-
1
-
-
84889677831
-
Mutational and fitness landscapes of an RNA virus revealed through population sequencing
-
Acevedo A, Brodsky L, Andino R. 2014. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505:686–690.
-
(2014)
Nature
, vol.505
, pp. 686-690
-
-
Acevedo, A1
Brodsky, L2
Andino, R.3
-
2
-
-
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. 31:1956–1978.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1956-1978
-
-
Bloom, JD.1
-
3
-
-
33846092128
-
A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments
-
Carrasco P, Daros JA, Agudelo-Romero P, Elena SF. 2007. A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments. J Virol Methods. 139:181–188.
-
(2007)
J Virol Methods
, vol.139
, pp. 181-188
-
-
Carrasco, P1
Daros, JA2
Agudelo-Romero, P3
Elena, SF.4
-
4
-
-
0035924939
-
The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analyses tautologous
-
Di Giulio M. 2001. The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analyses tautologous. J Theor Biol. 208:141–144.
-
(2001)
J Theor Biol
, vol.208
, pp. 141-144
-
-
Di Giulio, M.1
-
5
-
-
73649127602
-
The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages
-
Domingo-Calap P, Cuevas JM, Sanjuan R. 2009. The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages. PLoS Genet. 5:e1000742.
-
(2009)
PLoS Genet
, vol.5
, pp. e1000742
-
-
Domingo-Calap, P1
Cuevas, JM2
Sanjuan, R.3
-
6
-
-
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. 8:610–618.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 610-618
-
-
Eyre-Walker, A1
Keightley, PD.2
-
7
-
-
34250749323
-
High frequency of mutations that expand the host range of an RNA virus
-
Ferris MT, Joyce P, Burch CL. 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, MT1
Joyce, P2
Burch, CL.3
-
8
-
-
84901408859
-
A comprehensive, high-resolution map of a gene’s fitness landscape
-
Firnberg E, Labonte JW, Gray JJ, Ostermeier M. 2014. A comprehensive, high-resolution map of a gene’s fitness landscape. Mol Biol Evol. 31:1581–1592.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1581-1592
-
-
Firnberg, E1
Labonte, JW2
Gray, JJ3
Ostermeier, M.4
-
9
-
-
0014219557
-
Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations
-
Fitch WM. 1967. Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations. J Mol Biol. 26:499–507.
-
(1967)
J Mol Biol
, vol.26
, pp. 499-507
-
-
Fitch, WM.1
-
10
-
-
0001508130
-
Patterns of nucleotide substitution in pseudogenes and functional genes
-
Gojobori T, Li WH, Graur D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol. 17:245–250.
-
(1982)
J Mol Evol
, vol.17
, pp. 245-250
-
-
Gojobori, T1
Li, WH2
Graur, D.3
-
11
-
-
0016197604
-
Amino acid difference formula to help explain protein evolution
-
Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862–864.
-
(1974)
Science
, vol.185
, pp. 862-864
-
-
Grantham, R.1
-
12
-
-
0020083498
-
The meaning and use of the area under a receiver operating characteristic (ROC) curve
-
Hanley JA, McNeil BJ. 1982. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143:29–36.
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, JA1
McNeil, BJ.2
-
14
-
-
84881408157
-
Capturing the mutational landscape of the beta-lactamase TEM-1
-
Jacquier H, Birgy A, Le Nagard H, Mechulam Y, Schmitt E, Glodt J, Bercot B, Petit E, Poulain J, Barnaud G, et al. 2013. Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci U S A. 110:13067–13072.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 13067-13072
-
-
Jacquier, H1
Birgy, A2
Le Nagard, H3
Mechulam, Y4
Schmitt, E5
Glodt, J6
Bercot, B7
Petit, E8
Poulain, J9
Barnaud, G10
-
15
-
-
33749453792
-
Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms
-
Jiang C, Zhao Z. 2006. Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 88:527–534.
-
(2006)
Genomics
, vol.88
, pp. 527-534
-
-
Jiang, C1
Zhao, Z.2
-
17
-
-
33847289660
-
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes
-
Keller I, Bensasson D, Nichols RA. 2007. Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS Genet. 3:e22.
-
(2007)
PLoS Genet
, vol.3
, pp. e22
-
-
Keller, I1
Bensasson, D2
Nichols, RA.3
-
18
-
-
0025304132
-
Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors
-
Kleina LG, Miller JH. 1990. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol. 212:295–318.
-
(1990)
J Mol Biol
, vol.212
, pp. 295-318
-
-
Kleina, LG1
Miller, JH.2
-
19
-
-
0029960344
-
Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates
-
Kumar S. 1996. Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537–548.
-
(1996)
Genetics
, vol.143
, pp. 537-548
-
-
Kumar, S.1
-
21
-
-
0001952402
-
Evolution of DNA sequences
-
MacIntyre RJ, editor. New York: Plenum
-
Li WH, Luo CC, Wu CI. 1985. Evolution of DNA sequences. In: MacIntyre RJ, editor. Molecular evolutionary genetics. New York: Plenum.
