-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
DOI 10.1093/bioinformatics/bti263
-
Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105. (Pubitemid 40668057)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
0037424520
-
The main role of human thymine-DNA glycosylase is removal of thymine produced by deamination of 5-methylcytosine and not removal of ethenocytosine
-
DOI 10.1074/jbc.M211084200
-
Abu M., Waters TR. 2003. The main role of human thymine-DNA glycosylase is removal of thymine produced by deamination of 5-methylcytosine and not removal of ethenocytosine. J Biol Chem. 278:8739-8744. (Pubitemid 36800631)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.10
, pp. 8739-8744
-
-
Abu, M.1
Waters, T.R.2
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
21844464297
-
C→T mutagenesis and γ-radiation sensitivity due to deficiency in the Smug1 and Ung DNA glycosylases
-
DOI 10.1038/sj.emboj.7600689
-
An Q, Robins P, Lindahl T, Barnes D. 2005. C → T mutagenesis and γ-radiation sensitivity due to deficiency in the Smug1 and Ung DNA glycosylases. EMBOJ. 24:2205-2213. (Pubitemid 40961804)
-
(2005)
EMBO Journal
, vol.24
, Issue.12
, pp. 2205-2213
-
-
An, Q.1
Robins, P.2
Lindahl, T.3
Barnes, D.E.4
-
5
-
-
0034576553
-
The α/β uracil DNA glycosylases: A common origin with diverse fates
-
research0007.1-research0007.8
-
Aravind L, Koonin EV. 2000. The α/β uracil DNA glycosylases: a common origin with diverse fates. Genome Biol. 1: research0007.1-research0007. 8.
-
(2000)
Genome Biol.
, vol.1
-
-
Aravind, L.1
Koonin, E.V.2
-
6
-
-
34447564992
-
Mutation rate variation in multicellular eukaryotes: Causes and consequences
-
DOI 10.1038/nrg2158, PII NRG2158
-
Baer CF, Miyamoto MM, Denver DR. 2007. Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat Rev Genet. 8:619-631. (Pubitemid 47077282)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.8
, pp. 619-631
-
-
Baer, C.F.1
Miyamoto, M.M.2
Denver, D.R.3
-
7
-
-
0024472831
-
Polygenetic evidence of a role for 5-hydroxymethyluracil-DNA glycosylase in the maintenance of 5-methylcytosine in DNA
-
Boorstein RJ, Chiu LN, Teebor G. 1989. Phylogenetic evidence of a role for 5-hydroxymethyluracil-DNA glycosylase in the maintenance of 5-methylcytosine in DNA. Nucleic Acids Res. 17:7653-7661. (Pubitemid 19251939)
-
(1989)
Nucleic Acids Research
, vol.17
, Issue.19
, pp. 7653-7661
-
-
Boorstein, R.J.1
Chiu, L.-N.2
Teebor, G.W.3
-
8
-
-
0035834708
-
Definitive identification ofmammalian 5-hydroxymethyluracil DNAN-glycosylaseactivity as SMUG1
-
Boorstein RJ, Cummings A Jr, Marenstein DR, Chan MK, Ma Y, Neubert TA, Brown SM, Teebor GW. 2001. Definitive identification ofmammalian 5-hydroxymethyluracil DNAN-glycosylaseactivity as SMUG1. J Biol Chem. 276:41991-41997.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 41991-41997
-
-
Boorstein, R.J.1
Cummings Jr., A.2
Marenstein, D.R.3
Chan, M.K.4
Ma, Y.5
Neubert, T.A.6
Brown, S.M.7
Teebor, G.W.8
-
9
-
-
0022626963
-
Selection by genetic transformation of a Saccharomyces cerevisiae mutant defective for the nuclear uracil-DNA-glycosylase
-
Burgers PMJ, Klein MB. 1986. Selection by genetic transformation of a Saccharomyces cerevisiae mutant defective for the nuclear uracil-DNA-glycosylase J Bacteriol. 166:905-913. (Pubitemid 16098174)
-
(1986)
Journal of Bacteriology
, vol.166
, Issue.3
, pp. 905-913
-
-
Burgers, P.M.J.1
Klein, M.B.2
-
10
-
-
0035945231
-
Uracil-DNA glycosylase-deficient yeast exhibit a mitochondrial mutator phenotype
-
Chatterjee A, Singh KK. 2001. Uracil-DNA glycosylase-deficient yeast exhibit a mitochondrial mutator phenotype. Nucleic Acids Res. 29:4935-4940. (Pubitemid 34065407)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.24
, pp. 4935-4940
-
-
Chatterjee, A.1
Singh, K.K.2
-
11
-
-
0026097666
-
Role of uracil-DNA glycosylase in mutation avoidance by Streptococcus pneumoniae
-
Chen JD, Lacks SA 1991. Role of uracil-DNA glycosylase in mutation avoidance by Streptococcus pneumoniae. J Bacteriol. 173:283-290.
