resistance. J. Gen. Virol. 75(Pt 2), 341-351.
-
(1994)
J. Gen. Virol.
, vol.75
, Issue.PART 2
, pp. 341-351
-
-
Kellam, P.1
Boucher, C.A.2
Tijnagel, J.M.3
Larder, B.A.4
-
32
-
-
84863487617
-
Interactions between evolutionary processes at high mutation rates
-
Keller, T. E., Wilke, C. O., and Bull, J. J. (2012). Interactions between evolutionary processes at high mutation rates. Evolution 66, 2303-2314.
-
(2012)
Evolution
, vol.66
, pp. 2303-2314
-
-
Keller, T.E.1
Wilke, C.O.2
Bull, J.J.3
-
33
-
-
7344251198
-
The Neutral Theory of Molecular Evolution
-
Cambridge University Press
-
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
-
(1983)
Cambridge
-
-
Kimura, M.1
-
35
-
-
77952734936
-
High-throughput DNA sequencing-concepts and limitations
-
Kircher, M., and Kelso, J. (2010). High-throughput DNA sequencing-concepts and limitations. Bioessays 32, 524-536.
-
(2010)
Bioessays
, vol.32
, pp. 524-536
-
-
Kircher, M.1
Kelso, J.2
-
36
-
-
58549109637
-
Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
-
Knight, C. G., Platt, M., Rowe, W., Wedge, D. C., Khan, F., Day, P. J. R., et al. (2009). Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape. Nucleic Acids Res. 37, e6.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Knight, C.G.1
Platt, M.2
Rowe, W.3
Wedge, D.C.4
Khan, F.5
Day, P.J.R.6
-
37
-
-
70349577630
-
Revealing evolutionary pathways by fitness landscape reconstruction
-
Kogenaru, M., de Vos, M. G., and Tans, S. J. (2009). Revealing evolutionary pathways by fitness landscape reconstruction. Crit. Rev. Biochem. Mol. Biol. 44, 169-174.
-
(2009)
Crit. Rev. Biochem. Mol. Biol.
, vol.44
, pp. 169-174
-
-
Kogenaru, M.1
De Vos, M.G.2
Tans, S.J.3
-
38
-
-
27644472372
-
Orthologs, par-alogs, and evolutionary genomics
-
Koonin, E. V. (2005). Orthologs, par-alogs, and evolutionary genomics. Annu. Rev. Genet. 39, 309-338.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
39
-
-
77953809541
-
Constraints and plasticity in genome and molecular-phenome evolution
-
Koonin, E. V., and Wolf, Y I. (2010). Constraints and plasticity in genome and molecular-phenome evolution. Nat. Rev. Genet. 11, 487-498.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 487-498
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
40
-
-
73249126286
-
The dynamics of adaptation on correlated fitness landscapes
-
Kryazhimskiy, S., Tkacik, G., and Plotkin, J. B. (2009). The dynamics of adaptation on correlated fitness landscapes. Proc. Natl. Acad. Sci. U.S.A. 106,18638-18643.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 18638-18643
-
-
Kryazhimskiy, S.1
Tkacik, G.2
Plotkin, J.B.3
-
41
-
-
79955590028
-
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
-
doi:10.1371/journal.pgen.1002056
-
Kvitek, D. J., and Sherlock, G. (2011). Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet. 7, e1002056. doi:10.1371/journal.pgen.1002056
-
(2011)
PLoS Genet
, vol.7
-
-
Kvitek, D.J.1
Sherlock, G.2
-
42
-
-
79960137718
-
Genetic variation and the fate of beneficial mutations in asexual populations
-
Lang, G. I., Botstein, D., and Desai, M. M. (2011). Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 188, 647-661.
