-
1
-
-
35148899681
-
Stress-induced mutagenesis in bacteria
-
Foster PL (2007) Stress-induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 42: 373-397.
-
(2007)
Crit Rev Biochem Mol Biol
, vol.42
, pp. 373-397
-
-
Foster, P.L.1
-
2
-
-
0037849904
-
Stress-induced mutagenesis in bacteria
-
Bjedov I, Tenaillon O, Gerard B, Souza V, Denamur E, et al. (2003) Stress-induced mutagenesis in bacteria. Science 300: 1404-1409.
-
(2003)
Science
, vol.300
, pp. 1404-1409
-
-
Bjedov, I.1
Tenaillon, O.2
Gerard, B.3
Souza, V.4
Denamur, E.5
-
3
-
-
2542478884
-
Evolutionary significance of stress-induced mutagenesis in bacteria
-
Tenaillon O, Denamur E, Matic I (2004) Evolutionary significance of stress-induced mutagenesis in bacteria. Trends Microbiol 12: 264-270.
-
(2004)
Trends Microbiol
, vol.12
, pp. 264-270
-
-
Tenaillon, O.1
Denamur, E.2
Matic, I.3
-
4
-
-
0033536052
-
The role of transient hypermutators in adaptive mutation in Escherichia coli
-
Rosche WA, Foster PL (1999) The role of transient hypermutators in adaptive mutation in Escherichia coli. Proc Natl Acad Sci U S A 96: 6862-6867.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 6862-6867
-
-
Rosche, W.A.1
Foster, P.L.2
-
6
-
-
50149112177
-
Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis
-
Wrande M, Roth JR, Hughes D (2008) Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis. Proc Natl Acad Sci U S A 105: 11863-11868.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 11863-11868
-
-
Wrande, M.1
Roth, J.R.2
Hughes, D.3
-
7
-
-
0029151239
-
"Adaptive mutation": The debate goes on
-
Lenski RE, Sniegowski PD (1995) "Adaptive mutation": the debate goes on. Science 269: 285-288.
-
(1995)
Science
, vol.269
, pp. 285-288
-
-
Lenski, R.E.1
Sniegowski, P.D.2
-
8
-
-
0242363153
-
Adaptive mutation: General mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac
-
Slechta ES, Bunny KL, Kugelberg E, Kofoid E, Andersson DI, et al. (2003) Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc Natl Acad Sci U S A 100: 12847-12852.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 12847-12852
-
-
Slechta, E.S.1
Bunny, K.L.2
Kugelberg, E.3
Kofoid, E.4
Andersson, D.I.5
-
9
-
-
33646397599
-
Evolution of mutation rates in bacteria
-
Denamur E, Matic I (2006) Evolution of mutation rates in bacteria. Mol Microbiol 60: 820-827.
-
(2006)
Mol Microbiol
, vol.60
, pp. 820-827
-
-
Denamur, E.1
Matic, I.2
-
11
-
-
0034542564
-
The evolution of mutation rates: Separating causes from consequences
-
Sniegowski PD, Gerrish PJ, Johnson T, Shaver A (2000) The evolution of mutation rates: separating causes from consequences. Bioessays 22: 1057-1066.
-
(2000)
Bioessays
, vol.22
, pp. 1057-1066
-
-
Sniegowski, P.D.1
Gerrish, P.J.2
Johnson, T.3
Shaver, A.4
-
12
-
-
0036811766
-
Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations
-
Shaver AC, Dombrowski PG, Sweeney JY, Treis T, Zappala RM, et al. (2002) Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations. Genetics 162: 557-566.
-
(2002)
Genetics
, vol.162
, pp. 557-566
-
-
Shaver, A.C.1
Dombrowski, P.G.2
Sweeney, J.Y.3
Treis, T.4
Zappala, R.M.5
-
13
-
-
60549115416
-
Emergence of species in evolutionary "simulated annealing"
-
Heo M, Kang L, Shakhnovich EI (2009) Emergence of species in evolutionary "simulated annealing". Proc Natl Acad Sci U S A 106: 1869-1874.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 1869-1874
-
-
Heo, M.1
Kang, L.2
Shakhnovich, E.I.3
-
14
-
-
0032979190
-
Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria
-
Tenaillon O, Toupance B, Le Nagard H, Taddei F, Godelle B (1999) Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics 152: 485-493.