-
(1991)
J. Bacteriol.
, vol.173
, pp. 283-290
-
-
Chen, J.D.1
Lacks, S.A.2
-
12
-
-
0037799511
-
A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily
-
DOI 10.1093/nar/gkg319
-
Chung JH, Im EK, Park HY, Kwon JH, Lee S, Oh J, Hwang KC, Lee JH, Jang Y. 2003. A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily. Nucleic Acids Res. 31:2045-2055. (Pubitemid 37442072)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.8
, pp. 2045-2055
-
-
Chung, J.H.1
Im, E.K.2
Park, H.-Y.3
Kwon, J.H.4
Lee, S.5
Oh, J.6
Hwang, K.-C.7
Lee, J.H.8
Jang, Y.9
-
13
-
-
33846072878
-
The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data
-
DOI 10.1093/nar/gkl889
-
Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35: D169-D172. (Pubitemid 46056192)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam-Syed-Mohideen, A.S.5
McGarrell, D.M.6
Bandela, A.M.7
Cardenas, E.8
Garrity, G.M.9
Tiedje, J.M.10
-
14
-
-
70349507538
-
A genome-wide view of Caenorhabditis elegans base-substitution mutation processes
-
11 co-authors
-
Denver DR, Dolan PC, Wilhelm LJ, et al. (11 co-authors). 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
-
15
-
-
3343022751
-
An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases
-
DOI 10.1093/molbev/msg177
-
Denver DR, Swenson SL, Lynch M. 2003. An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Mol Biol Evol. 20:1603-1611. (Pubitemid 41070821)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.10
, pp. 1603-1611
-
-
Denver, D.R.1
Swenson, S.L.2
Lynch, M.3
-
16
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DOI 10.1128/AEM.03006-05
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 72:5069-5072. (Pubitemid 44078840)
-
(2006)
Applied and Environmental Microbiology
, vol.72
, Issue.7
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
17
-
-
18844434472
-
Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins
-
DOI 10.1042/BJ20041661
-
Dionne I, Bell SD. 2005. Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Biochem J. 387:859-863. (Pubitemid 40685722)
-
(2005)
Biochemical Journal
, vol.387
, Issue.3
, pp. 859-863
-
-
Dionne, I.1
Bell, S.D.2
-
18
-
-
0023782193
-
Purification and properties of mitochondrial uracil-DNA glycosylase from rat liver
-
Domena JD, Timmer RT, Dicharry SA, Mosbaugh DW. 1988. Purification and properties of mitochondrial uracil-DNA glycosylase from rat liver. Biochemistry 27:6742-6751.
-
(1988)
Biochemistry
, vol.27
, pp. 6742-6751
-
-
Domena, J.D.1
Timmer, R.T.2
Dicharry, S.A.3
Mosbaugh, D.W.4
-
20
-
-
0029078029
-
Biological basis of germline mutation: Comparisons of spontaneous germline mutation rates among Drosophila, mouse, and human
-
Drost JB, Lee WR. 1995. Biological basis of germline mutation: comparisons of spontaneous germline mutation rates among Drosophila, mouse, and human. Environ Mol Mutagen. 25 (Suppl. 26):48):48-64.
-
(1995)
Environ. Mol. Mutagen
, vol.25
, Issue.26 SUPPL.
, pp. 48-64
-
-
Drost, J.B.1
Lee, W.R.2
-
21
-
-
0020461949
-
Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli
-
Duncan BK, Weiss B. 1982. Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J Bacteriol. 151:750-755. (Pubitemid 13230469)
-
(1982)
Journal of Bacteriology
, vol.151
, Issue.2
, pp. 750-755
-
-
Duncan, B.K.1
Weiss, B.2
-
22
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-763. (Pubitemid 28552108)
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
23
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
DOI 10.1093/nar/gkh340
-
Edgar RC 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
24
-
-
0032786233
-
A phylogenomic study of DNA repair genes, proteins, and processes
-
Eisen J A, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res. 435:171-213.
