-
1
-
-
34447564992
-
Mutation rate variation in multicellular eukaryotes: causes and consequences
-
Baer, C. F., M. M. Miyamoto, and D. R. Denver, 2007 Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat. Rev. Genet. 8: 619-631.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 619-631
-
-
Baer, C.F.1
Miyamoto, M.M.2
Denver, D.R.3
-
2
-
-
33846597082
-
Physical and functional interactions between Escherichia coli MutY glycosylase and mismatch repair protein MutS
-
Bai, H., and A.-L. Lu, 2007 Physical and functional interactions between Escherichia coli MutY glycosylase and mismatch repair protein MutS. J. Bacteriol. 189: 902-910.
-
(2007)
J. Bacteriol.
, vol.189
, pp. 902-910
-
-
Bai, H.1
Lu, A.-L.2
-
3
-
-
0001057383
-
The viability of near-normal irradiated chromosomes
-
Bateman, A. J., 1959 The viability of near-normal irradiated chromosomes. Int. J. Radiat. Biol. 1: 170-180.
-
(1959)
Int. J. Radiat. Biol.
, vol.1
, pp. 170-180
-
-
Bateman, A.J.1
-
4
-
-
84953775974
-
Genome wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation
-
Behringer, M. G., and D. W. Hall, 2015 Genome wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation. G3 (Bethesda) 6: 149-160.
-
(2015)
G3 (Bethesda)
, vol.6
, pp. 149-160
-
-
Behringer, M.G.1
Hall, D.W.2
-
5
-
-
0035448545
-
The evolution of mycobacterial pathogenicity: clues from comparative genomics
-
Brosch, R., A. S. Pym, S. V. Gordon, and S. T. Cole, 2001 The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9: 452-458.
-
(2001)
Trends Microbiol.
, vol.9
, pp. 452-458
-
-
Brosch, R.1
Pym, A.S.2
Gordon, S.V.3
Cole, S.T.4
-
6
-
-
69549116107
-
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
-
Chen, K., J. W. Wallis, M. D. McLellan, D. E. Larson, J. M. Kalicki et al., 2009 BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6: 677-681.
-
(2009)
Nat. Methods
, vol.6
, pp. 677-681
-
-
Chen, K.1
Wallis, J.W.2
McLellan, M.D.3
Larson, D.E.4
Kalicki, J.M.5
-
7
-
-
84857877933
-
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
-
Clark, T. A., I. A. Murray, R. D. Morgan, A. O. Kislyuk, K. E. Spittle et al., 2012 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res. 40: e29.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Clark, T.A.1
Murray, I.A.2
Morgan, R.D.3
Kislyuk, A.O.4
Spittle, K.E.5
-
8
-
-
0032508046
-
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
-
Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher et al., 1998 Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
-
(1998)
Nature
, vol.393
, pp. 537-544
-
-
Cole, S.T.1
Brosch, R.2
Parkhill, J.3
Garnier, T.4
Churcher, C.5
-
9
-
-
34250900982
-
Base-excision repair of oxidative DNA damage
-
David, S. S., V. L. O'Shea, and S. Kundu, 2007 Base-excision repair of oxidative DNA damage. Nature 447: 941-950.
-
(2007)
Nature
, vol.447
, pp. 941-950
-
-
David, S.S.1
O'Shea, V.L.2
Kundu, S.3
-
10
-
-
78650114501
-
Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis
-
Debora, B. N., L. E. Vidales, R. Ramirez, M. Ramirez, E. A. Robleto et al., 2011 Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis. J. Bacteriol. 193: 236-245.
-
(2011)
J. Bacteriol.
, vol.193
, pp. 236-245
-
-
Debora, B.N.1
Vidales, L.E.2
Ramirez, R.3
Ramirez, M.4
Robleto, E.A.5
-
11
-
-
70349507538
-
A genome-wide view of Caenorhabditis elegans base-substitution mutation processes
-
Denver, D. R., P. C. Dolan, L. J. Wilhelm, W. Sung, J. I. Lucas-Lledó et al., 2009 A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proc. Natl. Acad. Sci. USA 106: 16310-16314.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 16310-16314
-
-
Denver, D.R.1
Dolan, P.C.2
Wilhelm, L.J.3
Sung, W.4
Lucas-Lledó, J.I.5
-
12
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A., E. Banks, R. Poplin, and K. V. GarimellaMaguire, J. R. et al., 2011 A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498.
