-
1
-
-
48249133274
-
A genome-wide view of the spectrum of spontaneous mutations in yeast
-
Lynch M, Sung W, Morris K, Coffey N, Landry CR, et al. (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A 105: 9272-7.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 9272-9277
-
-
Lynch, M.1
Sung, W.2
Morris, K.3
Coffey, N.4
Landry, C.R.5
-
2
-
-
0013997442
-
Frameshift mutations and the genetic code
-
Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, et al. (1966) Frameshift mutations and the genetic code. Cold Spring Harb Symp Quant Biol 31: 77-84.
-
(1966)
Cold Spring Harb Symp Quant Biol
, vol.31
, pp. 77-84
-
-
Streisinger, G.1
Okada, Y.2
Emrich, J.3
Newton, J.4
Tsugita, A.5
-
3
-
-
33646130830
-
Simple sequence repeats as advantageous mutators in evolution
-
Kashi Y, King DG, (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22: 253-9.
-
(2006)
Trends Genet
, vol.22
, pp. 253-259
-
-
Kashi, Y.1
King, D.G.2
-
4
-
-
1642441841
-
Catastrophe and what to do about it if you are a bacterium: the importance of frameshift mutants
-
Koch AL, (2004) Catastrophe and what to do about it if you are a bacterium: the importance of frameshift mutants. Crit Rev Microbiol 30: 1-6.
-
(2004)
Crit Rev Microbiol
, vol.30
, pp. 1-6
-
-
Koch, A.L.1
-
5
-
-
0028065674
-
Adaptive evolution of highly mutable loci in pathogenic bacteria
-
Moxon ER, Rainey PB, Nowak MA, Lenski RE, (1994) Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 4: 24-33.
-
(1994)
Curr Biol
, vol.4
, pp. 24-33
-
-
Moxon, E.R.1
Rainey, P.B.2
Nowak, M.A.3
Lenski, R.E.4
-
6
-
-
0027303887
-
Unusual mutational mechanisms and evolution
-
Rainey P, Moxon R, (1993) Unusual mutational mechanisms and evolution. Science 2601958; author reply 1959-60.
-
(1993)
Science
, vol.260
-
-
Rainey, P.1
Moxon, R.2
-
7
-
-
77952312601
-
Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences
-
Wernegreen JJ, Kauppinen SN, Degnan PH, (2010) Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences. Mol Biol Evol 27: 833-9.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 833-839
-
-
Wernegreen, J.J.1
Kauppinen, S.N.2
Degnan, P.H.3
-
8
-
-
0025329221
-
Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli
-
Wagner LA, Weiss RB, Driscoll R, Dunn DS, Gesteland RF, (1990) Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res 18: 3529-35.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 3529-3535
-
-
Wagner, L.A.1
Weiss, R.B.2
Driscoll, R.3
Dunn, D.S.4
Gesteland, R.F.5
-
9
-
-
0029870925
-
Programmed translational frameshifting
-
Farabaugh PJ, (1996) Programmed translational frameshifting. Microbiol Rev 60: 103-34.
-
(1996)
Microbiol Rev
, vol.60
, pp. 103-134
-
-
Farabaugh, P.J.1
-
10
-
-
0030457112
-
Programmed translational frameshifting
-
Farabaugh PJ, (1996) Programmed translational frameshifting. Annu Rev Genet 30: 507-28.
-
(1996)
Annu Rev Genet
, vol.30
, pp. 507-528
-
-
Farabaugh, P.J.1
-
11
-
-
0037139583
-
Recoding: translational bifurcations in gene expression
-
Baranov PV, Gesteland RF, Atkins JF, (2002) Recoding: translational bifurcations in gene expression. Gene 286: 187-201.
-
(2002)
Gene
, vol.286
, pp. 187-201
-
-
Baranov, P.V.1
Gesteland, R.F.2
Atkins, J.F.3
-
12
-
-
0042527531
-
Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Sulfolobus solfataricus via chemical rescue of an inactive mutant
-
Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, Moracci M, (2003) Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Sulfolobus solfataricus via chemical rescue of an inactive mutant. Biochemistry 42: 9525-31.