-
(1999)
Mutat Res.
, vol.435
, pp. 171-213
-
-
Eisen, J.A.1
Hanawalt, P.C.2
-
26
-
-
0029805081
-
A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase
-
DOI 10.1038/383735a0
-
Gallinari P, Jiricny J. 1996. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383:735-738. (Pubitemid 26360653)
-
(1996)
Nature
, vol.383
, Issue.6602
, pp. 735-738
-
-
Gallinari, P.1
Jiricny, J.2
-
27
-
-
11944256302
-
Procedures for the analysis of comparative data using phylogenetically independent contrasts
-
Garland T Jr, Harvey PH, Ives AR. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst Biol. 41:18-32.
-
(1992)
Syst. Biol.
, vol.41
, pp. 18-32
-
-
Garland Jr., T.1
Harvey, P.H.2
Ives, A.R.3
-
28
-
-
0033529945
-
A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil
-
DOI 10.1073/pnas.96.16.9045
-
Greagg MA, Fogg MJ, Panayotou G, Evans SJ, Connolly BA, Pearl LH. 1999. A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc Natl Acad Sci U S A. 96:9045-9050. (Pubitemid 29374704)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.16
, pp. 9045-9050
-
-
Greagg, M.A.1
Fogg, M.J.2
Panayotou, G.3
Evans, S.J.4
Connolly, B.A.5
Pearl, L.H.6
-
29
-
-
33645924354
-
dUTPase activity is critical to maintain genetic stability in Saccharomyces cerevisiae
-
DOI 10.1093/nar/gkl139
-
Guillet M, Van der Kemp PA, Boiteux S. 2006. dUTPase activity is critical to maintain genetic stability in Saccharomyces cerevisiae. Nucleic Acids Res. 34:2056-2066. (Pubitemid 44314204)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.7
, pp. 2056-2066
-
-
Guillet, M.1
Van Der Kemp, P.A.2
Boiteux, S.3
-
30
-
-
0002051540
-
BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser, 41:95-98.
-
(1999)
Nucl. Acids Symp. Ser.
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
31
-
-
0038074420
-
The versatile thymine DNA-glycosylase: A comparative characterization of the human, Drosophila and fission yeast orthologs
-
DOI 10.1093/nar/gkg344
-
Hardeland U, Bentele M, Jiricny J, Schär P. 2003. The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Nucleic Acids Res. 31:2261-2271. (Pubitemid 37442093)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.9
, pp. 2261-2271
-
-
Hardeland, U.1
Bentele, M.2
Jiricny, J.3
Schar, P.4
-
32
-
-
0033602148
-
Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors
-
DOI 10.1016/S0960-9822(99)80087-6
-
Haushalter KA, Stukenberg PT, Kirschner MW, Verdine GL. 1999. Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors. Curr Biol. 9:174-185. (Pubitemid 29120381)
-
(1999)
Current Biology
, vol.9
, Issue.4
, pp. 174-185
-
-
Haushalter, K.A.1
Stukenberg, P.T.2
Kirschner, M.W.3
Verdine, G.L.4
-
33
-
-
0033575886
-
The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
-
Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A. 1999. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401:301-304.
-
(1999)
Nature
, vol.401
, pp. 301-304
-
-
Hendrich, B.1
Hardeland, U.2
Ng, H.H.3
Jiricny, J.4
Bird, A.5
-
34
-
-
7544225525
-
Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis
-
DOI 10.1101/gad.1217204
-
Hoffman PD, Leonard JM, Lindberg GE, Bollmann SR, Hays JB. 2004. Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis. Genes Dev. 18:2676-2685. (Pubitemid 39453106)
-
(2004)
Genes and Development
, vol.18
, Issue.21
, pp. 2676-2685
-
-
Hoffman, P.D.1
Leonard, J.M.2
Lindberg, G.E.3
Bollmann, S.R.4
Hays, J.B.5
-
35
-
-
33749030720
-
Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori
-
DOI 10.1128/JB.00477-06
-
Huang S, Kang J, Blaser MJ. 2006. Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori. J Bacteriol. 188:6224-6234. (Pubitemid 44448564)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.17
, pp. 6224-6234
-
-
Huang, S.1
Kang, J.2
Blaser, M.J.3
-
36
-
-
0025790276
-
The spectrum of spontaneous mutations in a Saccharomyces cerevisiae uracil-DNA-glycosylase mutant limits the function of this enzyme to cytosine deamination repair
-
Impellizzeri KJ, Anderson B, Burgers PMJ. 1991. The spectrum of spontaneous mutations in a Saccharomyces cerevisiae uracil-DNA-glycosylase mutant limits the function of this enzyme to cytosine deamination repair. J Bacteriol. 173:6807-6810.