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
-
13
-
-
84937043154
-
The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia
-
Dillon, M. M., W. Sung, M. Lynch, and V. S. Cooper, 2015 The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia. Genetics 200: 935-946.
-
(2015)
Genetics
, vol.200
, pp. 935-946
-
-
Dillon, M.M.1
Sung, W.2
Lynch, M.3
Cooper, V.S.4
-
14
-
-
64349108498
-
DNA repair in Mycobacterium tuberculosis revisited
-
Dos Vultos, T., O. Mestre, T. Tonjum, and B. Gicquel, 2009 DNA repair in Mycobacterium tuberculosis revisited. FEMS Microbiol. Rev. 33: 471-487.
-
(2009)
FEMS Microbiol. Rev.
, vol.33
, pp. 471-487
-
-
Dos Vultos, T.1
Mestre, O.2
Tonjum, T.3
Gicquel, B.4
-
15
-
-
0025886466
-
A constant rate of spontaneous mutation in DNA-based microbes
-
Drake, J. W., 1991 A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 7160-7164
-
-
Drake, J.W.1
-
16
-
-
0020461949
-
Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli
-
Duncan, B. K., and B. Weiss, 1982 Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 151: 750-755.
-
(1982)
J. Bacteriol.
, vol.151
, pp. 750-755
-
-
Duncan, B.K.1
Weiss, B.2
-
17
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
Eyre-Walker, A., and P. D. Keightley, 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, A.1
Keightley, P.D.2
-
18
-
-
84941668361
-
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe
-
Farlow, A., H. Long, S. Arnoux, W. Sung, T. G. Doak et al., 2015 The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics 201: 737-744.
-
(2015)
Genetics
, vol.201
, pp. 737-744
-
-
Farlow, A.1
Long, H.2
Arnoux, S.3
Sung, W.4
Doak, T.G.5
-
19
-
-
79955460244
-
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
-
Ford, C. B., P. L. Lin, M. R. Chase, R. R. Shah, O. Iartchouk et al., 2011 Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet. 43: 482-486.
-
(2011)
Nat. Genet.
, vol.43
, pp. 482-486
-
-
Ford, C.B.1
Lin, P.L.2
Chase, M.R.3
Shah, R.R.4
Iartchouk, O.5
-
20
-
-
84879682699
-
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
-
Ford, C. B., R. R. Shah, M. K. Maeda, S. Gagneux, M. B. Murray et al., 2013 Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat. Genet. 45: 784-790.
-
(2013)
Nat. Genet.
, vol.45
, pp. 784-790
-
-
Ford, C.B.1
Shah, R.R.2
Maeda, M.K.3
Gagneux, S.4
Murray, M.B.5
-
21
-
-
84867383562
-
The presence of the DNA repair genes mutM, mutY, mutL, and mutS is related to proteome size in bacterial genomes
-
Garcia-Gonzales, A., R. J. Rivera-Rivera, and S. E. Massey, 2012 The presence of the DNA repair genes mutM, mutY, mutL, and mutS is related to proteome size in bacterial genomes. Front. Genet. 3: 1-11.
-
(2012)
Front. Genet.
, vol.3
, pp. 1-11
-
-
Garcia-Gonzales, A.1
Rivera-Rivera, R.J.2
Massey, S.E.3
-
22
-
-
84966300362
-
Fundamentals of Molecular Evolution
-
Sinauer Associates, Sunderland, MA.
-
Graur, D., and W. H. Li, 2000 Fundamentals of Molecular Evolution, Sinauer Associates, Sunderland, MA.