-
(2011)
Genetics
, vol.188
, pp. 647-661
-
-
Lang, G.I.1
Botstein, D.2
Desai, M.M.3
-
43
-
-
77649250720
-
Universal distribution of protein evolution rates as a consequence of protein folding physics
-
Lobkovsky, A. E., Wolf, Y.I., and Koonin, E. V. (2010). Universal distribution of protein evolution rates as a consequence of protein folding physics. Proc. Natl. Acad. Sci. U.S.A. 107, 2983-2988.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 2983-2988
-
-
Lobkovsky, A.E.1
Wolf, Y.I.2
Koonin, E.V.3
-
44
-
-
84855296907
-
Predictability of evolutionary trajectories in fitness landscapes
-
doi:10.1371/journal.pcbi.1002302
-
Lobkovsky, A. E., Wolf, Y I., and Koonin, E. V (2011). Predictability of evolutionary trajectories in fitness landscapes. PLoS Comput. Biol. 7, e1002302. doi:10.1371/journal.pcbi.1002302
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Lobkovsky, A.E.1
Wolf, Y.I.2
Koonin, E.V.3
-
45
-
-
64049093033
-
A framework for evolutionary systems biology
-
doi:10.1186/1752-0509-3-27
-
Loewe, L. (2009). A framework for evolutionary systems biology. BMCSyst. Biol. 3, 27. doi:10.1186/1752-0509-3-27
-
(2009)
BMCSyst. Biol.
, vol.3
, Issue.27
-
-
Loewe, L.1
-
46
-
-
67749098058
-
Stepwise acquisition of pyrimethamine resistance in the malaria parasite
-
Lozovsky, E. R., Chookajorn, T., Brown, K. M., Imwong, M., Shaw, P. J., Kamchonwongpaisan, S., et al. (2009). Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc. Natl. Acad. Sci. U.S.A. 106, 12025-12030.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 12025-12030
-
-
Lozovsky, E.R.1
Chookajorn, T.2
Brown, K.M.3
Imwong, M.4
Shaw, P.J.5
Kamchonwongpaisan, S.6
-
47
-
-
78449233935
-
Pervasive cryptic epistasis in molecular evolution
-
doi:10.1371/journal.pgen.1001162
-
Lunzer, M., Golding, G. B., and Dean, A. M. (2010). Pervasive cryptic epistasis in molecular evolution. PLoS Genet. 6, e1001162. doi:10.1371/journal.pgen.1001162
-
(2010)
PLoS Genet
, vol.6
-
-
Lunzer, M.1
Golding, G.B.2
Dean, A.M.3
-
48
-
-
27144538817
-
The biochemical architecture of an ancient adaptive landscape
-
Lunzer, M., Miller, S. P., Felsheim, R., and Dean, A. M. (2005). The biochemical architecture of an ancient adaptive landscape. Science 310, 499-501.
-
(2005)
Science
, vol.310
, pp. 499-501
-
-
Lunzer, M.1
Miller, S.P.2
Felsheim, R.3
Dean, A.M.4
-
49
-
-
34047099379
-
Distributions of epistasis in microbes fit predictions from a fitness landscape model
-
Martin, G., Elena, S. F., and Lenormand, T. (2007). Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nat. Genet. 39,555-560.
-
(2007)
Nat. Genet.
, vol.39
, pp. 555-560
-
-
Martin, G.1
Elena, S.F.2
Lenormand, T.3
-
50
-
-
0031029659
-
Evolution and dissemination of beta-lactamases accelerated by generations of beta-lactam antibiotics
-
Medeiros, A. A. (1997). Evolution and dissemination of beta-lactamases accelerated by generations of beta-lactam antibiotics. Clin. Infect. Dis. 24(Suppl. 1), 19-45.
-
(1997)
Clin. Infect. Dis.
, vol.24
, Issue.SUPPL. 1
, pp. 19-45
-
-
Medeiros, A.A.1
-
51
-
-
0031033277
-
Episodic adaptive evolution of primate lysozymes
-
Messier, W., and Stewart, C. B. (1997). Episodic adaptive evolution of primate lysozymes. Nature 385, 151-154.
-
(1997)
Nature
, vol.385
, pp. 151-154
-
-
Messier, W.1
Stewart, C.B.2
-
52
-
-
72849144434
-
Sequencing technologies-the next generation
-
Metzker, M. L. (2010). Sequencing technologies-the next generation. Nat. Rev. Genet. 11,31-46.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
53
-
-
84863393863
-
Repeatability and contingency in the evolution of a key innovation in phage lambda
-
Meyer, J. R., Dobias, D. T., Weitz, J. S., Barrick, J. E., Quick, R. T., and Lenski, R. E. (2012). Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335, 428-432.
-
(2012)
Science
, vol.335
, pp. 428-432
-
-
Meyer, J.R.1
Dobias, D.T.2
Weitz, J.S.3
Barrick, J.E.4
Quick, R.T.5
Lenski, R.E.6
-
54
-
-
78951475034
-
Mutational effects and population dynamics during viral adaptation challenge current models
-
Miller, C. R., Joyce, P., and Wichman, H.A. (2011). Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 187, 185-202.
