-
1
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770):111-114.
-
(2006)
Science
, vol.312
, Issue.5770
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
2
-
-
34548040966
-
Crystal structure of an ancient protein: Evolution by conformational epistasis
-
Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007) Crystal structure of an ancient protein: Evolution by conformational epistasis. Science 317(5844):1544-1548.
-
(2007)
Science
, vol.317
, Issue.5844
, pp. 1544-1548
-
-
Ortlund, E.A.1
Bridgham, J.T.2
Redinbo, M.R.3
Thornton, J.W.4
-
3
-
-
45849093668
-
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
-
Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 105(23):7899-7906.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.23
, pp. 7899-7906
-
-
Blount, Z.D.1
Borland, C.Z.2
Lenski, R.E.3
-
4
-
-
70349464621
-
An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
-
Bridgham JT, Ortlund EA, Thornton JW (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461(7263):515-519.
-
(2009)
Nature
, vol.461
, Issue.7263
, pp. 515-519
-
-
Bridgham, J.T.1
Ortlund, E.A.2
Thornton, J.W.3
-
5
-
-
77953262416
-
Permissive secondary mutations enable the evolution of influenza oseltamivir resistance
-
Bloom JD, Gong LI, Baltimore D (2010) Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328(5983):1272-1275.
-
(2010)
Science
, vol.328
, Issue.5983
, pp. 1272-1275
-
-
Bloom, J.D.1
Gong, L.I.2
Baltimore, D.3
-
6
-
-
84868365613
-
The spatial architecture of protein function and adaptation
-
McLaughlin RN, Jr, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R (2012) The spatial architecture of protein function and adaptation. Nature 491(7422):138-142.
-
(2012)
Nature
, vol.491
, Issue.7422
, pp. 138-142
-
-
McLaughlin, R.N.1
Poelwijk, F.J.2
Raman, A.3
Gosal, W.S.4
Ranganathan, R.5
-
7
-
-
84878935899
-
Epistasis among adaptive mutations in deer mouse hemoglobin
-
Natarajan C, et al. (2013) Epistasis among adaptive mutations in deer mouse hemoglobin. Science 340(6138):1324-1327.
-
(2013)
Science
, vol.340
, Issue.6138
, pp. 1324-1327
-
-
Natarajan, C.1
-
8
-
-
84879064073
-
Stability-mediated epistasis constrains the evolution of an influenza protein
-
Gong LI, Suchard MA, Bloom JD (2013) Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2:e00631.
-
(2013)
eLife
, vol.2
-
-
Gong, L.I.1
Suchard, M.A.2
Bloom, J.D.3
-
9
-
-
84906217983
-
Historical contingency and its biophysical basis in glucocorticoid receptor evolution
-
Harms MJ, Thornton JW (2014) Historical contingency and its biophysical basis in glucocorticoid receptor evolution. Nature 512(7513):203-207.
-
(2014)
Nature
, vol.512
, Issue.7513
, pp. 203-207
-
-
Harms, M.J.1
Thornton, J.W.2
-
11
-
-
0025526526
-
Mutational order: A major stochastic process in evolution
-
Mani GS, Clarke BC (1990) Mutational order: A major stochastic process in evolution. Proc R Soc Lond B Biol Sci 240(1297):29-37.
-
(1990)
Proc R Soc Lond B Biol Sci
, vol.240
, Issue.1297
, pp. 29-37
-
-
Mani, G.S.1
Clarke, B.C.2
-
12
-
-
0028977087
-
Experimental tests of the roles of adaptation, chance, and history in evolution
-
Travisano M, Mongold JA, Bennett AF, Lenski RE (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267(5194):87-90.
-
(1995)
Science
, vol.267
, Issue.5194
, pp. 87-90
-
-
Travisano, M.1
Mongold, J.A.2
Bennett, A.F.3
Lenski, R.E.4
-
13
-
-
46149093073
-
Replaying life's tape
-
Beatty J (2006) Replaying life's tape. J Philos 103(7):336-362.
-
(2006)
J Philos
, vol.103
, Issue.7
, pp. 336-362
-
-
Beatty, J.1
-
14
-
-
84979134212
-
Reversibility in evolution considered from the standpoint of genetics
-
Muller HJ (1939) Reversibility in evolution considered from the standpoint of genetics. Biol Rev Camb Philos Soc 14:261-280.