-
(2000)
-
-
Graur, D.1
Li, W.H.2
-
23
-
-
77951697965
-
Spontaneous mutation accumulation studies in evolutionary genetics
-
Halligan, D. L., and P. D. Keightley, 2009 Spontaneous mutation accumulation studies in evolutionary genetics. Annu. Rev. Ecol. Evol. Syst. 40: 151-172.
-
(2009)
Annu. Rev. Ecol. Evol. Syst.
, vol.40
, pp. 151-172
-
-
Halligan, D.L.1
Keightley, P.D.2
-
24
-
-
20844442964
-
Variation in efficiency of DNA mismatch repair at different sites in the yeast genome
-
Hawk, J. D., L. Stefanovic, J. C. Boyer, T. D. Petes, and R. A. Farber, 2005 Variation in efficiency of DNA mismatch repair at different sites in the yeast genome. Proc. Natl. Acad. Sci. USA 102: 8639-8643.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 8639-8643
-
-
Hawk, J.D.1
Stefanovic, L.2
Boyer, J.C.3
Petes, T.D.4
Farber, R.A.5
-
25
-
-
0029119607
-
DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences
-
Hemavathy, K. C., and V. Nagaraja, 1995 DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences. FEMS Immunol. Med. Microbiol. 11: 291-296.
-
(1995)
FEMS Immunol. Med. Microbiol.
, vol.11
, pp. 291-296
-
-
Hemavathy, K.C.1
Nagaraja, V.2
-
26
-
-
78049445172
-
Evidence that mutation is universally biased towards AT in bacteria
-
Hershberg, R., and D. A. Petrov, 2010 Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 6: e1001115.
-
(2010)
PLoS Genet.
, vol.6
-
-
Hershberg, R.1
Petrov, D.A.2
-
27
-
-
0141996214
-
Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8
-
Hoseki, J., A. Okamoto, R. Masui, T. Shibata, Y. Inoue et al., 2003 Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8. J. Mol. Biol. 333: 515-526.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 515-526
-
-
Hoseki, J.1
Okamoto, A.2
Masui, R.3
Shibata, T.4
Inoue, Y.5
-
28
-
-
84949501486
-
Univariate Discrete Distributions
-
Wiley-Interscience, Hoboken , NJ.
-
Johnson, N. L., and A. W. Kemp, 1993 Univariate Discrete Distributions, Wiley-Interscience, Hoboken , NJ.
-
(1993)
-
-
Johnson, N.L.1
Kemp, A.W.2
-
29
-
-
67650064592
-
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
-
Keightley, P. D., U. Trivedi, M. Thomson, F. Oliver, S. Kumar et al., 2009 Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19: 1195-1201.
-
(2009)
Genome Res.
, vol.19
, pp. 1195-1201
-
-
Keightley, P.D.1
Trivedi, U.2
Thomson, M.3
Oliver, F.4
Kumar, S.5
-
30
-
-
84901295203
-
Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
-
Keightley, P. D., R. W. Ness, D. L. Halligan, and P. R. Haddrill, 2014 Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics 196: 313-320.
-
(2014)
Genetics
, vol.196
, pp. 313-320
-
-
Keightley, P.D.1
Ness, R.W.2
Halligan, D.L.3
Haddrill, P.R.4
-
31
-
-
84922371114
-
Estimation of the spontaneous mutation rate in Heliconius melpomene
-
Keightley, P. D., A. Pinharanda, R. W. Ness, F. Simpson, K. K. Dasmahapatra et al., 2015 Estimation of the spontaneous mutation rate in Heliconius melpomene. Mol. Biol. Evol. 32: 239-243.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 239-243
-
-
Keightley, P.D.1
Pinharanda, A.2
Ness, R.W.3
Simpson, F.4
Dasmahapatra, K.K.5
-
32
-
-
0029026635
-
DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine
-
Kelman, Z., and M. O'Donnell, 1995 DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64: 171-200.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 171-200
-
-
Kelman, Z.1
O'Donnell, M.2
-
33
-
-
0029931416
-
Estimate of the genomic mutation rate deleterious to overall fitness in E
-
Kibota, T. T., and M. Lynch, 1996 Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature 381: 694-696.