-
(1991)
J. Bacteriol.
, vol.173
, pp. 6807-6810
-
-
Impellizzeri, K.J.1
Anderson, B.2
Burgers, P.M.J.3
-
37
-
-
0023650405
-
Thymine methyls and DNA-protein interactions
-
Ivarie R. 1987. Thymine methyls and DNA-protein interactions. Nucleic Acids Res. 15:9975-9983.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 9975-9983
-
-
Ivarie, R.1
-
38
-
-
0030035663
-
Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase
-
Kavli B, Slupphaug G, Mol CD, Arvai AS, Petersen SB, Tainer JA, Krokan HE. 1996. Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J. 15:3442-3447. (Pubitemid 26231951)
-
(1996)
EMBO Journal
, vol.15
, Issue.13
, pp. 3442-3447
-
-
Kavli, B.1
Slupphaug, G.2
Mol, C.D.3
Arvai, A.S.4
Petersen, S.B.5
Tainer, J.A.6
Krokan, H.E.7
-
39
-
-
18644363009
-
hUNG2 is the major repair enzyme for removal of uracil from U:A matches, U:G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup
-
DOI 10.1074/jbc.M207107200
-
Kavli B, Sundheim O, Akbari M, Otterlei M, Nilsen H, Skorpen F, Aas PA, Hagen L, Krokan HE, Slupphaug G. 2002. hUNG2 is the major repair enzyme for removal of uracil from U:A matches, U:G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup. J Biol Chem. 277:39926-39936. (Pubitemid 35190979)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.42
, pp. 39926-39936
-
-
Kavli, B.1
Sundheim, O.2
Akbari, M.3
Otterlei, M.4
Nilsen, H.5
Skorpen, F.6
Aas, P.A.7
Hagen, L.8
Krokan, H.E.9
Slupphaug, G.10
-
40
-
-
67650064592
-
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
-
Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML. 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
Blaxter, M.L.6
-
41
-
-
53049086145
-
Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus
-
Kiyonari S, Uchimura M, Shirai T, Ishino Y. 2008. Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J Biol Chem. 283:24185-24193.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 24185-24193
-
-
Kiyonari, S.1
Uchimura, M.2
Shirai, T.3
Ishino, Y.4
-
42
-
-
0030272402
-
Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms
-
DOI 10.1016/0378-1097(96)00325-4
-
Koulis A, Cowan DA, Pearl LH, Savva R. 1996. Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms. FEMS Microbiol Lett. 143:267-271. (Pubitemid 26317322)
-
(1996)
FEMS Microbiology Letters
, vol.143
, Issue.2-3
, pp. 267-271
-
-
Koulis, A.1
Cowan, D.A.2
Pearl, L.H.3
Savva, R.4
-
43
-
-
53449089755
-
Important role of the nucleotide excision repair pathway in Mycobacterium smegmatis in conferring protection against commonly encountered DNA-damaging agents
-
Kurthkoti K, Kumar P, Jain R, Varshney U. 2008. Important role of the nucleotide excision repair pathway in Mycobacterium smegmatis in conferring protection against commonly encountered DNA-damaging agents. Microbiology 154:2776-2785.
-
(2008)
Microbiology
, vol.154
, pp. 2776-2785
-
-
Kurthkoti, K.1
Kumar, P.2
Jain, R.3
Varshney, U.4
-
44
-
-
38049073294
-
The origins and early evolution of DNA mismatch repair genes-multiple horizontal gene transfers and co-evolution
-
Lin Z, Nei M, Ma H. 2007. The origins and early evolution of DNA mismatch repair genes-multiple horizontal gene transfers and co-evolution. Nucleic Acids Res. 35:7591-7603.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7591-7603
-
-
Lin, Z.1
Nei, M.2
Ma, H.3
-
46
-
-
0016257644
-
Heat-induced deamination of cytosine residues in deoxyribonucleic acid
-
Lindahl T, Nyberg B. 1974. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13:3405-3410.