-
(2003)
Biochemistry
, vol.42
, pp. 9525-9531
-
-
Cobucci-Ponzano, B.1
Trincone, A.2
Giordano, A.3
Rossi, M.4
Moracci, M.5
-
13
-
-
0038353117
-
Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting
-
Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, Moracci M, (2003) Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting. J Biol Chem 278: 14622-31.
-
(2003)
J Biol Chem
, vol.278
, pp. 14622-14631
-
-
Cobucci-Ponzano, B.1
Trincone, A.2
Giordano, A.3
Rossi, M.4
Moracci, M.5
-
14
-
-
54449100127
-
Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
-
Tamas I, Wernegreen JJ, Nystedt B, Kauppinen SN, Darby AC, et al. (2008) Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proc Natl Acad Sci U S A 105: 14934-9.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 14934-14939
-
-
Tamas, I.1
Wernegreen, J.J.2
Nystedt, B.3
Kauppinen, S.N.4
Darby, A.C.5
-
15
-
-
77954918654
-
Visualizing high error levels during gene expression in living bacterial cells
-
Meyerovich M, Mamou G, Ben-Yehuda S, (2010) Visualizing high error levels during gene expression in living bacterial cells. Proc Natl Acad Sci U S A 107: 11543-8.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 11543-11548
-
-
Meyerovich, M.1
Mamou, G.2
Ben-Yehuda, S.3
-
16
-
-
0025355475
-
Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme
-
Tsuchihashi Z, Kornberg A, (1990) Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc Natl Acad Sci U S A 87: 2516-20.
-
(1990)
Proc Natl Acad Sci U S A
, vol.87
, pp. 2516-2520
-
-
Tsuchihashi, Z.1
Kornberg, A.2
-
17
-
-
0026594057
-
Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon
-
Tsuchihashi Z, Brown PO, (1992) Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev 6: 511-9.
-
(1992)
Genes Dev
, vol.6
, pp. 511-519
-
-
Tsuchihashi, Z.1
Brown, P.O.2
-
18
-
-
84871226912
-
Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage
-
DOI: 10.1093/nar/gks944
-
Rockah-Shmuel L, Tawfik DS, (2012) Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. Nucleic Acids Res DOI: 10.1093/nar/gks944.
-
(2012)
Nucleic Acids Res
-
-
Rockah-Shmuel, L.1
Tawfik, D.S.2
-
19
-
-
0033052969
-
A hierarchical approach to protein molecular evolution
-
Bogarad LD, Deem MW, (1999) A hierarchical approach to protein molecular evolution. Proc Natl Acad Sci U S A 96 (6) (): 2591-5.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, Issue.6
, pp. 2591-2595
-
-
Bogarad, L.D.1
Deem, M.W.2
-
20
-
-
84875601072
-
Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space
-
10.1093/molbev/mst003
-
Toth-Petroczy A, Tawfik DS, (2013) Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space. Mol Biol Evol pp. 10.1093/molbev/mst003.
-
(2013)
Mol Biol Evol
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
21
-
-
76849094347
-
Back-translation for discovering distant protein homologies in the presence of frameshift mutations
-
Girdea M, Noe L, Kucherov G, (2009) Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms Mol Biol 5: 6.
-
(2009)
Algorithms Mol Biol
, vol.5
, pp. 6
-
-
Girdea, M.1
Noe, L.2
Kucherov, G.3
-
22
-
-
76849094347
-
Back-translation for discovering distant protein homologies in the presence of frameshift mutations
-
Girdea M, Noe L, Kucherov G, (2010) Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms Mol Biol 5: 6.
-
(2010)
Algorithms Mol Biol
, vol.5
, pp. 6
-
-
Girdea, M.1
Noe, L.2
Kucherov, G.3
-
23
-
-
0014935646
-
Natural selection and the concept of a protein space
-
Smith JM, (1970) Natural selection and the concept of a protein space. Nature 225: 563-4.
-
(1970)
Nature
, vol.225
, pp. 563-564
-
-
Smith, J.M.1
-
24
-
-
33748271469
-
An initial map of insertion and deletion (INDEL) variation in the human genome
-
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16: 1182-90.