-
(1996)
coli. Nature
, vol.381
, pp. 694-696
-
-
Kibota, T.T.1
Lynch, M.2
-
34
-
-
0038104364
-
Competition between MutY and mismatch repair at A-C mispairs in vivo
-
Kim, M., T. Huang, and J. H. Miller, 2003 Competition between MutY and mismatch repair at A-C mispairs in vivo. J. Bacteriol. 185: 4626-4629.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 4626-4629
-
-
Kim, M.1
Huang, T.2
Miller, J.H.3
-
35
-
-
84959609205
-
On the evolutionary adjustment of spontaneous mutation rates
-
Kimura, M., 2009 On the evolutionary adjustment of spontaneous mutation rates. Genet. Res. 9: 23.
-
(2009)
Genet. Res.
, vol.9
, pp. 23
-
-
Kimura, M.1
-
36
-
-
2342419732
-
DNA replication fidelity
-
Kunkel, T. A., 2004 DNA replication fidelity. J. Biol. Chem. 279: 16895-16898.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 16895-16898
-
-
Kunkel, T.A.1
-
38
-
-
84896523433
-
Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast
-
Lang, G. I., L. Parsons, and A. E. Gammie, 2013 Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3 (Bethesda) 3: 1453-1465.
-
(2013)
G3 (Bethesda)
, vol.3
, pp. 1453-1465
-
-
Lang, G.I.1
Parsons, L.2
Gammie, A.E.3
-
39
-
-
84867339877
-
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
-
Lee, H., E. Popodi, H. Tang, and P. L. Foster, 2012 Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl. Acad. Sci. USA 109: E2774-E2783.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. E2774-E2783
-
-
Lee, H.1
Popodi, E.2
Tang, H.3
Foster, P.L.4
-
40
-
-
80052396623
-
New family of deamination repair enzymes in uracil-DNA glycosylase superfamily
-
Lee, H. W., B. N. Dominy, and W. Cao, 2011 New family of deamination repair enzymes in uracil-DNA glycosylase superfamily. J. Biol. Chem. 286: 31282-31287.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 31282-31287
-
-
Lee, H.W.1
Dominy, B.N.2
Cao, W.3
-
41
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
42
-
-
68549104404
-
The sequence alignment/map (SAM) format and SAMtools
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
43
-
-
84943608703
-
Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans.
-
Long, H., S. Kucukyildirim, W. Sung, E. Williams, H. Lee et al., 2015a Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Mol. Biol. Evol. 32: 2383-2392.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 2383-2392
-
-
Long, H.1
Kucukyildirim, S.2
Sung, W.3
Williams, E.4
Lee, H.5
-
44
-
-
84928236984
-
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens ATCC948
-
Long, H., W. Sung, S. F. Miller, M. Ackerman, T. G. Doak et al., 2015b Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens ATCC948. Genome Biol. Evol. 7: 262-271.
-
(2015)
Genome Biol. Evol.
, vol.7
, pp. 262-271
-
-
Long, H.1
Sung, W.2
Miller, S.F.3
Ackerman, M.4
Doak, T.G.5
-
45
-
-
84855910162
-
Roles of endonuclease V, uracil-DNA glycosylase, and mismatch repair in Bacillus subtilis DNA base-deamination-induced mutagenesis
-
López-Olmos, K., M. P. Hernández, J. A. Contreras-Garduño, E. A. Robleto, P. Setlow et al., 2012 Roles of endonuclease V, uracil-DNA glycosylase, and mismatch repair in Bacillus subtilis DNA base-deamination-induced mutagenesis. J. Bacteriol. 194: 243-252.
-
(2012)
J. Bacteriol.
, vol.194
, pp. 243-252
-
-
López-Olmos, K.1
Hernández, M.P.2
Contreras-Garduño, J.A.3
Robleto, E.A.4
Setlow, P.5
-
46
-
-
34250709215
-
The Origins of Genome Architecture
-
Sinauer Associates, Sunderland, MA.
