-
1
-
-
0027355635
-
Development of enzyme-based methods for DNA sequence analysis and their applications in the genome projects
-
Wu R. Development of enzyme-based methods for DNA sequence analysis and their applications in the genome projects. Adv Enzymol Relat Areas Mol Biol 1993, 67:431-468.
-
(1993)
Adv Enzymol Relat Areas Mol Biol
, vol.67
, pp. 431-468
-
-
Wu, R.1
-
3
-
-
84857567316
-
Overview of DNA sequencing strategies
-
Chapter7. Unit 7.1
-
Shendure J.A., Porreca G.J., Church G.M., Gardner A.F., Hendrickson C.L., Kieleczawa J., Slatko B.E. Overview of DNA sequencing strategies. Curr Protoc Mol Biol 2011, Chapter7. Unit 7.1.
-
(2011)
Curr Protoc Mol Biol
-
-
Shendure, J.A.1
Porreca, G.J.2
Church, G.M.3
Gardner, A.F.4
Hendrickson, C.L.5
Kieleczawa, J.6
Slatko, B.E.7
-
4
-
-
52949096084
-
Next-generation DNA sequencing methods
-
Mardis E.R. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402.
-
(2008)
Annu Rev Genomics Hum Genet
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
5
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J., Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
6
-
-
73349130030
-
Perspectives and challenges of emerging single-molecule DNA sequencing technologies
-
Xu M., Fujita D., Hanagata N. Perspectives and challenges of emerging single-molecule DNA sequencing technologies. Small 2009, 5:2638-2649.
-
(2009)
Small
, vol.5
, pp. 2638-2649
-
-
Xu, M.1
Fujita, D.2
Hanagata, N.3
-
7
-
-
79959212998
-
Landscape of next-generation sequencing technologies
-
Niedringhaus T.P., Milanova D., Kerby M.B., Snyder M.P., Barron A.E. Landscape of next-generation sequencing technologies. Anal Chem 2011, 83:4327-4341.
-
(2011)
Anal Chem
, vol.83
, pp. 4327-4341
-
-
Niedringhaus, T.P.1
Milanova, D.2
Kerby, M.B.3
Snyder, M.P.4
Barron, A.E.5
-
10
-
-
79955025118
-
Next generation sequencing based approaches to epigenomics
-
Hirst M., Marra M.A. Next generation sequencing based approaches to epigenomics. Brief Funct Genomics 2010, 9:455-465.
-
(2010)
Brief Funct Genomics
, vol.9
, pp. 455-465
-
-
Hirst, M.1
Marra, M.A.2
-
12
-
-
77953381898
-
Tackling the methylome: recent methodological advances in genome-wide methylation profiling
-
Estecio M.R., Issa J.P. Tackling the methylome: recent methodological advances in genome-wide methylation profiling. Genome Med 2009, 1:106.
-
(2009)
Genome Med
, vol.1
, pp. 106
-
-
Estecio, M.R.1
Issa, J.P.2
-
13
-
-
77955446294
-
Protocol matters: which methylome are you actually studying?
-
Robinson M.D., Statham A.L., Speed T.P., Clark S.J. Protocol matters: which methylome are you actually studying?. Epigenomics 2010, 2:587-598.
-
(2010)
Epigenomics
, vol.2
, pp. 587-598
-
-
Robinson, M.D.1
Statham, A.L.2
Speed, T.P.3
Clark, S.J.4
-
14
-
-
77957937011
-
Quantitative comparison of genome-wide DNA methylation mapping technologies
-
Bock C., Tomazou E.M., Brinkman A.B., Muller F., Simmer F., Gu H., Jager N., Gnirke A., Stunnenberg H.G., Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28:1106-1114.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1106-1114
-
-
Bock, C.1
Tomazou, E.M.2
Brinkman, A.B.3
Muller, F.4
Simmer, F.5
Gu, H.6
Jager, N.7
Gnirke, A.8
Stunnenberg, H.G.9
Meissner, A.10
-
15
-
-
66149123748
-
The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain
-
Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain. Science 2009, 324:929-930.