-
(1985)
Molecular evolutionary genetics
-
-
Li, WH1
Luo, CC2
Wu, CI.3
-
22
-
-
75749103383
-
Rate, molecular spectrum, and consequences of human mutation
-
Lynch M. 2010. Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci U S A. 107:961–968.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 961-968
-
-
Lynch, M.1
-
23
-
-
79251553136
-
Diminishing returns from beneficial mutations and pervasive epistasis shape the fitness landscape for rifampicin resistance in Pseudomonas aeruginosa
-
MacLean RC, Perron GG, Gardner A. 2010. Diminishing returns from beneficial mutations and pervasive epistasis shape the fitness landscape for rifampicin resistance in Pseudomonas aeruginosa. Genetics 186:1345–1354.
-
(2010)
Genetics
, vol.186
, pp. 1345-1354
-
-
MacLean, RC1
Perron, GG2
Gardner, A.3
-
24
-
-
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. 89:225–252.
-
(2014)
Q Rev Biol
, vol.89
, pp. 225-252
-
-
McCandlish, DM1
Stoltzfus, A.2
-
25
-
-
78951475034
-
Mutational effects and population dynamics during viral adaptation challenge current models
-
Miller CR, Joyce P, Wichman HA. 2011. Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 187:185–202.
-
(2011)
Genetics
, vol.187
, pp. 185-202
-
-
Miller, CR1
Joyce, P2
Wichman, HA.3
-
26
-
-
0018415510
-
Two types of amino acid substitutions in protein evolution
-
Miyata T, Miyazawa S, Yasunaga T. 1979. Two types of amino acid substitutions in protein evolution. J Mol Evol. 12:219–236.
-
(1979)
J Mol Evol
, vol.12
, pp. 219-236
-
-
Miyata, T1
Miyazawa, S2
Yasunaga, T.3
-
27
-
-
33644772171
-
Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition
-
Morton BR, Bi IV, McMullen MD, Gaut BS. 2006. Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics 172:569–577.
-
(2006)
Genetics
, vol.172
, pp. 569-577
-
-
Morton, BR1
Bi, IV2
McMullen, MD3
Gaut, BS.4
-
28
-
-
77955475761
-
Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1
-
Peris JB, Davis P, Cuevas JM, Nebot MR, Sanjuan R. 2010. Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1. Genetics 185:603–609.
-
(2010)
Genetics
, vol.185
, pp. 603-609
-
-
Peris, JB1
Davis, P2
Cuevas, JM3
Nebot, MR4
Sanjuan, R.5
-
29
-
-
0033573925
-
Patterns of nucleotide substitution in Drosophila and mammalian genomes
-
Petrov DA, Hartl DL. 1999. Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci U S A. 96:1475–1479.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 1475-1479
-
-
Petrov, DA1
Hartl, DL.2
-
30
-
-
84919430559
-
Uneven genetic robustness of HIV-1 integrase
-
Rihn SJ, Hughes J, Wilson SJ, Bieniasz PD. 2015. Uneven genetic robustness of HIV-1 integrase. J Virol. 89:552–567.
-
(2015)
J Virol
, vol.89
, pp. 552-567
-
-
Rihn, SJ1
Hughes, J2
Wilson, SJ3
Bieniasz, PD.4
-
31
-
-
84879544085
-
Extreme genetic fragility of the HIV-1 capsid
-
Rihn SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, Bieniasz PD. 2013. Extreme genetic fragility of the HIV-1 capsid. PLoS Pathog. 9:e1003461.
-
(2013)
PLoS Pathog
, vol.9
, pp. e1003461
-
-
Rihn, SJ1
Wilson, SJ2
Loman, NJ3
Alim, M4
Bakker, SE5
Bhella, D6
Gifford, RJ7
Rixon, FJ8
Bieniasz, PD.9
-
32
-
-
84875703570
-
Analyses of the effects of all ubiquitin point mutants on yeast growth rate
-
Roscoe BP, Thayer KM, Zeldovich KB, Fushman D, Bolon DN. 2013. Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J Mol Biol. 425:1363–1377.
-
(2013)
J Mol Biol
, vol.425
, pp. 1363-1377
-
-
Roscoe, BP1
Thayer, KM2
Zeldovich, KB3
Fushman, D4
Bolon, DN.5
-
33
-
-
0037910313
-
Patterns of transitional mutation biases within and among mammalian genomes
-
Rosenberg MS, Subramanian S, Kumar S. 2003. Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol. 20:988–993.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 988-993
-
-
Rosenberg, MS1
Subramanian, S2
Kumar, S.3
-
34
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuan R, Moya A, Elena SF. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A. 101:8396–8401.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 8396-8401
-
-
Sanjuan, R1
Moya, A2
Elena, SF.3
-
35
-
-
0025953766
-
Spontaneous mutation in the Escherichia coli lacI gene
-
Schaaper RM, Dunn RL. 1991. Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129:317–326.