-
(1939)
Biol Rev Camb Philos Soc
, vol.14
, pp. 261-280
-
-
Muller, H.J.1
-
15
-
-
0017728436
-
A systems-analytical approach to macro-evolutionary phenomena
-
Riedl R (1977) A systems-analytical approach to macro-evolutionary phenomena. Q Rev Biol 52(4):351-370.
-
(1977)
Q Rev Biol
, vol.52
, Issue.4
, pp. 351-370
-
-
Riedl, R.1
-
17
-
-
79956314177
-
Path dependence and historical contingency in biology
-
Palgrave Macmillan, New York
-
Szathmáry E (2006) Path dependence and historical contingency in biology. Understanding Change: Models, Methodologies, and Metaphors (Palgrave Macmillan, New York), pp 140-157.
-
(2006)
Understanding Change: Models, Methodologies, and Metaphors
, pp. 140-157
-
-
Szathmáry, E.1
-
18
-
-
84861422981
-
Amino acid coevolution induces an evolutionary Stokes shift
-
Pollock DD, Thiltgen G, Goldstein RA (2012) Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci USA 109(21):E1352-E1359.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.21
, pp. E1352-E1359
-
-
Pollock, D.D.1
Thiltgen, G.2
Goldstein, R.A.3
-
19
-
-
0014935646
-
Natural selection and the concept of a protein space
-
Smith JM (1970) Natural selection and the concept of a protein space. Nature 225(5232):563-564.
-
(1970)
Nature
, vol.225
, Issue.5232
, pp. 563-564
-
-
Smith, J.M.1
-
22
-
-
0036797562
-
Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans
-
Cordell HJ (2002) Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11(20):2463-2468.
-
(2002)
Hum Mol Genet
, vol.11
, Issue.20
, pp. 2463-2468
-
-
Cordell, H.J.1
-
23
-
-
54149088214
-
Epistasis - The essential role of gene interactions in the structure and evolution of genetic systems
-
Phillips PC (2008) Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9(11):855-867.
-
(2008)
Nat Rev Genet
, vol.9
, Issue.11
, pp. 855-867
-
-
Phillips, P.C.1
-
24
-
-
84902775598
-
Empirical fitness landscapes and the predictability of evolution
-
de Visser JAGM, Krug J (2014) Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 15(7):480-490.
-
(2014)
Nat Rev Genet
, vol.15
, Issue.7
, pp. 480-490
-
-
De Visser, J.A.G.M.1
Krug, J.2
-
26
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6(9):678-687.
-
(2005)
Nat Rev Genet
, vol.6
, Issue.9
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
27
-
-
78449233935
-
Pervasive cryptic epistasis in molecular evolution
-
Lunzer M, Golding GB, Dean AM (2010) Pervasive cryptic epistasis in molecular evolution. PLoS Genet 6(10):e1001162.
-
(2010)
PLoS Genet
, vol.6
, Issue.10
-
-
Lunzer, M.1
Golding, G.B.2
Dean, A.M.3
-
28
-
-
77957346489
-
Genome-wide analysis of a long-term evolution experiment with Drosophila
-
Burke MK, et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467(7315):587-590.
-
(2010)
Nature
, vol.467
, Issue.7315
, pp. 587-590
-
-
Burke, M.K.1
-
29
-
-
79952270576
-
Prevalence of epistasis in the evolution of influenza A surface proteins
-
Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB (2011) Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet 7(2):e1001301.
-
(2011)
PLoS Genet
, vol.7
, Issue.2
-
-
Kryazhimskiy, S.1
Dushoff, J.2
Bazykin, G.A.3
Plotkin, J.B.4
-
30
-
-
79957948242
-
Negative epistasis between beneficial mutations in an evolving bacterial population
-
Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF (2011) Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332(6034):1193-1196.
-
(2011)
Science
, vol.332
, Issue.6034
, pp. 1193-1196
-
-
Khan, A.I.1
Dinh, D.M.2
Schneider, D.3
Lenski, R.E.4
Cooper, T.F.5
-
31
-
-
79957958115
-
Diminishing returns epistasis among beneficial mutations decelerates adaptation
-
Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332(6034):1190-1192.