-
(2009)
Science
, vol.324
, pp. 929-930
-
-
Kriaucionis, S.1
Heintz, N.2
-
16
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
Tahiliani M., Koh K.P., Shen Y., Pastor W.A., Bandukwala H., Brudno Y., Agarwal S., Iyer L.M., Liu D.R., Aravind L., et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
-
(2009)
Science
, vol.324
, pp. 930-935
-
-
Tahiliani, M.1
Koh, K.P.2
Shen, Y.3
Pastor, W.A.4
Bandukwala, H.5
Brudno, Y.6
Agarwal, S.7
Iyer, L.M.8
Liu, D.R.9
Aravind, L.10
-
17
-
-
79959987448
-
5-Hydroxymethylcytosine, the sixth base of the genome
-
Munzel M., Globisch D., Carell T. 5-Hydroxymethylcytosine, the sixth base of the genome. Angew Chem Int Ed Engl 2011, 50:6460-6468.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, pp. 6460-6468
-
-
Munzel, M.1
Globisch, D.2
Carell, T.3
-
18
-
-
77749277177
-
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
-
Huang Y., Pastor W.A., Shen Y., Tahiliani M., Liu D.R., Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE 2010, 5:e8888.
-
(2010)
PLoS ONE
, vol.5
-
-
Huang, Y.1
Pastor, W.A.2
Shen, Y.3
Tahiliani, M.4
Liu, D.R.5
Rao, A.6
-
19
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito S., Shen L., Dai Q., Wu S.C., Collins L.B., Swenberg J.A., He C., Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333:1300-1303.
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
Shen, L.2
Dai, Q.3
Wu, S.C.4
Collins, L.B.5
Swenberg, J.A.6
He, C.7
Zhang, Y.8
-
20
-
-
33645389087
-
N6-methyladenine: the other methylated base of DNA
-
Ratel D., Ravanat J.L., Berger F., Wion D. N6-methyladenine: the other methylated base of DNA. Bioessays 2006, 28:309-315.
-
(2006)
Bioessays
, vol.28
, pp. 309-315
-
-
Ratel, D.1
Ravanat, J.L.2
Berger, F.3
Wion, D.4
-
21
-
-
0038713344
-
Immunity through DNA deamination
-
Neuberger M.S., Harris R.S., Di Noia J., Petersen-Mahrt S.K. Immunity through DNA deamination. Trends Biochem Sci 2003, 28:305-312.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 305-312
-
-
Neuberger, M.S.1
Harris, R.S.2
Di Noia, J.3
Petersen-Mahrt, S.K.4
-
22
-
-
53849113697
-
Base J: discovery, biosynthesis, and possible functions
-
Borst P., Sabatini R. Base J: discovery, biosynthesis, and possible functions. Annu Rev Microbiol 2008, 62:235-251.
-
(2008)
Annu Rev Microbiol
, vol.62
, pp. 235-251
-
-
Borst, P.1
Sabatini, R.2
-
23
-
-
79953148257
-
Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA
-
Ekanayake D.K., Minning T., Weatherly B., Gunasekera K., Nilsson D., Tarleton R., Ochsenreiter T., Sabatini R. Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA. Mol Cell Biol 2011, 31:1690-1700.
-
(2011)
Mol Cell Biol
, vol.31
, pp. 1690-1700
-
-
Ekanayake, D.K.1
Minning, T.2
Weatherly, B.3
Gunasekera, K.4
Nilsson, D.5
Tarleton, R.6
Ochsenreiter, T.7
Sabatini, R.8
-
24
-
-
33646184968
-
The wild-type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides
-
Vengrova S., Dalgaard J.Z. The wild-type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides. EMBO Rep 2006, 7:59-65.