-
(1999)
Genetics
, vol.152
, pp. 485-493
-
-
Tenaillon, O.1
Toupance, B.2
Le Nagard, H.3
Taddei, F.4
Godelle, B.5
-
15
-
-
33644759282
-
The evolution of mutation rate in finite asexual populations
-
Andre JB, Godelle B (2006) The evolution of mutation rate in finite asexual populations. Genetics 172: 611-626.
-
(2006)
Genetics
, vol.172
, pp. 611-626
-
-
Andre, J.B.1
Godelle, B.2
-
16
-
-
0030620272
-
Role of mutator alleles in adaptive evolution
-
Taddei F, Radman M, Maynard-Smith J, Toupance B, Gouyon PH, et al. (1997) Role of mutator alleles in adaptive evolution. Nature 387: 700-702.
-
(1997)
Nature
, vol.387
, pp. 700-702
-
-
Taddei, F.1
Radman, M.2
Maynard-Smith, J.3
Toupance, B.4
Gouyon, P.H.5
-
17
-
-
0031745665
-
Protein design: A perspective from simple tractable models
-
Shakhnovich EI (1998) Protein design: a perspective from simple tractable models. Fold Des 3: R45-58.
-
(1998)
Fold Des
, vol.3
-
-
Shakhnovich, E.I.1
-
18
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich E (2006) Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev 106: 1559-1588.
-
(2006)
Chem Rev
, vol.106
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
19
-
-
0141817914
-
Assembly and molecular activities of the MutS tetramer
-
Bjornson KP, Blackwell LJ, Sage H, Baitinger C, Allen D, et al. (2003) Assembly and molecular activities of the MutS tetramer. J Biol Chem 278: 34667-34673.
-
(2003)
J Biol Chem
, vol.278
, pp. 34667-34673
-
-
Bjornson, K.P.1
Blackwell, L.J.2
Sage, H.3
Baitinger, C.4
Allen, D.5
-
21
-
-
0030711638
-
Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12
-
Tsui HC, Feng G, Winkler ME (1997) Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12. J Bacteriol 179: 7476-7487.
-
(1997)
J Bacteriol
, vol.179
, pp. 7476-7487
-
-
Tsui, H.C.1
Feng, G.2
Winkler, M.E.3
-
22
-
-
0030777211
-
Highly variable mutation rates in commensal and pathogenic Escherichia coli
-
Matic I, Radman M, Taddei F, Picard B, Doit C, et al. (1997) Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science 277: 1833-1834.
-
(1997)
Science
, vol.277
, pp. 1833-1834
-
-
Matic, I.1
Radman, M.2
Taddei, F.3
Picard, B.4
Doit, C.5
-
23
-
-
0029992026
-
Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells
-
Feng G, Tsui HC, Winkler ME (1996) Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol 178: 2388-2396.
-
(1996)
J Bacteriol
, vol.178
, pp. 2388-2396
-
-
Feng, G.1
Tsui, H.C.2
Winkler, M.E.3
-
24
-
-
0037515830
-
Molecular analysis of mutS expression and mutation in natural isolates of pathogenic Escherichia coli
-
Li B, Tsui HC, LeClerc JE, Dey M, Winkler ME, et al. (2003) Molecular analysis of mutS expression and mutation in natural isolates of pathogenic Escherichia coli. Microbiology 149: 1323-1331.
-
(2003)
Microbiology
, vol.149
, pp. 1323-1331
-
-
Li, B.1
Tsui, H.C.2
Leclerc, J.E.3
Dey, M.4
Winkler, M.E.5
-
25
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
26
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307: 1962-1965.