-
(1974)
Biochemistry
, vol.13
, pp. 3405-3410
-
-
Lindahl, T.1
Nyberg, B.2
-
47
-
-
65349159321
-
Evolution of mutation rates: Phylogenomic analysis of the photolyase/cryptochrome family
-
Lucas-Lledó J I, Lynch M. 2009. Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. Mol Biol Evol. 26:1143-1153.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1143-1153
-
-
Lucas-Lledó, J.I.1
Lynch, M.2
-
49
-
-
75749103383
-
Rate, molecular spectrum, and consequences of human mutation
-
Lynch M. 2010. Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci USA. 107:961-968.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 961-968
-
-
Lynch, M.1
-
51
-
-
0037509930
-
Mammalian 5-formyluracil-DNA glycosylase. 2. Role of SMUG1 uracil-DNA glycosylase in repair of 5-formyluracil and other oxidized and deaminated base lesions
-
DOI 10.1021/bi0273213
-
Masaoka A, Matsubara M, Hasegawa R, Tanaka T, Kurisu S, Terato H, Ohyama Y, Karino N, Matsuda A, Ide H. 2003. Mammalian 5-formyluracil-DNA glycosylase. 2. Role of SMUG1 uracil-DNA glycosylase in repair of 5-formyluracil and other oxidized and deaminated base lesions. Biochemistry 42:5003-5012. (Pubitemid 36532054)
-
(2003)
Biochemistry
, vol.42
, Issue.17
, pp. 5003-5012
-
-
Masaoka, A.1
Matsubara, M.2
Hasegawa, R.3
Tanaka, T.4
Kurisu, S.5
Terato, H.6
Ohyama, Y.7
Karino, N.8
Matsuda, A.9
Ide, H.10
-
53
-
-
0035788426
-
Escherichia coli DNA glycosylase Mug: A growth-regulated enzyme required for mutation avoidance in stationary-phase cells
-
DOI 10.1046/j.1365-2958.2001.02559.x
-
Mokkapati SK, Fernández de Henestrosa AR, Bhagwat AS. 2001. Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells. Mol Microbiol. 41:1101-1111. (Pubitemid 36124706)
-
(2001)
Molecular Microbiology
, vol.41
, Issue.5
, pp. 1101-1111
-
-
Mokkapati, S.K.1
Fernandez De Henestrosa, A.R.2
Bhagwat, A.S.3
-
54
-
-
33745759756
-
Genomic GC level, optimal growth temperature, and genome size in prokaryotes
-
DOI 10.1016/j.bbrc.2006.06.054, PII S0006291X06013088
-
Musto H, Naya H, Zavala A, Romero H, Alvarez-Valín, Bernardi G. 2006. Genomic GC level, optimal growth temperature, and genome size in prokaryotes. Biochem Biophys Res Commun. 347:1-3. (Pubitemid 44015646)
-
(2006)
Biochemical and Biophysical Research Communications
, vol.347
, Issue.1
, pp. 1-3
-
-
Musto, H.1
Naya, H.2
Zavala, A.3
Romero, H.4
Alvarez-Valin, F.5
Bernardi, G.6
-
56
-
-
0035421186
-
Excision of deaminated cytosine from the vertebrate genome: Role of the SMUG1 uracil-DNA glycosylase
-
DOI 10.1093/emboj/20.15.4278
-
Nilsen H, Haushalter KA, Robins P, Barnes DE, Verdine GL, Lindahl T. 2001. Excision of deaminated cytosine from the vertebrate genome: role of the SMUG1 uracil-DNA glycosylase. EMBO J. 20:4278-4286. (Pubitemid 32751843)
-
(2001)
EMBO Journal
, vol.20
, Issue.15
, pp. 4278-4286
-
-
Nilsen, H.1
Haushalter, K.A.2
Robins, P.3
Barnes, D.E.4
Verdine, G.L.5
Lindahl, T.6
-
57
-
-
0033636312
-
Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication
-
Nilsen H, Rosewell I, Robins P, Skjelbred CF, Andersen S, Slupphaug G, Daly G, Krokan HE, Lindahl T, Barnes DE. 2000. Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication. Mol Cell. 5:1059-1065.
-
(2000)
Mol. Cell.