-
(2006)
EMBO Rep
, vol.7
, pp. 59-65
-
-
Vengrova, S.1
Dalgaard, J.Z.2
-
25
-
-
75549086595
-
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes
-
Roberts R.J., Vincze T., Posfai J., Macelis D. REBASE - a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010, 38:D234-D236.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
26
-
-
35348999539
-
Phosphorothioation of DNA in bacteria by dnd genes
-
Wang L., Chen S., Xu T., Taghizadeh K., Wishnok J.S., Zhou X., You D., Deng Z., Dedon P.C. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 2007, 3:709-710.
-
(2007)
Nat Chem Biol
, vol.3
, pp. 709-710
-
-
Wang, L.1
Chen, S.2
Xu, T.3
Taghizadeh, K.4
Wishnok, J.S.5
Zhou, X.6
You, D.7
Deng, Z.8
Dedon, P.C.9
-
27
-
-
79952590206
-
DNA phosphorothioation is widespread and quantized in bacterial genomes
-
Wang L., Chen S., Vergin K.L., Giovannoni S.J., Chan S.W., DeMott M.S., Taghizadeh K., Cordero O.X., Cutler M., Timberlake S., et al. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci USA 2011, 108:2963-2968.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 2963-2968
-
-
Wang, L.1
Chen, S.2
Vergin, K.L.3
Giovannoni, S.J.4
Chan, S.W.5
DeMott, M.S.6
Taghizadeh, K.7
Cordero, O.X.8
Cutler, M.9
Timberlake, S.10
-
28
-
-
64349112326
-
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more
-
Marinus M.G., Casadesus J. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 2009, 33:488-503.
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 488-503
-
-
Marinus, M.G.1
Casadesus, J.2
-
29
-
-
73449107182
-
Dam and its role in pathogenicity of Salmonella enterica
-
Giacomodonato M.N., Sarnacki S.H., Llana M.N., Cerquetti M.C. Dam and its role in pathogenicity of Salmonella enterica. J Infect Dev Ctries 2009, 3:484-490.
-
(2009)
J Infect Dev Ctries
, vol.3
, pp. 484-490
-
-
Giacomodonato, M.N.1
Sarnacki, S.H.2
Llana, M.N.3
Cerquetti, M.C.4
-
30
-
-
71849115781
-
Epigenetic regulation of the bacterial cell cycle
-
Collier J. Epigenetic regulation of the bacterial cell cycle. Curr Opin Microbiol 2009, 12:722-729.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 722-729
-
-
Collier, J.1
-
31
-
-
36749067835
-
A DNA methylation ratchet governs progression through a bacterial cell cycle
-
Collier J., McAdams H.H., Shapiro L. A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA 2007, 104:17111-17116.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 17111-17116
-
-
Collier, J.1
McAdams, H.H.2
Shapiro, L.3
-
32
-
-
76949108806
-
The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
-
Srikhanta Y.N., Fox K.L., Jennings M.P. The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat Rev Microbiol 2010, 8:196-206.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 196-206
-
-
Srikhanta, Y.N.1
Fox, K.L.2
Jennings, M.P.3
-
33
-
-
84856473209
-
Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli
-
Militello K.T., Simon R.D., Qureshi M., Maines R., Van Horne M.L., Hennick S.M., Jayakar S.K., Pounder S. Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli. FEMS Microbiol Lett 2011, 10.1111/j.1574-6968.2011.02482.
-
(2011)
FEMS Microbiol Lett
-
-
Militello, K.T.1
Simon, R.D.2
Qureshi, M.3
Maines, R.4
Van Horne, M.L.5
Hennick, S.M.6
Jayakar, S.K.7
Pounder, S.8
-
38
-
-
25444474703
-
Mitochondria take center stage in aging and neurodegeneration
-
Beal M.F. Mitochondria take center stage in aging and neurodegeneration. Ann Neurol 2005, 58:495-505.
-
(2005)
Ann Neurol
, vol.58
, pp. 495-505
-
-
Beal, M.F.1
-
39
-
-
2942523593
-
Endogenous DNA damage in humans: a review of quantitative data
-
De Bont R., van Larebeke N. Endogenous DNA damage in humans: a review of quantitative data. Mutagenesis 2004, 19:169-185.