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
27
-
-
0030620273
-
Evolution of high mutation rates in experimental populations of
-
Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387: 703-705.
-
(1997)
E. Coli. Nature
, vol.387
, pp. 703-705
-
-
Sniegowski, P.D.1
Gerrish, P.J.2
Lenski, R.E.3
-
28
-
-
0033555421
-
Diminishing returns from mutation supply rate in asexual populations
-
de Visser JAGM, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE (1999) Diminishing returns from mutation supply rate in asexual populations. Science 283: 404-406.
-
(1999)
Science
, vol.283
, pp. 404-406
-
-
de Visser, J.A.G.M.1
Zeyl, C.W.2
Gerrish, P.J.3
Blanchard, J.L.4
Lenski, R.E.5
-
30
-
-
67650314825
-
The fixation probability of rare mutators in finite asexual populations
-
Wylie CS, Ghim CM, Kessler D, Levine H (2009) The fixation probability of rare mutators in finite asexual populations. Genetics 181: 1595-1612.
-
(2009)
Genetics
, vol.181
, pp. 1595-1612
-
-
Wylie, C.S.1
Ghim, C.M.2
Kessler, D.3
Levine, H.4
-
32
-
-
25444468618
-
Noise in gene expression: Origins, consequences, and control
-
Raser JM, O'Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309: 2010-2013.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
33
-
-
0242442569
-
DNA mismatch repair: Molecular mechanisms and biological function
-
Schofield MJ, Hsieh P (2003) DNA mismatch repair: molecular mechanisms and biological function. Annu Rev Microbiol 57: 579-608.
-
(2003)
Annu Rev Microbiol
, vol.57
, pp. 579-608
-
-
Schofield, M.J.1
Hsieh, P.2
-
34
-
-
0032808947
-
The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes
-
Drake JW (1999) The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann N Y Acad Sci 870: 100-107.
-
(1999)
Ann N Y Acad Sci
, vol.870
, pp. 100-107
-
-
Drake, J.W.1
-
35
-
-
0033166541
-
Mismatch repair is diminished during stationary-phase mutation
-
Harris RS, Feng G, Ross KJ, Sidhu R, Thulin C, et al. (1999) Mismatch repair is diminished during stationary-phase mutation. Mutat Res 437: 51-60.
-
(1999)
Mutat Res
, vol.437
, pp. 51-60
-
-
Harris, R.S.1
Feng, G.2
Ross, K.J.3
Sidhu, R.4
Thulin, C.5
-
36
-
-
34447255483
-
Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo
-
Mendillo ML, Putnam CD, Kolodner RD (2007) Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo. J Biol Chem 282: 16345-16354.
-
(2007)
J Biol Chem
, vol.282
, pp. 16345-16354
-
-
Mendillo, M.L.1
Putnam, C.D.2
Kolodner, R.D.3
-
37
-
-
47649125318
-
Tuning gene expression to changing environments: From rapid responses to evolutionary adaptation
-
Lopez-Maury L, Marguerat S, Bahler J (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet 9: 583-593.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 583-593
-
-
Lopez-Maury, L.1
Marguerat, S.2
Bahler, J.3
-
38
-
-
1542285166
-
A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae
-
Huisinga KL, Pugh BF (2004) A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell 13: 573-585.
-
(2004)
Mol Cell
, vol.13
, pp. 573-585
-
-
Huisinga, K.L.1
Pugh, B.F.2
-
39
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, et al. (2006) Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell 24: 853-865.
-
(2006)
Mol Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
Balazsi, G.2
Kohanski, M.A.3
Isaacs, F.J.4
Murphy, K.F.5
-
40
-
-
0034703744
-
Evolutionary implications of the frequent horizontal transfer of mismatch repair genes
-
Denamur E, Lecointre G, Darlu P, Tenaillon O, Acquaviva C, et al. (2000) Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 103: 711-721.