-
Lynch, M., 2007 The Origins of Genome Architecture, Sinauer Associates, Sunderland, MA.
-
(2007)
-
-
Lynch, M.1
-
47
-
-
77955090647
-
Evolution of the mutation rate
-
Lynch, M., 2010 Evolution of the mutation rate. Trends Genet. 26: 345-352.
-
(2010)
Trends Genet.
, vol.26
, pp. 345-352
-
-
Lynch, M.1
-
48
-
-
80052736277
-
The lower bound to the evolution of mutation rates
-
Lynch, M., 2011 The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 1107-1118
-
-
Lynch, M.1
-
49
-
-
84869212334
-
Evolutionary layering and the limits to cellular perfection
-
Lynch, M., 2012 Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 18851-18856
-
-
Lynch, M.1
-
50
-
-
48249133274
-
A genome-wide view of the spectrum of spontaneous mutations in yeast
-
Lynch, M., W. Sung, K. Morris, N. Coffey, C. R. Landry et al., 2008 A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl. Acad. Sci. USA 105: 9272-9277.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 9272-9277
-
-
Lynch, M.1
Sung, W.2
Morris, K.3
Coffey, N.4
Landry, C.R.5
-
51
-
-
77749301852
-
Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis
-
Malshetty, V. S., R. Jain, T. Srinath, K. Kurthkoti, and U. Varshney, 2010 Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis. Microbiology 156: 940-949.
-
(2010)
Microbiology
, vol.156
, pp. 940-949
-
-
Malshetty, V.S.1
Jain, R.2
Srinath, T.3
Kurthkoti, K.4
Varshney, U.5
-
52
-
-
77956295988
-
The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. H. M., E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky et al., 2010 The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.H.M.1
Banks, E.2
Sivachenko, A.3
Cibulskis, K.4
Kernytsky, A.5
-
53
-
-
0035479142
-
Deletional bias and the evolution of bacterial genomes
-
Mira, A., H. Ochman, and N. A. Moran, 2001 Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589-596.
-
(2001)
Trends Genet.
, vol.17
, pp. 589-596
-
-
Mira, A.1
Ochman, H.2
Moran, N.A.3
-
54
-
-
85007151998
-
Complete genome sequences of a Mycobacterium smegmatis laboratory strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains
-
Mohan, A., J. Padiadpu, P. Baloni, and N. Chandra, 2015 Complete genome sequences of a Mycobacterium smegmatis laboratory strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains. Genome Announc. 3: e01520-e01514.
-
(2015)
Genome Announc.
, vol.3
, pp. e01520-e01514
-
-
Mohan, A.1
Padiadpu, J.2
Baloni, P.3
Chandra, N.4
-
55
-
-
70549103951
-
Comparative genomic and phylogeographic analysis of Mycobacterium leprae
-
Monot, M., N. Honore, T. Garnier, N. Zidane, D. Sherafi et al., 2009 Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat. Genet. 41: 1282-1289.
-
(2009)
Nat. Genet.
, vol.41
, pp. 1282-1289
-
-
Monot, M.1
Honore, N.2
Garnier, T.3
Zidane, N.4
Sherafi, D.5
-
56
-
-
0002129633
-
The genetic structure of natural populations of Drosophila melanogaster I. Spontaneous mutation rate of polygenes controlling viability.
-
Mukai, T., 1964 The genetic structure of natural populations of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability. Genetics 50: 1-19.
-
(1964)
Genetics
, vol.50
, pp. 1-19
-
-
Mukai, T.1
-
57
-
-
33747830026
-
Artificial transmutation of the gene
-
Muller, H. J., 1927 Artificial transmutation of the gene. Science 66: 84-87.
-
(1927)
Science
, vol.66
, pp. 84-87
-
-
Muller, H.J.1
-
58
-
-
0000775877
-
The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature
-
Muller, H. J., 1928 The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature. Genetics 13: 279-357.