-
(2004)
Mutagenesis
, vol.19
, pp. 169-185
-
-
De Bont, R.1
van Larebeke, N.2
-
40
-
-
58949084649
-
Base excision repair of oxidative DNA damage and association with cancer and aging
-
Maynard S., Schurman S.H., Harboe C., de Souza-Pinto N.C., Bohr V.A. Base excision repair of oxidative DNA damage and association with cancer and aging. Carcinogenesis 2009, 30:2-10.
-
(2009)
Carcinogenesis
, vol.30
, pp. 2-10
-
-
Maynard, S.1
Schurman, S.H.2
Harboe, C.3
de Souza-Pinto, N.C.4
Bohr, V.A.5
-
41
-
-
65549096318
-
Free radical induced oxidative damage to DNA: relation to brain aging and neurological disorders
-
Rao K.S. Free radical induced oxidative damage to DNA: relation to brain aging and neurological disorders. Indian J Biochem Biophys 2009, 46:9-15.
-
(2009)
Indian J Biochem Biophys
, vol.46
, pp. 9-15
-
-
Rao, K.S.1
-
42
-
-
0027278557
-
Instability and decay of the primary structure of DNA
-
Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
-
(1993)
Nature
, vol.362
, pp. 709-715
-
-
Lindahl, T.1
-
43
-
-
0024195429
-
DNA damage produced by ionizing radiation in mammalian cells: identities, mechanisms of formation, and reparability
-
Ward J.F. DNA damage produced by ionizing radiation in mammalian cells: identities, mechanisms of formation, and reparability. Prog Nucleic Acid Res Mol Biol 1988, 35:95-125.
-
(1988)
Prog Nucleic Acid Res Mol Biol
, vol.35
, pp. 95-125
-
-
Ward, J.F.1
-
44
-
-
0035834708
-
Definitive identification of mammalian 5-hydroxymethyluracil DNA N-glycosylase activity as SMUG1
-
Boorstein R.J., Cummings A., Marenstein D.R., Chan M.K., Ma Y., Neubert T.A., Brown S.M., Teebor G.W. Definitive identification of mammalian 5-hydroxymethyluracil DNA N-glycosylase activity as SMUG1. J Biol Chem 2001, 276:41991-41997.
-
(2001)
J Biol Chem
, vol.276
, pp. 41991-41997
-
-
Boorstein, R.J.1
Cummings, 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
-
45
-
-
4344647877
-
Cellular repair of oxidatively induced DNA base lesions is defective in prostate cancer cell lines, PC-3 and DU-145
-
Trzeciak A.R., Nyaga S.G., Jaruga P., Lohani A., Dizdaroglu M., Evans M.K. Cellular repair of oxidatively induced DNA base lesions is defective in prostate cancer cell lines, PC-3 and DU-145. Carcinogenesis 2004, 25:1359-1370.
-
(2004)
Carcinogenesis
, vol.25
, pp. 1359-1370
-
-
Trzeciak, A.R.1
Nyaga, S.G.2
Jaruga, P.3
Lohani, A.4
Dizdaroglu, M.5
Evans, M.K.6
-
46
-
-
0028074299
-
DNA methylation and cancer
-
Laird P.W., Jaenisch R. DNA methylation and cancer. Hum Mol Genet 1994, 3 Spec No:1487-1495.
-
(1994)
Hum Mol Genet
, vol.3 Spec No
, pp. 1487-1495
-
-
Laird, P.W.1
Jaenisch, R.2
-
47
-
-
77950406088
-
Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases
-
Nick McElhinny S.A., Watts B.E., Kumar D., Watt D.L., Lundstrom E.B., Burgers P.M., Johansson E., Chabes A., Kunkel T.A. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc Natl Acad Sci USA 2010, 107:4949-4954.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 4949-4954
-
-
Nick McElhinny, S.A.1
Watts, B.E.2
Kumar, D.3
Watt, D.L.4
Lundstrom, E.B.5
Burgers, P.M.6
Johansson, E.7
Chabes, A.8
Kunkel, T.A.9
-
48
-
-
77956921247
-
Genome instability due to ribonucleotide incorporation into DNA
-
Nick McElhinny S.A., Kumar D., Clark A.B., Watt D.L., Watts B.E., Lundstrom E.B., Johansson E., Chabes A., Kunkel T.A. Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 2010, 6:774-781.