-
(2011)
Science
, vol.332
, Issue.6034
, pp. 1190-1192
-
-
Chou, H.H.1
Chiu, H.C.2
Delaney, N.F.3
Segrè, D.4
Marx, C.J.5
-
32
-
-
84867781208
-
Epistasis as the primary factor in molecular evolution
-
Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA (2012) Epistasis as the primary factor in molecular evolution. Nature 490(7421):535-538.
-
(2012)
Nature
, vol.490
, Issue.7421
, pp. 535-538
-
-
Breen, M.S.1
Kemena, C.2
Vlasov, P.K.3
Notredame, C.4
Kondrashov, F.A.5
-
33
-
-
84866944595
-
Genomic analysis of a key innovation in an experimental Escherichia coli population
-
Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489(7417):513-518.
-
(2012)
Nature
, vol.489
, Issue.7417
, pp. 513-518
-
-
Blount, Z.D.1
Barrick, J.E.2
Davidson, C.J.3
Lenski, R.E.4
-
34
-
-
84890116570
-
Long-term dynamics of adaptation in asexual populations
-
Wiser MJ, Ribeck N, Lenski RE (2013) Long-term dynamics of adaptation in asexual populations. Science 342(6164):1364-1367.
-
(2013)
Science
, vol.342
, Issue.6164
, pp. 1364-1367
-
-
Wiser, M.J.1
Ribeck, N.2
Lenski, R.E.3
-
35
-
-
0032571568
-
Contingency and determinism in replicated adaptive radiations of island lizards
-
Losos JB, Jackman TR, Larson A, Queiroz K, Rodriguez-Schettino L (1998) Contingency and determinism in replicated adaptive radiations of island lizards. Science 279(5359):2115-2118.
-
(1998)
Science
, vol.279
, Issue.5359
, pp. 2115-2118
-
-
Losos, J.B.1
Jackman, T.R.2
Larson, A.3
Queiroz, K.4
Rodriguez-Schettino, L.5
-
36
-
-
79953738501
-
Initial mutations direct alternative pathways of protein evolution
-
Salverda MLM, et al. (2011) Initial mutations direct alternative pathways of protein evolution. PLoS Genet 7(3):e1001321.
-
(2011)
PLoS Genet
, vol.7
, Issue.3
-
-
Salverda, M.L.M.1
-
37
-
-
84863393863
-
Repeatability and contingency in the evolution of a key innovation in phage lambda
-
Meyer JR, et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335(6067):428-432.
-
(2012)
Science
, vol.335
, Issue.6067
, pp. 428-432
-
-
Meyer, J.R.1
-
38
-
-
84878427504
-
Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution
-
Dickinson BC, Leconte AM, Allen B, Esvelt KM, Liu DR (2013) Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc Natl Acad Sci USA 110(22):9007-9012.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.22
, pp. 9007-9012
-
-
Dickinson, B.C.1
Leconte, A.M.2
Allen, B.3
Esvelt, K.M.4
Liu, D.R.5
-
39
-
-
84866697042
-
Fitness conferred by replaced amino acids declines with time
-
Naumenko SA, Kondrashov AS, Bazykin GA (2012) Fitness conferred by replaced amino acids declines with time. Biol Lett 8(5):825-828.
-
(2012)
Biol Lett
, vol.8
, Issue.5
, pp. 825-828
-
-
Naumenko, S.A.1
Kondrashov, A.S.2
Bazykin, G.A.3
-
40
-
-
84874768052
-
Estimating the rate of irreversibility in protein evolution
-
Soylemez O, Kondrashov FA (2012) Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 4(12):1213-1222.
-
(2012)
Genome Biol Evol
, vol.4
, Issue.12
, pp. 1213-1222
-
-
Soylemez, O.1
Kondrashov, F.A.2
-
41
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444(7121):929-932.
-
(2006)
Nature
, vol.444
, Issue.7121
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
42
-
-
36148966864
-
Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context
-
Wang ZO, Pollock DD (2007) Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J Mol Evol 65(5):485-495.
-
(2007)
J Mol Evol
, vol.65
, Issue.5
, pp. 485-495
-
-
Wang, Z.O.1
Pollock, D.D.2
-
43
-
-
77953718211
-
Sequence space and the ongoing expansion of the protein universe
-
Povolotskaya IS, Kondrashov FA (2010) Sequence space and the ongoing expansion of the protein universe. Nature 465(7300):922-926.