, vol.5
, pp. 1059-1065
-
-
Nilsen, H.1
Rosewell, I.2
Robins, P.3
Skjelbred, C.F.4
Andersen, S.5
Slupphaug, G.6
Daly, G.7
Krokan, H.E.8
Lindahl, T.9
Barnes, D.E.10
-
58
-
-
48249091623
-
The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant
-
Nordman J, Wright A. 2008. The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant. Proc Natl Acad Sci USA. 105:10197-10202.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 10197-10202
-
-
Nordman, J.1
Wright, A.2
-
59
-
-
33644633050
-
Catalytic promiscuity and the divergent evolution of DNA repair enzyme
-
O'Brien PJ. 2006. Catalytic promiscuity and the divergent evolution of DNA repair enzyme. Chem Rev. 106:720-752.
-
(2006)
Chem. Rev.
, vol.106
, pp. 720-752
-
-
O'Brien, P.J.1
-
60
-
-
0037743666
-
Mismatch uracil glycosylase from Escherichia coli. A general mismatch or a specific DNA glycosylase?
-
DOI 10.1074/jbc.M210860200
-
O'Neill RJ, Vorob'eva OV, Shahbakhti H, Zmuda E, Bhagwat AS, Baldwin GS. 2003. Mismatch uracil glycosylase from Escherichia coli. A general mismatch or a specific DNA glycosylase? J Biol Chem. 278:20526-20532. (Pubitemid 36806349)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.23
, pp. 20526-20532
-
-
O'Neill, R.J.1
Vorob'Eva, O.V.2
Shahbakhti, H.3
Zmuda, E.4
Bhagwat, A.S.5
Baldwin, G.S.6
-
61
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
Ossowski S, Schneeberger K, Lucas-LLedó J I, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M. 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
Shaw, R.G.6
Weigel, D.7
Lynch, M.8
-
62
-
-
0028097770
-
Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters
-
Pagel M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc Lond B. 255:37-45. (Pubitemid 24044170)
-
(1994)
Proceedings of the Royal Society B: Biological Sciences
, vol.255
, Issue.1342
, pp. 37-45
-
-
Pagel, M.1
-
63
-
-
33646735054
-
Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo
-
DOI 10.1086/503444
-
Pagel M, Meade A. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am Nat. 167:808-825. (Pubitemid 43998042)
-
(2006)
American Naturalist
, vol.167
, Issue.6
, pp. 808-825
-
-
Pagel, M.1
Meade, A.2
-
64
-
-
0026718777
-
A method for the analysis of comparative data
-
Pagel MD. 1992. A method for the analysis of comparative data. J Theor Biol. 156:431-442.
-
(1992)
J. Theor Biol.
, vol.156
, pp. 431-442
-
-
Pagel, M.D.1
-
65
-
-
0034734383
-
Structure and function in the uracil-DNA glycosylase superfamily
-
DOI 10.1016/S0921-8777(00)00025-2, PII S0921877700000252
-
Pearl LH. 2000. Structure and function in the uracil-dna glycosylase superfamily. Mutat Res. 460:165-181. (Pubitemid 30628589)
-
(2000)
Mutation Research - DNA Repair
, vol.460
, Issue.3-4
, pp. 165-181
-
-
Pearl, L.H.1
-
66
-
-
4444268722
-
Trypanosoma cruzi contains a single detectable uracil-DNA glycosylase and repairs uracil exclusively via short patch base excision repair
-
DOI 10.1016/j.jmb.2004.07.043, PII S0022283604008721
-
Pena Diaz J, Akbari M, Sundheim O, Farez-Vidal ME, Andersen S, Sneve R, Gonzalez-Pacanowska D, Krokan HE, Slupphaug G. 2004. Trypanosoma cruzi contains a single detectable uracil-DNA glycosylase and repairs uracil exclusively via short patch base excision repair. J Mol Biol. 342:787-799. (Pubitemid 39165650)
-
(2004)
Journal of Molecular Biology
, vol.342
, Issue.3
, pp. 787-799
-
-
Pena-Diaz, J.1
Akbari, M.2
Sundheim, O.3
Esther Farez-Vidal, M.4
Andersen, S.5
Sneve, R.6
Gonzalez-Pacanowska, D.7
Krokan, H.E.8
Slupphaug, G.9
-
67
-
-
34547645005
-
Uracil-DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms
-
DOI 10.1093/nar/gkm372
-
Pettersen HS, Sundheim O, Gilljam KM, Slupphaug G, Krokan HE, Kavli B. 2007. Uracil-DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms. Nucleic Acids Res. 35:3879-3892. (Pubitemid 47244612)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.12
, pp. 3879-3892
-
-
Pettersen, H.S.1
Sundheim, O.2
Gilljam, K.M.3
Slupphaug, G.4
Krokan, H.E.5
Kavli, B.6
-
68
-
-
0034665836
-
Increased spontaneous mutation frequency in human cells expressing the phage PBS2-encoded inhibitor of uracil-DNA glycosylase
-
Radany EH, Dornfeld KJ, Sanderson RJ, Savage MK, Majumdar A, Seidman MM, Mosbaugh DW. 2000. Increased spontaneous mutation frequency in human cells expressing the phage PBS2-encoded inhibitor of uracil-DNA glycosylase. Mutat Res. 461:41-58.