-
(2006)
Genome Res
, vol.16
, pp. 1182-1190
-
-
Mills, R.E.1
Luttig, C.T.2
Larkins, C.E.3
Beauchamp, A.4
Tsui, C.5
-
25
-
-
0023256559
-
Slipped-strand mispairing: a major mechanism for DNA sequence evolution
-
Levinson G, Gutman GA, (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-21.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 203-221
-
-
Levinson, G.1
Gutman, G.A.2
-
26
-
-
0036897944
-
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review
-
Li YC, Korol AB, Fahima T, Beiles A, Nevo E, (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11: 2453-65.
-
(2002)
Mol Ecol
, vol.11
, pp. 2453-2465
-
-
Li, Y.C.1
Korol, A.B.2
Fahima, T.3
Beiles, A.4
Nevo, E.5
-
27
-
-
0042531995
-
Polymerase slippage in relation to the uniformity of tetrameric repeat stretches
-
Klintschar M, Wiegand P, (2003) Polymerase slippage in relation to the uniformity of tetrameric repeat stretches. Forensic Sci Int 135: 163-6.
-
(2003)
Forensic Sci Int
, vol.135
, pp. 163-166
-
-
Klintschar, M.1
Wiegand, P.2
-
28
-
-
0036893298
-
A DNA sequence evolution analysis generalized by simulation and the markov chain monte carlo method implicates strand slippage in a majority of insertions and deletions
-
Nishizawa M, Nishizawa K, (2002) A DNA sequence evolution analysis generalized by simulation and the markov chain monte carlo method implicates strand slippage in a majority of insertions and deletions. J Mol Evol 55: 706-17.
-
(2002)
J Mol Evol
, vol.55
, pp. 706-717
-
-
Nishizawa, M.1
Nishizawa, K.2
-
29
-
-
58449126084
-
The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
-
Moran NA, McLaughlin HJ, Sorek R, (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323: 379-82.
-
(2009)
Science
, vol.323
, pp. 379-382
-
-
Moran, N.A.1
McLaughlin, H.J.2
Sorek, R.3
-
30
-
-
12344307147
-
Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes
-
Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA, (2005) Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 14: 59-69.
-
(2005)
Hum Mol Genet
, vol.14
, pp. 59-69
-
-
Bhangale, T.R.1
Rieder, M.J.2
Livingston, R.J.3
Nickerson, D.A.4
-
31
-
-
67649369319
-
Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria
-
Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, et al. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26: 1523-31.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1523-1531
-
-
Chen, J.Q.1
Wu, Y.2
Yang, H.3
Bergelson, J.4
Kreitman, M.5
-
32
-
-
37549023418
-
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage
-
de la Chaux N, Messer PW, Arndt PF, (2007) DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evol Biol 7: 191.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 191
-
-
de la Chaux, N.1
Messer, P.W.2
Arndt, P.F.3
-
33
-
-
0018966254
-
Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli
-
Szomolanyi E, Kiss A, Venetianer P, (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene 10: 219-25.
-
(1980)
Gene
, vol.10
, pp. 219-225
-
-
Szomolanyi, E.1
Kiss, A.2
Venetianer, P.3
-
34
-
-
44349161622
-
Intense neutral drifts yield robust and evolvable consensus proteins
-
Bershtein S, Goldin K, Tawfik DS, (2008) Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 379: 1029-44.
-
(2008)
J Mol Biol
, vol.379
, pp. 1029-1044
-
-
Bershtein, S.1
Goldin, K.2
Tawfik, D.S.3
-
35
-
-
0035883519
-
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
-
Kobayashi I, (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Research 29: 3742-3756.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 3742-3756
-
-
Kobayashi, I.1
-
36
-
-
43349095997
-
Real-time kinetics of restriction-modification gene expression after entry into a new host cell
-
Mruk I, Blumenthal RM, (2008) Real-time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic Acids Res 36: 2581-93.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2581-2593
-
-
Mruk, I.1
Blumenthal, R.M.2
-
37
-
-
35148814896
-
A simple selection strategy for evolving highly efficient enzymes
-
Neuenschwander M, Butz M, Heintz C, Kast P, Hilvert D, (2007) A simple selection strategy for evolving highly efficient enzymes. Nat Biotechnol 25: 1145-7.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1145-1147
-
-
Neuenschwander, M.1
Butz, M.2
Heintz, C.3
Kast, P.4
Hilvert, D.5
-
38
-
-
70349333227
-
The evolutionary consequences of erroneous protein synthesis
-
Drummond DA, Wilke CO, (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10: 715-24.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 715-724
-
-
Drummond, D.A.1
Wilke, C.O.2
-
39
-
-
0022872027
-
Escherichia coli K-12 restricts DNA containing 5-methylcytosine
-
Raleigh EA, Wilson G, (1986) Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A 83: 9070-4.