-
(2010)
Nature
, vol.465
, Issue.7300
, pp. 922-926
-
-
Povolotskaya, I.S.1
Kondrashov, F.A.2
-
44
-
-
84903742512
-
Why human disease-associated residues appear as the wild-type in other species: Genome-scale structural evidence for the compensation hypothesis
-
Xu J, Zhang J (2014) Why human disease-associated residues appear as the wild-type in other species: Genome-scale structural evidence for the compensation hypothesis. Mol Biol Evol 31(7):1787-1792.
-
(2014)
Mol Biol Evol
, vol.31
, Issue.7
, pp. 1787-1792
-
-
Xu, J.1
Zhang, J.2
-
45
-
-
0033582946
-
Coevolving protein residues: Maximum likelihood identification and relationship to structure
-
Pollock DD, Taylor WR, Goldman N (1999) Coevolving protein residues: Maximum likelihood identification and relationship to structure. J Mol Biol 287(1):187-198.
-
(1999)
J Mol Biol
, vol.287
, Issue.1
, pp. 187-198
-
-
Pollock, D.D.1
Taylor, W.R.2
Goldman, N.3
-
46
-
-
1542642309
-
Protein evolution with dependence among codons due to tertiary structure
-
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL (2003) Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 20(10):1692-1704.
-
(2003)
Mol Biol Evol
, vol.20
, Issue.10
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
47
-
-
33748126145
-
Assessing site-interdependent phylogenetic models of sequence evolution
-
Rodrigue N, Philippe H, Lartillot N (2006) Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol 23(9):1762-1775.
-
(2006)
Mol Biol Evol
, vol.23
, Issue.9
, pp. 1762-1775
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
48
-
-
34547809931
-
Quantifying the impact of protein tertiary structure on molecular evolution
-
Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL (2007) Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol 24(8):1769-1782.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1769-1782
-
-
Choi, S.C.1
Hobolth, A.2
Robinson, D.M.3
Kishino, H.4
Thorne, J.L.5
-
49
-
-
84890067204
-
Protein evolution along phylogenetic histories under structurally constrained substitution models
-
Arenas M, Dos Santos HG, Posada D, Bastolla U (2013) Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics 29(23):3020-3028.
-
(2013)
Bioinformatics
, vol.29
, Issue.23
, pp. 3020-3028
-
-
Arenas, M.1
Dos Santos, H.G.2
Posada, D.3
Bastolla, U.4
-
50
-
-
84988220710
-
A model of substitution trajectories in sequence space and long-term protein evolution
-
Usmanova DR, Ferretti L, Povolotskaya IS, Vlasov PK, Kondrashov FA (2015) A model of substitution trajectories in sequence space and long-term protein evolution. Mol Biol Evol 32(2):542-554.
-
(2015)
Mol Biol Evol
, vol.32
, Issue.2
, pp. 542-554
-
-
Usmanova, D.R.1
Ferretti, L.2
Povolotskaya, I.S.3
Vlasov, P.K.4
Kondrashov, F.A.5
-
51
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11(5):725-736.
-
(1994)
Mol Biol Evol
, vol.11
, Issue.5
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
52
-
-
34547675965
-
An empirical codon model for protein sequence evolution
-
Kosiol C, Holmes I, Goldman N (2007) An empirical codon model for protein sequence evolution. Mol Biol Evol 24(7):1464-1479.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.7
, pp. 1464-1479
-
-
Kosiol, C.1
Holmes, I.2
Goldman, N.3
-
53
-
-
39749161509
-
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
-
Yang Z, Nielsen R (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25(3):568-579.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.3
, pp. 568-579
-
-
Yang, Z.1
Nielsen, R.2
-
54
-
-
77949536563
-
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
-
Rodrigue N, Philippe H, Lartillot N (2010) Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci USA 107(10):4629-4634.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.10
, pp. 4629-4634
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
55
-
-
84858184390
-
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models
-
Tamuri AU, dos Reis M, Goldstein RA (2012) Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 190(3):1101-1115.
-
(2012)
Genetics
, vol.190
, Issue.3
, pp. 1101-1115
-
-
Tamuri, A.U.1
Dos Reis, M.2
Goldstein, R.A.3
-
56
-
-
84905001681
-
An experimentally determined evolutionary model dramatically improves phylogenetic fit
-
Bloom JD (2014) An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol 31(8):1956-1978.