-
(2010)
Nat Chem Biol
, vol.6
, pp. 774-781
-
-
Nick McElhinny, S.A.1
Kumar, D.2
Clark, A.B.3
Watt, D.L.4
Watts, B.E.5
Lundstrom, E.B.6
Johansson, E.7
Chabes, A.8
Kunkel, T.A.9
-
49
-
-
52049113518
-
DNA damage: detection strategies
-
Kumari S., Rastogi R.P., Singh K.L., Singh S.P., Sinha R.P. DNA damage: detection strategies. EXCLI J 2008, 7:44-62.
-
(2008)
EXCLI J
, vol.7
, pp. 44-62
-
-
Kumari, S.1
Rastogi, R.P.2
Singh, K.L.3
Singh, S.P.4
Sinha, R.P.5
-
50
-
-
0027164447
-
Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases
-
Nelson M., Raschke E., McClelland M. Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1993, 21:3139-3154.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 3139-3154
-
-
Nelson, M.1
Raschke, E.2
McClelland, M.3
-
52
-
-
0032524408
-
Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data
-
Rao B.S., Buckler-White A. Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data. Nucleic Acids Res 1998, 26:2505-2507.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 2505-2507
-
-
Rao, B.S.1
Buckler-White, A.2
-
53
-
-
34249785952
-
YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica
-
Broadbent S.E., Balbontin R., Casadesus J., Marinus M.G., van der Woude M. YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica. J Bacteriol 2007, 189:4325-4327.
-
(2007)
J Bacteriol
, vol.189
, pp. 4325-4327
-
-
Broadbent, S.E.1
Balbontin, R.2
Casadesus, J.3
Marinus, M.G.4
van der Woude, M.5
-
54
-
-
0035111893
-
NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain
-
Bart A., Pannekoek Y., Dankert J., van der Ende A. NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain. Infect Immun 2001, 69:1816-1820.
-
(2001)
Infect Immun
, vol.69
, pp. 1816-1820
-
-
Bart, A.1
Pannekoek, Y.2
Dankert, J.3
van der Ende, A.4
-
55
-
-
79960572626
-
The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
-
Cohen-Karni D., Xu D., Apone L., Fomenkov A., Sun Z., Davis P.J., Kinney S.R., Yamada-Mabuchi M., Xu S.Y., Davis T., et al. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc Natl Acad Sci USA 2011, 108:11040-11045.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 11040-11045
-
-
Cohen-Karni, D.1
Xu, D.2
Apone, L.3
Fomenkov, A.4
Sun, Z.5
Davis, P.J.6
Kinney, S.R.7
Yamada-Mabuchi, M.8
Xu, S.Y.9
Davis, T.10
-
56
-
-
77956500617
-
A unique family of Mrr-like modification-dependent restriction endonucleases
-
Zheng Y., Cohen-Karni D., Xu D., Chin H.G., Wilson G., Pradhan S., Roberts R.J. A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res 2010, 38:5527-5534.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5527-5534
-
-
Zheng, Y.1
Cohen-Karni, D.2
Xu, D.3
Chin, H.G.4
Wilson, G.5
Pradhan, S.6
Roberts, R.J.7
-
57
-
-
80054739563
-
The hunt for 5-hydroxymethylcytosine: the sixth base
-
Song C.X., He C. The hunt for 5-hydroxymethylcytosine: the sixth base. Epigenomics 2011, 3:521-523.