-
(1986)
Proc Natl Acad Sci U S A
, vol.83
, pp. 9070-9074
-
-
Raleigh, E.A.1
Wilson, G.2
-
40
-
-
79959807202
-
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences
-
McDonald MJ, Wang WC, Huang HD, Leu JY, (2010) Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol 9: e1000622.
-
(2010)
PLoS Biol
, vol.9
-
-
McDonald, M.J.1
Wang, W.C.2
Huang, H.D.3
Leu, J.Y.4
-
41
-
-
77952082576
-
Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus
-
Cobucci-Ponzano B, Guzzini L, Benelli D, Londei P, Perrodou E, et al. (2010) Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus. J Proteome Res 9: 2496-507.
-
(2010)
J Proteome Res
, vol.9
, pp. 2496-2507
-
-
Cobucci-Ponzano, B.1
Guzzini, L.2
Benelli, D.3
Londei, P.4
Perrodou, E.5
-
42
-
-
33644747335
-
Why are phenotypic mutation rates much higher than genotypic mutation rates?
-
Burger R, Willensdorfer M, Nowak MA, (2006) Why are phenotypic mutation rates much higher than genotypic mutation rates? Genetics 172: 197-206.
-
(2006)
Genetics
, vol.172
, pp. 197-206
-
-
Burger, R.1
Willensdorfer, M.2
Nowak, M.A.3
-
43
-
-
65549084298
-
Potential role of phenotypic mutations in the evolution of protein expression and stability
-
Goldsmith M, Tawfik DS, (2009) Potential role of phenotypic mutations in the evolution of protein expression and stability. Proc Natl Acad Sci U S A 106: 6197-202.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6197-6202
-
-
Goldsmith, M.1
Tawfik, D.S.2
-
44
-
-
45149112698
-
The look-ahead effect of phenotypic mutations
-
Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E, (2008) The look-ahead effect of phenotypic mutations. Biol Direct 3: 18.
-
(2008)
Biol Direct
, vol.3
, pp. 18
-
-
Whitehead, D.J.1
Wilke, C.O.2
Vernazobres, D.3
Bornberg-Bauer, E.4
-
45
-
-
79551622326
-
Evolution of molecular error rates and the consequences for evolvability
-
Rajon E, Masel J, (2011) Evolution of molecular error rates and the consequences for evolvability. Proc Natl Acad Sci U S A 108: 1082-7.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 1082-1087
-
-
Rajon, E.1
Masel, J.2
-
46
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
47
-
-
79959842126
-
Genomic island variability facilitates Prochlorococcus-virus coexistence
-
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D, (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474: 604-8.
-
(2011)
Nature
, vol.474
, pp. 604-608
-
-
Avrani, S.1
Wurtzel, O.2
Sharon, I.3
Sorek, R.4
Lindell, D.5
-
48
-
-
79251528560
-
Mutation detection with next-generation resequencing through a mediator genome
-
Wurtzel O, Dori-Bachash M, Pietrokovski S, Jurkevitch E, Sorek R, (2010) Mutation detection with next-generation resequencing through a mediator genome. PLoS One 5: e15628.
-
(2010)
PLoS One
, vol.5
-
-
Wurtzel, O.1
Dori-Bachash, M.2
Pietrokovski, S.3
Jurkevitch, E.4
Sorek, R.5
-
49
-
-
77954257799
-
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: W529-33.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
50
-
-
0029068629
-
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing
-
Reinisch KM, Chen L, Verdine GL, Lipscomb WN, (1995) The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82: 143-53.
-
(1995)
Cell
, vol.82
, pp. 143-153
-
-
Reinisch, K.M.1
Chen, L.2
Verdine, G.L.3
Lipscomb, W.N.4
-
51
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-62.
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
|