-
(2014)
Mol Biol Evol
, vol.31
, Issue.8
, pp. 1956-1978
-
-
Bloom, J.D.1
-
57
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320(2):369-387.
-
(2002)
J Mol Biol
, vol.320
, Issue.2
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
58
-
-
0025082684
-
Additivity of mutational effects in proteins
-
Wells JA (1990) Additivity of mutational effects in proteins. Biochemistry 29(37):8509-8517.
-
(1990)
Biochemistry
, vol.29
, Issue.37
, pp. 8509-8517
-
-
Wells, J.A.1
-
59
-
-
0027441807
-
Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability
-
Serrano L, Day AG, Fersht AR (1993) Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 233(2):305-312.
-
(1993)
J Mol Biol
, vol.233
, Issue.2
, pp. 305-312
-
-
Serrano, L.1
Day, A.G.2
Fersht, A.R.3
-
60
-
-
79959992592
-
A biophysical protein folding model accounts for most mutational fitness effects in viruses
-
Wylie CS, Shakhnovich EI (2011) A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci USA 108(24):9916-9921.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.24
, pp. 9916-9921
-
-
Wylie, C.S.1
Shakhnovich, E.I.2
-
61
-
-
84891364264
-
Mutational effects on stability are largely conserved during protein evolution
-
Ashenberg O, Gong LI, Bloom JD (2013) Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci USA 110(52):21071-21076.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.52
, pp. 21071-21076
-
-
Ashenberg, O.1
Gong, L.I.2
Bloom, J.D.3
-
62
-
-
0014296201
-
Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles
-
Kimura M (1968) Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genet Res 11(3):247-269.
-
(1968)
Genet Res
, vol.11
, Issue.3
, pp. 247-269
-
-
Kimura, M.1
-
63
-
-
84905454017
-
Modeling evolution using the probability of fixation: History and implications
-
McCandlish DM, Stoltzfus A (2014) Modeling evolution using the probability of fixation: History and implications. Q Rev Biol 89(3):225-252.
-
(2014)
Q Rev Biol
, vol.89
, Issue.3
, pp. 225-252
-
-
McCandlish, D.M.1
Stoltzfus, A.2
-
64
-
-
74549207309
-
Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details
-
Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details. Protein Eng Des Sel 22(9):553-560.
-
(2009)
Protein Eng Des Sel
, vol.22
, Issue.9
, pp. 553-560
-
-
Potapov, V.1
Cohen, M.2
Schreiber, G.3
-
65
-
-
79551470095
-
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
-
Kellogg EH, Leaver-Fay A, Baker D (2011) Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 79(3):830-838.
-
(2011)
Proteins
, vol.79
, Issue.3
, pp. 830-838
-
-
Kellogg, E.H.1
Leaver-Fay, A.2
Baker, D.3
-
66
-
-
0028949615
-
Proteins and temperature
-
Somero GN (1995) Proteins and temperature. Annu Rev Physiol 57:43-68.
-
(1995)
Annu Rev Physiol
, vol.57
, pp. 43-68
-
-
Somero, G.N.1
-
67
-
-
0028896311
-
A relationship between protein stability and protein function
-
Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) A relationship between protein stability and protein function. Proc Natl Acad Sci USA 92(2):452-456.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, Issue.2
, pp. 452-456
-
-
Shoichet, B.K.1
Baase, W.A.2
Kuroki, R.3
Matthews, B.W.4
-
68
-
-
79958774937
-
Protein stability, flexibility and function
-
Teilum K, Olsen JG, Kragelund BB (2011) Protein stability, flexibility and function. Biochim Biophys Acta 1814(8):969-976.
-
(2011)
Biochim Biophys Acta
, vol.1814
, Issue.8
, pp. 969-976
-
-
Teilum, K.1
Olsen, J.G.2
Kragelund, B.B.3
-
69
-
-
84893786232
-
Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases
-
Howell SC, Inampudi KK, Bean DP, Wilson CJ (2014) Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases. Structure 22(2):218-229.
-
(2014)
Structure
, vol.22
, Issue.2
, pp. 218-229
-
-
Howell, S.C.1
Inampudi, K.K.2
Bean, D.P.3
Wilson, C.J.4
-
70
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuán R, Moya A, Elena SF (2004) The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101(22):8396-8401.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.22
, pp. 8396-8401
-
-
Sanjuán, R.1
Moya, A.2
Elena, S.F.3
-
71
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8(8):610-618.