-
(2000)
Mutat Res.
, vol.461
, pp. 41-58
-
-
Radany, E.H.1
Dornfeld, K.J.2
Sanderson, R.J.3
Savage, M.K.4
Majumdar, A.5
Seidman, M.M.6
Mosbaugh, D.W.7
-
69
-
-
40649104519
-
Mutagenesis of uracil-DNA glycosylase deficient mutants of the extremely thermophilic eubacterium Thermus thermophilus
-
Sakai T, Tokishita SI, Mochizuki K, Motomiya A, Yamagata H, Ohta T. 2008. Mutagenesis of uracil-DNA glycosylase deficient mutants of the extremely thermophilic eubacterium Thermus thermophilus. DNA Repair 7:663-669.
-
(2008)
DNA Repair
, vol.7
, pp. 663-669
-
-
Sakai, T.1
Tokishita, S.I.2
Mochizuki, K.3
Motomiya, A.4
Yamagata, H.5
Ohta, T.6
-
70
-
-
0035804794
-
Characterization of the full length uracil-DNA glycosylase in the extreme thermophile Thermotoga maritima
-
DOI 10.1016/S0921-8777(00)00083-5, PII S0921877700000835
-
Sandigursky M, Faje A, Franklin WA. 2001. Characterization of the full length uracil-DNA glycosylase in the extreme thermophile Thermotoga maritima. Mutat Res. 485:187-195. (Pubitemid 32232302)
-
(2001)
Mutation Research - DNA Repair
, vol.485
, Issue.3
, pp. 187-195
-
-
Sandigursky, M.1
Faje, A.2
Franklin, W.A.3
-
71
-
-
0033587149
-
Thermostable uracil-DNA glycosylase from Thermotoga maritima, a member of a novel class of DNA repair enzymes
-
DOI 10.1016/S0960-9822(99)80237-1
-
Sandigursky M, Franklin WA. 1999. Thermostable uracil-DNA glycosylase from Thermotoga maritima, a member of a novel class of DNA repair enzymes. Curr Biol. 9:531-534. (Pubitemid 29257108)
-
(1999)
Current Biology
, vol.9
, Issue.10
, pp. 531-534
-
-
Sandigursky, M.1
Franklin, W.A.2
-
72
-
-
0034705405
-
Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus
-
DOI 10.1074/jbc.M001995200
-
Sandigursky M, Franklin WA. 2000. Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus. J Biol Chem. 275:19146-19149. (Pubitemid 30422884)
-
(2000)
Journal of Biological Chemistry
, vol.275
, Issue.25
, pp. 19146-19149
-
-
Sandigursky, M.1
Franklin, W.A.2
-
73
-
-
0032555065
-
4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase
-
DOI 10.1073/pnas.95.15.8508
-
4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. Proc Natl Acad Sci U S A. 95:8508-8513. (Pubitemid 28350518)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.15
, pp. 8508-8513
-
-
Saparbaev, M.1
Laval, J.2
-
74
-
-
0037124349
-
A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site
-
DOI 10.1093/emboj/cdf309
-
Sartori AA, Fitz-Gibbon S, Yang H, Miller JH, Jiricny J. 2002. A novel uracil-DNA glycosylase with broad substrate specificity and an anusual active site. EMBO J. 21:3182-3191. (Pubitemid 34670401)
-
(2002)
EMBO Journal
, vol.21
, Issue.12
, pp. 3182-3191
-
-
Sartori, A.A.1
Fitz-Gibbon, S.2
Yang, H.3
Miller, J.H.4
Jiricny, J.5
-
75
-
-
14544277543
-
Variation in the strength of selected codon usage bias among bacteria
-
DOI 10.1093/nar/gki242
-
Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33:1141-1153. (Pubitemid 41439907)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.4
, pp. 1141-1153
-
-
Sharp, P.M.1
Bailes, E.2
Grocock, R.J.3
Peden, J.F.4
Sockett, R.E.5
-
76
-
-
0028933306
-
Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase
-
Slupphaug G, Eftedal I, Kavli B, Bharati S, Helle NM, Haug T, Levine DW, Krokan HE. 1995. Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase. Biochemistry 34:128-138.