-
(2011)
Genetics
, vol.187
, pp. 185-202
-
-
Miller, C.R.1
Joyce, P.2
Wichman, H.A.3
-
55
-
-
33750287639
-
Direct demonstration of an adaptive constraint
-
Miller, S. P., Lunzer, M., and Dean, A. M. (2006). Direct demonstration of an adaptive constraint. Science 314, 458-461.
-
(2006)
Science
, vol.314
, pp. 458-461
-
-
Miller, S.P.1
Lunzer, M.2
Dean, A.M.3
-
56
-
-
77749254888
-
Fitness flux and ubiquity of adaptive evolution
-
Mustonen, V., and Lassig, M. (2010). Fitness flux and ubiquity of adaptive evolution. Proc. Natl. Acad. Sci. U.S.A. 107,4248-4253.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 4248-4253
-
-
Mustonen, V.1
Lassig, M.2
-
57
-
-
0031720920
-
Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp
-
Nakatsu, C. H., Korona, R., Lenski, R. E., de Bruijn, F. J., Marsh, T. L., and Forney, L. J. (1998). Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp. J. Bacteriol. 180,4325-4331.
-
(1998)
J. Bacteriol.
, vol.180
, pp. 4325-4331
-
-
Nakatsu, C.H.1
Korona, R.2
Lenski, R.E.3
De Bruijn, F.J.4
Marsh, T.L.5
Forney, L.J.6
-
58
-
-
77957959525
-
The neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum
-
Nei, M., Suzuki, Y., and Nozawa, M. (2010). The neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum. Genet. 11,265-289.
-
(2010)
Genet
, vol.11
, pp. 265-289
-
-
Nei, M.1
Suzuki, Y.2
Nozawa, M.3
-
59
-
-
77649246045
-
Evolutionary trajectories of beta-lactamase ctx-m-1 cluster enzymes: predicting antibioticresistance
-
doi:10.1371/journal.ppat.1000735
-
Novais, A., Comas, I., Baquero, F., Cantón, R., Coque, T. M., Moya, A., et al. (2010). Evolutionary trajectories of beta-lactamase ctx-m-1 cluster enzymes: predicting antibioticresistance. PLoSPathog. 6,e1000735. doi:10.1371/journal.ppat.1000735
-
(2010)
PLoSPathog
, vol.6
-
-
Novais, A.1
Comas, I.2
Baquero, F.3
Cantón, R.4
Coque, T.M.5
Moya, A.6
-
60
-
-
51949110360
-
Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases
-
O'Maille, P. E., Malone, A., Dellas, N., Andes Hess, B. Jr., Smentek, L., Sheehan, I., et al. (2008). Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat. Chem. Biol. 4, 617-623.
-
(2008)
Nat. Chem. Biol.
, vol.4
, pp. 617-623
-
-
O'Maille, P.E.1
Malone, A.2
Dellas, N.3
Andes Hess Jr, B.4
Smentek, L.5
Sheehan, I.6
-
61
-
-
77951557120
-
Non-homologous isofunc-tional enzymes: a systematic analysis of alternative solutions in enzyme evolution
-
Omelchenko, M. V., Galperin, M. Y., Wolf, Y. I., and Koonin, E. V. (2010). Non-homologous isofunc-tional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol. Direct 5, 31.
-
(2010)
Biol. Direct
, vol.5
, pp. 31
-
-
Omelchenko, M.V.1
Galperin, M.Y.2
Wolf, Y.I.3
Koonin, E.V.4
-
62
-
-
37349107011
-
The genetic basis of parallel and divergent phe-notypic responses in evolving populations of Escherichia coli
-
Ostrowski, E. A., Woods, R. J., and Lenski, R. E. (2008). The genetic basis of parallel and divergent phe-notypic responses in evolving populations of Escherichia coli. Proc. Biol. Sci. 275, 277-284.
-
(2008)
Proc. Biol. Sci.
, vol.275
, pp. 277-284
-
-
Ostrowski, E.A.1
Woods, R.J.2
Lenski, R.E.3
-
63
-
-
80052031934
-
Systems-biology approaches for predicting genomic evolution
-
Papp, B., Notebaart, R. A., and Pal, C. (2011). Systems-biology approaches for predicting genomic evolution. Nat. Rev. Genet. 12,591-602.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 591-602
-
-
Papp, B.1
Notebaart, R.A.2
Pal, C.3
-
64
-
-
33747849237
-
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli
-
Pelosi, L., Kuhn, L., Guetta, D., Garin, J., Geiselmann, J., Lenski, R. E., et al. (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
-
65
-
-
33846551980
-
Empirical fitness landscapes reveal accessible evolutionary paths
-
Poelwijk, F. J., Kiviet, D. J., Weinreich, D. M., and Tans, S. J. (2007). Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445, 383-386.