-
(2000)
Cell
, vol.103
, pp. 711-721
-
-
Denamur, E.1
Lecointre, G.2
Darlu, P.3
Tenaillon, O.4
Acquaviva, C.5
-
42
-
-
58149464666
-
Fluctuations in mass-action equilibrium of protein binding networks
-
268102
-
Yan KK, Walker D, Maslov S (2008) Fluctuations in mass-action equilibrium of protein binding networks. Phys Rev Lett 101: 268102.
-
(2008)
Phys Rev Lett
, vol.101
-
-
Yan, K.K.1
Walker, D.2
Maslov, S.3
-
43
-
-
36549097257
-
Enumeration of all compact conformations of copolymers with random sequence of links
-
Shakhnovich E, Gutin A (1990) Enumeration of all compact conformations of copolymers with random sequence of links. Journal of Chemical Physics 93: 5967-5971.
-
(1990)
Journal of Chemical Physics
, vol.93
, pp. 5967-5971
-
-
Shakhnovich, E.1
Gutin, A.2
-
45
-
-
4243392673
-
Proteins with selected sequences fold into unique native conformation
-
Shakhnovich EI (1994) Proteins with selected sequences fold into unique native conformation. Physical Review Letters 72: 3907-3910.
-
(1994)
Physical Review Letters
, vol.72
, pp. 3907-3910
-
-
Shakhnovich, E.I.1
-
46
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du R, Pande V, Grosberg A, Tanaka T, Shakhnovich EI (1998) On the transition coordinate for protein folding. Journal of Chemical Physics 108: 334-350.
-
(1998)
Journal of Chemical Physics
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.2
Grosberg, A.3
Tanaka, T.4
Shakhnovich, E.I.5
-
47
-
-
0035370662
-
Multiple protein folding nuclei and the transition state ensemble in two-state proteins
-
Klimov DK, Thirumalai D (2001) Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 43: 465-475.
-
(2001)
Proteins
, vol.43
, pp. 465-475
-
-
Klimov, D.K.1
Thirumalai, D.2
-
48
-
-
34047232678
-
Positive and negative design in stability and thermal adaptation of natural proteins
-
Berezovsky IN, Zeldovich KB, Shakhnovich EI (2007) Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol 3: e52.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Berezovsky, I.N.1
Zeldovich, K.B.2
Shakhnovich, E.I.3
-
49
-
-
34547607777
-
A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds
-
Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI (2007) A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol 3: e139.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, B.E.3
Shakhnovich, E.I.4
-
50
-
-
43949093427
-
Understanding protein evolution: From protein physics to Darwinian selection
-
Zeldovich KB, Shakhnovich EI (2008) Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem 59: 105-127.
-
(2008)
Annu Rev Phys Chem
, vol.59
, pp. 105-127
-
-
Zeldovich, K.B.1
Shakhnovich, E.I.2
-
51
-
-
33846515095
-
Thermodynamics of neutral protein evolution
-
Bloom JD, Raval A, Wilke CO (2007) Thermodynamics of neutral protein evolution. Genetics 175: 255-266.
-
(2007)
Genetics
, vol.175
, pp. 255-266
-
-
Bloom, J.D.1
Raval, A.2
Wilke, C.O.3
-
52
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
53
-
-
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 U S A 104: 16152-16157.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
54
-
-
34047118521
-
Tunability and noise dependence in differentiation dynamics
-
Suel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz MB (2007) Tunability and noise dependence in differentiation dynamics. Science 315: 1716-1719.
-
(2007)
Science
, vol.315
, pp. 1716-1719
-
-
Suel, G.M.1
Kulkarni, R.P.2
Dworkin, J.3
Garcia-Ojalvo, J.4
Elowitz, M.B.5
-
55
-
-
35348813628
-
Propagation of large concentration changes in reversible protein-binding networks
-
Maslov S, Ispolatov I (2007) Propagation of large concentration changes in reversible protein-binding networks. Proc Natl Acad Sci U S A 104: 13655-13660.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 13655-13660
-
-
Maslov, S.1
Ispolatov, I.2
|