-
(1995)
Biochemistry
, vol.34
, pp. 128-138
-
-
Slupphaug, G.1
Eftedal, I.2
Kavli, B.3
Bharati, S.4
Helle, N.M.5
Haug, T.6
Levine, D.W.7
Krokan, H.E.8
-
77
-
-
34548534747
-
Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis
-
DOI 10.1016/j.dnarep.2007.05.001, PII S156878640700184X
-
Srinath T, Bharti SK, Varshney U. 2007. Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis. DNA Repair 6:1517-1528. (Pubitemid 47385403)
-
(2007)
DNA Repair
, vol.6
, Issue.10
, pp. 1517-1528
-
-
Srinath, T.1
Bharti, S.K.2
Varshney, U.3
-
78
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
DOI 10.1093/bioinformatics/btl446
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
79
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web servers
-
Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 57:758-771.
-
(2008)
Syst. Biol.
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
80
-
-
0034702867
-
Escherichia coli double-strand uracil-DNA glycosylase: Involvement in uracil-mediated DNA base excision repair and stimulation of activity by endonuclease IV
-
DOI 10.1021/bi0007066
-
Sung JS, Mosbaugh DW. 2000. Escherichia coli double-strand uracil-DNA glycosylase: involvement in uracil-mediated DNA base excision repair and stimulation of activity by endonuclease IV. Biochemistry 39:10224-10235. (Pubitemid 30663045)
-
(2000)
Biochemistry
, vol.39
, Issue.33
, pp. 10224-10235
-
-
Sung, J.-S.1
Mosbaugh, D.W.2
-
81
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
DOI 10.1080/10635150701472164, PII 780704285
-
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577. (Pubitemid 47171631)
-
(2007)
Systematic Biology
, vol.56
, Issue.4
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
82
-
-
0012670425
-
Uracil incorporation: A source of pulse-labelled DNA fragments in the replication of the Escherichia coli chromosome
-
Tye BK, Chien J, Lehman IR, Duncan BK, Warner HR. 1978. Uracil incorporation: a source of pulse-labeled DNA fragments in the replication of the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 75:233-237. (Pubitemid 8290773)
-
(1978)
Proceedings of the National Academy of Sciences of the United States of America
, vol.75
, Issue.1
, pp. 233-237
-
-
Tye, B.K.1
Chien, J.2
Lehman, I.R.3
-
83
-
-
0042090471
-
Importance of Uracil DNA Glycosylase in Pseudomonas aeruginosa and Mycobacterium smegmatis, G+C-rich Bacteria, in Mutation Prevention, Tolerance to Acidified Nitrite, and Endurance in Mouse Macrophages
-
DOI 10.1074/jbc.M302121200
-
Venkatesh J, Kumar P, Krishna PSM, Manjunath R, Varshney U. 2003. Importance of uracil DNA glycosylase in Pseudomonas aeruginosa and Mycobacterium smegmatis, G+C-rich bacteria, in mutation prevention, tolerance to acidified nitrite, and endurance in mouse macrophages. J Biol Chem. 278:24350-24358. (Pubitemid 37548586)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.27
, pp. 24350-24358
-
-
Venkatesh, J.1
Kumar, P.2
Krishna, P.S.M.3
Manjunath, R.4
Varshney, U.5
-
84
-
-
0032493637
-
Kinetics of the action of thymine DNA glycosylase
-
DOI 10.1074/jbc.273.32.20007
-
Waters TR, Swann PF. 1998. Kinetics of the action of thymine DNA glycosylase. J Biol Chem. 273:20007-20014. (Pubitemid 28377551)
-
(1998)
Journal of Biological Chemistry
, vol.273
, Issue.32
, pp. 20007-20014
-
-
Waters, T.R.1
Swann, P.F.2
-
85
-
-
51749095104
-
Phylocom: Software for the analysis of phylogenetic community structure and trait evolution
-
Webb CO, Ackerly DD, Kembel SW. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098-2100.
-
(2008)
Bioinformatics
, vol.24
, pp. 2098-2100
-
-
Webb, C.O.1
Ackerly, D.D.2
Kembel, S.W.3
|