-
(2007)
Nat Rev Genet
, vol.8
, Issue.8
, pp. 610-618
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
72
-
-
84881408157
-
Capturing the mutational landscape of the beta-lactamase TEM-1
-
Jacquier H, et al. (2013) Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci USA 110(32):13067-13072.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.32
, pp. 13067-13072
-
-
Jacquier, H.1
-
73
-
-
84895727363
-
A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments
-
Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD (2014) A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments. Genetics 196(3):841-852.
-
(2014)
Genetics
, vol.196
, Issue.3
, pp. 841-852
-
-
Bank, C.1
Hietpas, R.T.2
Wong, A.3
Bolon, D.N.4
Jensen, J.D.5
-
75
-
-
0035252648
-
How enzymes adapt: Lessons from directed evolution
-
Arnold FH, Wintrode PL, Miyazaki K, Gershenson A (2001) How enzymes adapt: Lessons from directed evolution. Trends Biochem Sci 26(2):100-106.
-
(2001)
Trends Biochem Sci
, vol.26
, Issue.2
, pp. 100-106
-
-
Arnold, F.H.1
Wintrode, P.L.2
Miyazaki, K.3
Gershenson, A.4
-
76
-
-
0036139093
-
Why are proteins marginally stable?
-
Taverna DM, Goldstein RA (2002) Why are proteins marginally stable? Proteins 46(1):105-109.
-
(2002)
Proteins
, vol.46
, Issue.1
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
77
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103(15):5869-5874.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.15
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
78
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369(5):1318-1332.
-
(2007)
J Mol Biol
, vol.369
, Issue.5
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
79
-
-
33846515095
-
Thermodynamics of neutral protein evolution
-
Bloom JD, Raval A, Wilke CO (2007) Thermodynamics of neutral protein evolution. Genetics 175(1):255-266.
-
(2007)
Genetics
, vol.175
, Issue.1
, pp. 255-266
-
-
Bloom, J.D.1
Raval, A.2
Wilke, C.O.3
-
80
-
-
36049027813
-
Protein stability imposes limits on organism complexity and speed of molecular evolution
-
Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104(41):16152-16157.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.41
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
81
-
-
0028808763
-
Context-dependent optimal substitution matrices
-
Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8(7):641-645.
-
(1995)
Protein Eng
, vol.8
, Issue.7
, pp. 641-645
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
82
-
-
0345062357
-
Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
-
Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291(1):177-196.
-
(1999)
J Mol Biol
, vol.291
, Issue.1
, pp. 177-196
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
83
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23(9):1751-1761.
-
(2006)
Mol Biol Evol
, vol.23
, Issue.9
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
84
-
-
84988239865
-
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
-
Risso VA, et al. (2015) Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol Biol Evol 32(2):440-455.
-
(2015)
Mol Biol Evol
, vol.32
, Issue.2
, pp. 440-455
-
-
Risso, V.A.1
-
86
-
-
84886298744
-
Selection biases the prevalence and type of epistasis along adaptive trajectories
-
Draghi JA, Plotkin JB (2013) Selection biases the prevalence and type of epistasis along adaptive trajectories. Evolution 67(11):3120-3131.
-
(2013)
Evolution
, vol.67
, Issue.11
, pp. 3120-3131
-
-
Draghi, J.A.1
Plotkin, J.B.2
-
87
-
-
84901650146
-
The changing geometry of a fitness landscape along an adaptive walk
-
Greene D, Crona K (2014) The changing geometry of a fitness landscape along an adaptive walk. PLOS Comput Biol 10(5):e1003520.
-
(2014)
PLOS Comput Biol
, vol.10
, Issue.5
-
-
Greene, D.1
Crona, K.2
-
88
-
-
70649097086
-
Lethal mutagenesis in viruses and bacteria
-
Chen P, Shakhnovich EI (2009) Lethal mutagenesis in viruses and bacteria. Genetics 183(2):639-650.
-
(2009)
Genetics
, vol.183
, Issue.2
, pp. 639-650
-
-
Chen, P.1
Shakhnovich, E.I.2
-
89
-
-
84898811791
-
Strong evidence for protein epistasis, weak evidence against it
-
Pollock DD, Goldstein RA (2014) Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci USA 111(15):E1450.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.15
-
-
Pollock, D.D.1
Goldstein, R.A.2
-
91
-
-
84878410814
-
The role of epistasis in protein evolution
-
discussion E2-E3
-
McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB (2013) The role of epistasis in protein evolution. Nature 497(7451):E1-E2, discussion E2-E3.