-
(2007)
Nature
, vol.445
, pp. 383-386
-
-
Poelwijk, F.J.1
Kiviet, D.J.2
Weinreich, D.M.3
Tans, S.J.4
-
66
-
-
78650592680
-
Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes
-
Poelwijk, F. J., Tanase-Nicola, S., Kiviet, D. J., and Tans, S. J. (2011). Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes. J. Theor. Biol. 272,141-144.
-
(2011)
J. Theor. Biol.
, vol.272
, pp. 141-144
-
-
Poelwijk, F.J.1
Tanase-Nicola, S.2
Kiviet, D.J.3
Tans, S.J.4
-
67
-
-
54349117265
-
Constructing and analyzing the fitness landscape of an experimental evolutionary process
-
Reetz,M. T.,andSanchis, J. (2008). Constructing and analyzing the fitness landscape of an experimental evolutionary process. Chembiochem 9, 2260-2267.
-
(2008)
Chembiochem
, vol.9
, pp. 2260-2267
-
-
Reetz, M.T.1
andSanchis, J.2
-
68
-
-
70449533747
-
The genetics of adaptation for eight microvirid bacterio-phages
-
Rokyta, D. R., Abdo, Z., and Wichman, H. A. (2009). The genetics of adaptation for eight microvirid bacterio-phages. J. Mol. Evol. 69, 229-239.
-
(2009)
J. Mol. Evol.
, vol.69
, pp. 229-239
-
-
Rokyta, D.R.1
Abdo, Z.2
Wichman, H.A.3
-
69
-
-
70450242805
-
Exploring protein fitness landscapes by directed evolution
-
Romero, P. A., and Arnold, F. H. (2009). Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol. 10, 866-876.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 866-876
-
-
Romero, P.A.1
Arnold, F.H.2
-
70
-
-
77955885732
-
Predictive models for population performance on real biological fitness landscapes
-
Rowe, W., Wedge, D. C., Platt, M., Kell, D. B., and Knowles, J. (2010).Predictive models for population performance on real biological fitness landscapes. Bioinformatics 26, 2145-2152.
-
(2010)
Bioinformatics
, vol.26
, pp. 2145-2152
-
-
Rowe, W.1
Wedge, D.C.2
Platt, M.3
Kell, D.B.4
Knowles, J.5
-
71
-
-
79953738501
-
Initial mutations direct alternative pathways of protein evolution
-
doi:10.1371/journal.pgen.1001321
-
Salverda, M. L., Dellus, E., Gorter, F. A., Debets, A. J., van der Oost, J., Hoekstra, R. F., et al. (2011). Initial mutations direct alternative pathways of protein evolution. PLoS Genet. 7, e1001321. doi:10.1371/journal.pgen.1001321
-
(2011)
PLoS Genet
, vol.7
-
-
Salverda, M.L.1
Dellus, E.2
Gorter, F.A.3
Debets, A.J.4
van der Oost, J.5
Hoekstra, R.F.6
-
72
-
-
0033045013
-
Overdominant alleles in a population of variable size
-
Slatkin, M., and Muirhead, C. A. (1999). Overdominant alleles in a population of variable size. Genetics 152, 775-781.
-
(1999)
Genetics
, vol.152
, pp. 775-781
-
-
Slatkin, M.1
Muirhead, C.A.2
-
73
-
-
0023666025
-
Adaptive evolution in the stomach lysozymes of foregut fermenters
-
Stewart, C. B., Schilling, J. W., and Wilson,A. C. (1987). Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330, 401-404.
-
(1987)
Nature
, vol.330
, pp. 401-404
-
-
Stewart, C.B.1
Schilling, J.W.2
Wilson, A.C.3
-
74
-
-
0026325886
-
Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection
-
Swanson, K. W., Irwin, D. M., and Wilson, A. C. (1991). Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection. J.Mol. Evol. 33,418-425.