-
(1928)
Genetics
, vol.13
, pp. 279-357
-
-
Muller, H.J.1
-
59
-
-
84946572905
-
Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
-
Ness, R. W., A. D. Morgan, R. B. Vasanthakrishnan, N. Colegrave, and P. D. Keightley, 2015 Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome Res. 25: 1739-1749.
-
(2015)
Genome Res.
, vol.25
, pp. 1739-1749
-
-
Ness, R.W.1
Morgan, A.D.2
Vasanthakrishnan, R.B.3
Colegrave, N.4
Keightley, P.D.5
-
60
-
-
0021910963
-
Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells
-
Nikolaskaya, I. I., N. G. Lopatina, E. V. Sharkova, and S. V. Suchkov, P. Somody et al., 1985 Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells. Biochem. Int. 10: 405-413.
-
(1985)
Biochem. Int.
, vol.10
, pp. 405-413
-
-
Nikolaskaya, I.I.1
Lopatina, N.G.2
Sharkova, E.V.3
Suchkov, S.V.4
Somody, P.5
-
61
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
Ossowski, S., K. Schneeberger, J. I. Lucas-Lledó, N. Warthmann, R. M. Clark et al., 2010 The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
-
(2010)
Science
, vol.327
, pp. 92-94
-
-
Ossowski, S.1
Schneeberger, K.2
Lucas-Lledó, J.I.3
Warthmann, N.4
Clark, R.M.5
-
62
-
-
0034734383
-
Structure and function in the uracil-DNA glycosylase superfamily
-
Pearl, L. H., 2000 Structure and function in the uracil-DNA glycosylase superfamily. Mutat. Res. 460: 165-181.
-
(2000)
Mutat. Res.
, vol.460
, pp. 165-181
-
-
Pearl, L.H.1
-
63
-
-
0032530427
-
Uracil DNA glycosylase from Mycobacterium smegmatis and its distinct biochemical properties
-
Purnapatre, K., and U. Varshney, 1998 Uracil DNA glycosylase from Mycobacterium smegmatis and its distinct biochemical properties. Eur. J. Biochem. 256: 580-588.
-
(1998)
Eur. J. Biochem.
, vol.256
, pp. 580-588
-
-
Purnapatre, K.1
Varshney, U.2
-
64
-
-
84963641621
-
R: A Language and Environment for Statistical Computing
-
R Foundation for Statistical Computing, Vienna, Austria.
-
R Development Core Team, 2014 R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.
-
(2014)
-
-
-
65
-
-
84930090059
-
DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader
-
Rock, J. M., U. F. Lang, M. R. Chase, C. B. Ford, E. R. Gerrick et al., 2015 DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nat. Genet. 47: 677-681.
-
(2015)
Nat. Genet.
, vol.47
, pp. 677-681
-
-
Rock, J.M.1
Lang, U.F.2
Chase, M.R.3
Ford, C.B.4
Gerrick, E.R.5
-
66
-
-
0037124349
-
A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site
-
Sartori, A. A., S. Fitz-Gibbon, H. Yang, J. H. Miller, and J. Jiricny, 2002 A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site. EMBO J. 21: 3182-3191.
-
(2002)
EMBO J.
, vol.21
, pp. 3182-3191
-
-
Sartori, A.A.1
Fitz-Gibbon, S.2
Yang, H.3
Miller, J.H.4
Jiricny, J.5
-
67
-
-
0027482444
-
Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli
-
Schaaper, R. M., 1993 Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 268: 23762-23765.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 23762-23765
-
-
Schaaper, R.M.1
-
68
-
-
0025953766
-
Spontaneous mutation in the Escherichia coli lac I gene
-
Schaaper, R. M., and R. L. Dunn, 1991 Spontaneous mutation in the Escherichia coli lac I gene. Genetics 129: 317-326.
-
(1991)
Genetics
, vol.129
, pp. 317-326
-
-
Schaaper, R.M.1
Dunn, R.L.2
-
69
-
-
0024374370
-
The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical
-
Schlagman, S. L., and S. Hattman, 1989 The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical. Nucleic Acids Res. 17: 9101-9112.