-
(1991)
Genetics
, vol.129
, pp. 317-326
-
-
Schaaper, RM1
Dunn, RL.2
-
36
-
-
84864070833
-
Quantifying the adaptive potential of an antibiotic resistance enzyme
-
Schenk MF, Szendro IG, Krug J, de Visser JA. 2012. Quantifying the adaptive potential of an antibiotic resistance enzyme. PLoS Genet. 8:e1002783.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002783
-
-
Schenk, MF1
Szendro, IG2
Krug, J3
de Visser, JA.4
-
37
-
-
84881056465
-
Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster
-
Schrider DR, Houle D, Lynch M, Hahn MW. 2013. Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster. Genetics 194:937–954.
-
(2013)
Genetics
, vol.194
, pp. 937-954
-
-
Schrider, DR1
Houle, D2
Lynch, M3
Hahn, MW.4
-
38
-
-
0030899906
-
Inference for phylogenies under a hybrid parsimony method: evolutionary-symmetric transversion parsimony
-
Sinsheimer JS, Lake JA, Little RJ. 1997. Inference for phylogenies under a hybrid parsimony method: evolutionary-symmetric transversion parsimony. Biometrics 53:23–38.
-
(1997)
Biometrics
, vol.53
, pp. 23-38
-
-
Sinsheimer, JS1
Lake, JA2
Little, RJ.3
-
39
-
-
69249205499
-
Climbing mount probable: mutation as a cause of nonrandomness in evolution
-
Stoltzfus A, Yampolsky LY. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered. 100:637–647.
-
(2009)
J Hered
, vol.100
, pp. 637-647
-
-
Stoltzfus, A1
Yampolsky, LY.2
-
40
-
-
3242768556
-
A universal evolutionary index for amino acid changes
-
Tang H, Wyckoff GJ, Lu J, Wu CI. 2004. A universal evolutionary index for amino acid changes. Mol Biol Evol. 21:1548–1556.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1548-1556
-
-
Tang, H1
Wyckoff, GJ2
Lu, J3
Wu, CI.4
-
41
-
-
84905197658
-
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
-
Thyagarajan B, Bloom JD. 2014. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. Elife 3.
-
(2014)
Elife
, vol.3
-
-
Thyagarajan, B1
Bloom, JD.2
-
42
-
-
0015439090
-
Non-randomness of base replacement in point mutation
-
Vogel F. 1972. Non-randomness of base replacement in point mutation. J Mol Evol. 1:334–367.
-
(1972)
J Mol Evol
, vol.1
, pp. 334-367
-
-
Vogel, F.1
-
43
-
-
0017363167
-
Higher frequencies of transitions among point mutations
-
Vogel F, Kopun M. 1977. Higher frequencies of transitions among point mutations. J Mol Evol. 9:159–180.
-
(1977)
J Mol Evol
, vol.9
, pp. 159-180
-
-
Vogel, F1
Kopun, M.2
-
44
-
-
0001062055
-
The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance
-
Wakeley J. 1996. The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. Trends Ecol Evol. 11:158–162.
-
(1996)
Trends Ecol Evol
, vol.11
, pp. 158-162
-
-
Wakeley, J.1
-
45
-
-
84900431101
-
High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
-
Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, et al. 2014. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep. 4:4942.
-
(2014)
Sci Rep
, vol.4
, pp. 4942
-
-
Wu, NC1
Young, AP2
Al-Mawsawi, LQ3
Olson, CA4
Feng, J5
Qi, H6
Chen, SH7
Lu, IH8
Lin, CY9
Chin, RG10
-
46
-
-
0031916709
-
The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes
-
Xia X. 1998. The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. Mol Biol Evol. 15:336–344.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 336-344
-
-
Xia, X.1
-
47
-
-
0035050426
-
Bias in the introduction of variation as an orienting factor in evolution
-
Yampolsky LY, Stoltzfus A. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev. 3:73–83.
-
(2001)
Evol Dev
, vol.3
, pp. 73-83
-
-
Yampolsky, LY1
Stoltzfus, A.2
-
48
-
-
25444482352
-
The exchangeability of amino acids in proteins
-
Yampolsky LY, Stoltzfus A. 2005. The exchangeability of amino acids in proteins. Genetics 170:1459–1472.
-
(2005)
Genetics
, vol.170
, pp. 1459-1472
-
-
Yampolsky, LY1
Stoltzfus, A.2
-
49
-
-
0033921902
-
Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
-
Zhang J. 2000. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol. 50:56–68.
-
(2000)
J Mol Evol
, vol.50
, pp. 56-68
-
-
Zhang, J.1
-
50
-
-
13444269389
-
Moderate mutation rate in the SARS coronavirus genome and its implications
-
Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang YP, Boerwinkle E, Fu YX. 2004. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 4:21.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 21
-
-
Zhao, Z1
Li, H2
Wu, X3
Zhong, Y4
Zhang, K5
Zhang, YP6
Boerwinkle, E7
Fu, YX.8
|