-
(1991)
J. Mol. Evol.
, vol.33
, pp. 418-425
-
-
Swanson, K.W.1
Irwin, D.M.2
Wilson, A.C.3
-
75
-
-
84856258903
-
The molecular diversity of adaptive convergence
-
Tenaillon, O., Rodriguez-Verdugo, A., Gaut, R. L., McDonald, P., Bennett, A. F., Long, A. D., et al. (2012). The molecular diversity of adaptive convergence. Science 335, 457-461.
-
(2012)
Science
, vol.335
, pp. 457-461
-
-
Tenaillon, O.1
Rodriguez-Verdugo, A.2
Gaut, R.L.3
McDonald, P.4
Bennett, A.F.5
Long, A.D.6
-
76
-
-
84555171441
-
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
-
Toprak, E., Veres, A., Michel, J. B., Chait, R., Hartl, D. L., and Kishony, R. (2012). Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 44, 101-105.
-
(2012)
Nat. Genet.
, vol.44
, pp. 101-105
-
-
Toprak, E.1
Veres, A.2
Michel, J.B.3
Chait, R.4
Hartl, D.L.5
Kishony, R.6
-
77
-
-
65249177164
-
Directed enzyme evolution: climbing fitness peaks one amino acid at a time
-
Tracewell, C. A., and Arnold, F. H. (2009). Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr. Opin. Chem. Biol. 13, 3-9.
-
(2009)
Curr. Opin. Chem. Biol.
, vol.13
, pp. 3-9
-
-
Tracewell, C.A.1
Arnold, F.H.2
-
78
-
-
32244448130
-
Defining the sequence-recognition profile of DNA-binding molecules
-
Warren, C. L., Kratochvil, N. C., Hauschild, K. E., Foister, S., Brezin-ski, M. L., Dervan, P. B. Jr., et al. (2006). Defining the sequence-recognition profile of DNA-binding molecules. Proc. Natl. Acad. Sci. U.S.A. 103, 867-872.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 867-872
-
-
Warren, C.L.1
Kratochvil, N.C.2
Hauschild, K.E.3
Foister, S.4
Brezin-ski, M.L.5
Dervan Jr, P.B.6
-
79
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich, D. M., Delaney, N. F., Depristo, M. A., and Hartl, D. L. (2006). Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
80
-
-
21044435697
-
Perspective: sign epistasis and genetic constraint on evolutionary trajectories
-
Weinreich, D. M., Watson, R. A., and Chao, L. (2005). Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59,1165-1174.
-
(2005)
Evolution
, vol.59
, pp. 1165-1174
-
-
Weinreich, D.M.1
Watson, R.A.2
Chao, L.3
-
81
-
-
0033575348
-
Different trajectories of parallel evolution during viral adaptation
-
Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M., and Bull, J. J. (1999). Different trajectories of parallel evolution during viral adaptation. Science 285,422-424.
-
(1999)
Science
, vol.285
, pp. 422-424
-
-
Wichman, H.A.1
Badgett, M.R.2
Scott, L.A.3
Boulianne, C.M.4
Bull, J.J.5
-
82
-
-
20444382446
-
Adaptive molecular evolution for 13,000 phage generations: a possible arms race
-
Wichman, H. A., Millstein, J., and Bull, J. J. (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
-
83
-
-
33745166593
-
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli
-
Woods, R., Schneider, D., Winkworth, C. L., Riley, M. A., and Lenski, R. E. (2006). Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103,9107-9112.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 9107-9112
-
-
Woods, R.1
Schneider, D.2
Winkworth, C.L.3
Riley, M.A.4
Lenski, R.E.5
-
84
-
-
0000907353
-
The roles of mutation, inbreeding, crossbreeding and selection in evolution
-
ed. D. F. Jones, (Brooklyn: Brooklyn Botanic Garden)
-
Wright, S. (1932). The roles of mutation, inbreeding, crossbreeding and selection in evolution, in Proceedings of the Sixth International Congress of Genetics, Vol. 1, ed. D. F. Jones, (Brooklyn: Brooklyn Botanic Garden), 356-366.
-
(1932)
Proceedings of the Sixth International Congress of Genetics
, vol.1
, pp. 356-366
-
-
Wright, S.1
-
85
-
-
0001416961
-
Surfaces of selective value revisited
-
Wright, S. (1988). Surfaces of selective value revisited. Am. Nat. 131, 115-123.
-
(1988)
Am. Nat.
, vol.131
, pp. 115-123
-
-
Wright, S.1
|