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 9101-9112
-
-
Schlagman, S.L.1
Hattman, S.2
-
70
-
-
84930226215
-
The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding
-
Sharma, G., S. Upadhyay, M. Srilalitha, V. K. Nandicoori, and S. Khosla, 2015 The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding. Nucleic Acids Res. 43: 3922-3937.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 3922-3937
-
-
Sharma, G.1
Upadhyay, S.2
Srilalitha, M.3
Nandicoori, V.K.4
Khosla, S.5
-
71
-
-
84884753898
-
DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis
-
Shell, S. S., E. G. Prestwich, S. H. Baek, R. R. Shah, C. M. Sassetti et al., 2013 DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PLoS Pathog. 9: e1003419.
-
(2013)
PLoS Pathog.
, vol.9
-
-
Shell, S.S.1
Prestwich, E.G.2
Baek, S.H.3
Shah, R.R.4
Sassetti, C.M.5
-
72
-
-
75249096198
-
To catch a killer What can mycobacterial models teach us about Mycobacterium tuberculosis pathogenesis?
-
Shiloh, M. U., and P. A. DiGiuseppe Champion, 2010 To catch a killer. What can mycobacterial models teach us about Mycobacterium tuberculosis pathogenesis? Curr. Opin. Microbiol. 13: 86-92.
-
(2010)
Curr. Opin. Microbiol.
, vol.13
, pp. 86-92
-
-
Shiloh, M.U.1
DiGiuseppe Champion, P.A.2
-
73
-
-
67649407565
-
Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis
-
Smith, N. H., R. G. Hewinson, K. Kremer, R. Brosch, and S. V. Gordon, 2009 Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis. Nat. Rev. Microbiol. 7: 537-544.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 537-544
-
-
Smith, N.H.1
Hewinson, R.G.2
Kremer, K.3
Brosch, R.4
Gordon, S.V.5
-
74
-
-
0025081151
-
Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis
-
Snapper, S. B., R. E. Melton, S. Mustafa, T. Kieser, and W. R. Jacobs, Jr., 1990 Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol. Microbiol. 4: 1911-1919.
-
(1990)
Mol. Microbiol.
, vol.4
, pp. 1911-1919
-
-
Snapper, S.B.1
Melton, R.E.2
Mustafa, S.3
Kieser, T.4
Jacobs, W.R.5
-
75
-
-
84874623094
-
Mutation rates: how low can you go? Curr
-
Sniegowski, P., and Y. Raynes, 2013 Mutation rates: how low can you go? Curr. Biol. 23: R147-R149.
-
(2013)
Biol.
, vol.23
, pp. R147-R149
-
-
Sniegowski, P.1
Raynes, Y.2
-
76
-
-
0030931719
-
Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination
-
Sreevatsan, S., X. Pan, K. E. Stockbauer, N. D. Connell, B. N. Kreiswirth et al., 1997 Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94: 9869-9874.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 9869-9874
-
-
Sreevatsan, S.1
Pan, X.2
Stockbauer, K.E.3
Connell, N.D.4
Kreiswirth, B.N.5
-
77
-
-
34548534747
-
Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis
-
Srinath, T., S. K. Bharti, and U. Varshney, 2007 Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis. DNA Repair (Amst.) 6: 1517-1528.
-
(2007)
DNA Repair (Amst.)