-
(2013)
Nature
, vol.497
, Issue.7451
, pp. E1-E2
-
-
McCandlish, D.M.1
Rajon, E.2
Shah, P.3
Ding, Y.4
Plotkin, J.B.5
-
92
-
-
77953287348
-
Mechanistic revisions of phenomenological modeling strategies in molecular evolution
-
Rodrigue N, Philippe H (2010) Mechanistic revisions of phenomenological modeling strategies in molecular evolution. Trends Genet 26(6):248-252.
-
(2010)
Trends Genet
, vol.26
, Issue.6
, pp. 248-252
-
-
Rodrigue, N.1
Philippe, H.2
-
93
-
-
84938520945
-
Codon models as a vehicle for reconciling population genetics with inter-specific sequence data
-
eds Cannarozzi GM, Schneider A (Oxford Univ Press, Oxford)
-
Thorne JL, Lartillot N, Rodrigue N, Choi SC (2012) Codon models as a vehicle for reconciling population genetics with inter-specific sequence data. Codon Evolution: Mechanisms and Models, eds Cannarozzi GM, Schneider A (Oxford Univ Press, Oxford), pp 97-110.
-
(2012)
Codon Evolution: Mechanisms and Models
, pp. 97-110
-
-
Thorne, J.L.1
Lartillot, N.2
Rodrigue, N.3
Choi, S.C.4
-
94
-
-
84864029746
-
Bringing molecules back into molecular evolution
-
Wilke CO (2012) Bringing molecules back into molecular evolution. PLOS Comput Biol 8(6):e1002572.
-
(2012)
PLOS Comput Biol
, vol.8
, Issue.6
-
-
Wilke, C.O.1
-
95
-
-
84864697376
-
Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
-
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29(8):1917-1932.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.8
, pp. 1917-1932
-
-
Bryant, D.1
Bouckaert, R.2
Felsenstein, J.3
Rosenberg, N.A.4
RoyChoudhury, A.5
-
96
-
-
84888597013
-
Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models
-
De Maio N, Schlötterer C, Kosiol C (2013) Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol Biol Evol 30(10):2249-2262.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.10
, pp. 2249-2262
-
-
De Maio, N.1
Schlötterer, C.2
Kosiol, C.3
-
97
-
-
84883240912
-
A phylogenetic model for the detection of epistatic interactions
-
Nasrallah CA, Huelsenbeck JP (2013) A phylogenetic model for the detection of epistatic interactions. Mol Biol Evol 30(9):2197-2208.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.9
, pp. 2197-2208
-
-
Nasrallah, C.A.1
Huelsenbeck, J.P.2
-
98
-
-
52449148668
-
The role of compensatory neutral mutations in molecular evolution
-
Kimura M (1985) The role of compensatory neutral mutations in molecular evolution. J Genet 64:7-19.
-
(1985)
J Genet
, vol.64
, pp. 7-19
-
-
Kimura, M.1
-
99
-
-
0037035388
-
Evolution of functionally conserved enhancers can be accelerated in large populations: A population-genetic model
-
Carter AJR, Wagner GP (2002) Evolution of functionally conserved enhancers can be accelerated in large populations: A population-genetic model. Proc Biol Sci 269(1494):953-960.
-
(2002)
Proc Biol Sci
, vol.269
, Issue.1494
, pp. 953-960
-
-
Carter, A.J.R.1
Wagner, G.P.2
-
100
-
-
1942453330
-
Stochastic tunnels in evolutionary dynamics
-
Iwasa Y, Michor F, Nowak MA (2004) Stochastic tunnels in evolutionary dynamics. Genetics 166(3):1571-1579.
-
(2004)
Genetics
, vol.166
, Issue.3
, pp. 1571-1579
-
-
Iwasa, Y.1
Michor, F.2
Nowak, M.A.3
-
102
-
-
84861434946
-
The interface of protein structure, protein biophysics, and molecular evolution
-
Liberles DA, et al. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21(6):769-785.
-
(2012)
Protein Sci
, vol.21
, Issue.6
, pp. 769-785
-
-
Liberles, D.A.1
|