-
(2011)
Epigenomics
, vol.3
, pp. 521-523
-
-
Song, C.X.1
He, C.2
-
59
-
-
36148996882
-
Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi
-
Ekanayake D.K., Cipriano M.J., Sabatini R. Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi. Nucleic Acids Res 2007, 35:6367-6377.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 6367-6377
-
-
Ekanayake, D.K.1
Cipriano, M.J.2
Sabatini, R.3
-
60
-
-
34249856759
-
Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania
-
Genest P.A., Ter Riet B., Cijsouw T., van Luenen H.G., Borst P. Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Res 2007, 35:2116-2124.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 2116-2124
-
-
Genest, P.A.1
Ter Riet, B.2
Cijsouw, T.3
van Luenen, H.G.4
Borst, P.5
-
61
-
-
0030722989
-
Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei
-
van Leeuwen F., Wijsman E.R., Kieft R., van der Marel G.A., van Boom J.H., Borst P. Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes Dev 1997, 11:3232-3241.
-
(1997)
Genes Dev
, vol.11
, pp. 3232-3241
-
-
van Leeuwen, F.1
Wijsman, E.R.2
Kieft, R.3
van der Marel, G.A.4
van Boom, J.H.5
Borst, P.6
-
63
-
-
77950630162
-
Recent advances in single-molecule sequencing
-
Treffer R., Deckert V. Recent advances in single-molecule sequencing. Curr Opin Biotechnol 2010, 21:4-11.
-
(2010)
Curr Opin Biotechnol
, vol.21
, pp. 4-11
-
-
Treffer, R.1
Deckert, V.2
-
64
-
-
41749104588
-
Single-molecule DNA sequencing of a viral genome
-
Harris T.D., Buzby P.R., Babcock H., Beer E., Bowers J., Braslavsky I., Causey M., Colonell J., Dimeo J., Efcavitch J.W., et al. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109.
-
(2008)
Science
, vol.320
, pp. 106-109
-
-
Harris, T.D.1
Buzby, P.R.2
Babcock, H.3
Beer, E.4
Bowers, J.5
Braslavsky, I.6
Causey, M.7
Colonell, J.8
Dimeo, J.9
Efcavitch, J.W.10
-
65
-
-
79956308473
-
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
-
Pastor W.A., Pape U.J., Huang Y., Henderson H.R., Lister R., Ko M., McLoughlin E.M., Brudno Y., Mahapatra S., Kapranov P., et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011, 473:394-397.
-
(2011)
Nature
, vol.473
, pp. 394-397
-
-
Pastor, W.A.1
Pape, U.J.2
Huang, Y.3
Henderson, H.R.4
Lister, R.5
Ko, M.6
McLoughlin, E.M.7
Brudno, Y.8
Mahapatra, S.9
Kapranov, P.10
-
66
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
-
67
-
-
77957051540
-
Real-time DNA sequencing from single polymerase molecules
-
Korlach J., Bjornson K.P., Chaudhuri B.P., Cicero R.L., Flusberg B.A., Gray J.J., Holden D., Saxena R., Wegener J., Turner S.W. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 2010, 472:431-455.
-
(2010)
Methods Enzymol
, vol.472
, pp. 431-455
-
-
Korlach, J.1
Bjornson, K.P.2
Chaudhuri, B.P.3
Cicero, R.L.4
Flusberg, B.A.5
Gray, J.J.6
Holden, D.7
Saxena, R.8
Wegener, J.9
Turner, S.W.10
-
68
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg B.A., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., Clark T.A., Korlach J., Turner S.W. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7:461-465.
-
(2010)
Nat Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
Travers, K.J.4
Olivares, E.C.5
Clark, T.A.6
Korlach, J.7
Turner, S.W.8
-
69
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers K.J., Chin C.S., Rank D.R., Eid J.S., Turner S.W. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010, 38:e159.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Travers, K.J.1
Chin, C.S.2
Rank, D.R.3
Eid, J.S.4
Turner, S.W.5
-
70
-
-
84856453032
-
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine
-
Song X.S., Clark T.A., Lu X.Y., Kislyuk A., Dai Q., Turner S.W., He C., Korlach J. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods 2011, 10.1038/nmeth.1779.