, vol.6
, pp. 1517-1528
-
-
Srinath, T.1
Bharti, S.K.2
Varshney, U.3
-
79
-
-
0037052965
-
A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus
-
Starkuviene, V., and H.-J. Fritz, 2002 A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res. 30: 2097-2102.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2097-2102
-
-
Starkuviene, V.1
Fritz, H.-J.2
-
80
-
-
84868599895
-
Drift-barrier hypothesis and mutation rate evolution
-
Sung, W., M. S. Ackerman, S. F. Miller, T. G. Doak, and M. Lynch, 2012a Drift-barrier hypothesis and mutation rate evolution. Proc. Natl. Acad. Sci. USA 109: 18488-18492.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 18488-18492
-
-
Sung, W.1
Ackerman, M.S.2
Miller, S.F.3
Doak, T.G.4
Lynch, M.5
-
81
-
-
84868579284
-
Extraordinary genome stability in the ciliate Paramecium tetraurelia
-
Sung, W., A. E. Tucker, T. G. Doak, E. Choi, W. K. Thomas et al., 2012b Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc. Natl. Acad. Sci. USA 109: 19339-19344.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 19339-19344
-
-
Sung, W.1
Tucker, A.E.2
Doak, T.G.3
Choi, E.4
Thomas, W.K.5
-
82
-
-
84936850349
-
Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments
-
Sung, W., M. S. Ackerman, J.-F. Gout, S. F. Miller, E.Williams et al., 2015 Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments. Mol. Biol. Evol. 32: 1672-1683.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 1672-1683
-
-
Sung, W.1
Ackerman, M.S.2
Gout, J.-F.3
Miller, S.F.4
Williams, E.5
-
83
-
-
84923070685
-
The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens
-
van der Veen, S., and C. M. Tang, 2015 The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens. Nat. Rev. Microbiol. 13: 83-94.
-
(2015)
Nat. Rev. Microbiol.
, vol.13
, pp. 83-94
-
-
van der Veen, S.1
Tang, C.M.2
-
84
-
-
0036628726
-
Biological consequences of free radical-damaged DNA bases
-
Wallace, S. S., 2002 Biological consequences of free radical-damaged DNA bases. Free Radic. Biol. Med. 33: 1-14.
-
(2002)
Free Radic. Biol. Med.
, vol.33
, pp. 1-14
-
-
Wallace, S.S.1
-
85
-
-
70350469035
-
The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination
-
Wanner, R. M., D. Castor, C. Güthlein, E. C. Böttger, B. Springer et al., 2009 The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination. J. Bacteriol. 191: 6312-6319.
-
(2009)
J. Bacteriol.
, vol.191
, pp. 6312-6319
-
-
Wanner, R.M.1
Castor, D.2
Güthlein, C.3
Böttger, E.C.4
Springer, B.5
-
86
-
-
84856220271
-
Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli
-
Wielgoss, S., J. E. Barrick, O. Tenaillon, S. Cruveiller, B. Chane-Woon-Ming et al., 2011 Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3 (Bethesda) 1: 183-186.
-
(2011)
G3 (Bethesda)
, vol.1
, pp. 183-186
-
-
Wielgoss, S.1
Barrick, J.E.2
Tenaillon, O.3
Cruveiller, S.4
Chane-Woon-Ming, B.5
-
87
-
-
70350694443
-
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
Ye, K., M. H. Schulz, Q. Long, R. Apweiler, and Z. Ning, 2009 Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865-2871.
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-2871
-
-
Ye, K.1
Schulz, M.H.2
Long, Q.3
Apweiler, R.4
Ning, Z.5
-
88
-
-
0034707047
-
The DNA damage response: putting checkpoints in perspective
-
Zhou, B. B., and S. J. Elledge, 2000 The DNA damage response: putting checkpoints in perspective. Nature 408: 433-439.
-
(2000)
Nature
, vol.408
, pp. 433-439
-
-
Zhou, B.B.1
Elledge, S.J.2
-
89
-
-
84966424770
-
Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology
-
Zhu, L., J. Zhong, X. Jia, G. Liu, Y. Kang et al., 2016 Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology. Nucleic Acids Res. 44: 730-743.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. 730-743
-
-
Zhu, L.1
Zhong, J.2
Jia, X.3
Liu, G.4
Kang, Y.5
-
90
-
-
84901824457
-
Precise estimates of mutation rate and spectrum in yeast
-
Zhu, Y. O., M. L. Siegal, D. W. Hall, and D. A. Petrov, 2014 Precise estimates of mutation rate and spectrum in yeast. Proc. Natl. Acad. Sci. USA 111: E2310-E2318.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. E2310-E2318
-
-
Zhu, Y.O.1
Siegal, M.L.2
Hall, D.W.3
Petrov, D.A.4
|