-
(2011)
Nat Methods
-
-
Song, X.S.1
Clark, T.A.2
Lu, X.Y.3
Kislyuk, A.4
Dai, Q.5
Turner, S.W.6
He, C.7
Korlach, J.8
-
71
-
-
84857877933
-
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
-
Clark T.A., Murray I.A., Morgan R.D., Kislyuk A.O., Spittle K.E., Boitano M., Fomenkov A., Roberts R.J., Korlach J. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 2011, 10.1093/nar/gkr1146.
-
(2011)
Nucleic Acids Res
-
-
Clark, T.A.1
Murray, I.A.2
Morgan, R.D.3
Kislyuk, A.O.4
Spittle, K.E.5
Boitano, M.6
Fomenkov, A.7
Roberts, R.J.8
Korlach, J.9
-
72
-
-
84861802222
-
Direct detection and sequencing of damaged DNA bases
-
Clark T.A., Spittle K.E., Turner S.W., Korlach J. Direct detection and sequencing of damaged DNA bases. Genome Integr 2011, 2:10.
-
(2011)
Genome Integr
, vol.2
, pp. 10
-
-
Clark, T.A.1
Spittle, K.E.2
Turner, S.W.3
Korlach, J.4
-
73
-
-
34547175132
-
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases
-
Berman A.J., Kamtekar S., Goodman J.L., Lazaro J.M., de Vega M., Blanco L., Salas M., Steitz T.A. Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J 2007, 26:3494-3505.
-
(2007)
EMBO J
, vol.26
, pp. 3494-3505
-
-
Berman, A.J.1
Kamtekar, S.2
Goodman, J.L.3
Lazaro, J.M.4
de Vega, M.5
Blanco, L.6
Salas, M.7
Steitz, T.A.8
-
74
-
-
1642588255
-
Structures of mismatch replication errors observed in a DNA polymerase
-
Johnson S.J., Beese L.S. Structures of mismatch replication errors observed in a DNA polymerase. Cell 2004, 116:803-816.
-
(2004)
Cell
, vol.116
, pp. 803-816
-
-
Johnson, S.J.1
Beese, L.S.2
-
75
-
-
80455173836
-
Nanopore sensors for nucleic acid analysis
-
Venkatesan B.M., Bashir R. Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 2011, 6:615-624.
-
(2011)
Nat Nanotechnol
, vol.6
, pp. 615-624
-
-
Venkatesan, B.M.1
Bashir, R.2
-
76
-
-
77958487369
-
Identification of epigenetic DNA modifications with a protein nanopore
-
Wallace E.V., Stoddart D., Heron A.J., Mikhailova E., Maglia G., Donohoe T.J., Bayley H. Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun (Camb) 2010, 46:8195-8197.
-
(2010)
Chem Commun (Camb)
, vol.46
, pp. 8195-8197
-
-
Wallace, E.V.1
Stoddart, D.2
Heron, A.J.3
Mikhailova, E.4
Maglia, G.5
Donohoe, T.J.6
Bayley, H.7
-
77
-
-
80053530116
-
Nucleotide discrimination with DNA immobilized in the MspA nanopore
-
Manrao E.A., Derrington I.M., Pavlenok M., Niederweis M., Gundlach J.H. Nucleotide discrimination with DNA immobilized in the MspA nanopore. PLoS ONE 2011, 6:e25723.
-
(2011)
PLoS ONE
, vol.6
-
-
Manrao, E.A.1
Derrington, I.M.2
Pavlenok, M.3
Niederweis, M.4
Gundlach, J.H.5
-
78
-
-
79851474623
-
Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules
-
Wanunu M., Cohen-Karni D., Johnson R.R., Fields L., Benner J., Peterman N., Zheng Y., Klein M.L., Drndic M. Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules. J Am Chem Soc 2011, 133:486-492.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 486-492
-
-
Wanunu, M.1
Cohen-Karni, D.2
Johnson, R.R.3
Fields, L.4
Benner, J.5
Peterman, N.6
Zheng, Y.7
Klein, M.L.8
Drndic, M.9
-
79
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
Clarke J., Wu H.C., Jayasinghe L., Patel A., Reid S., Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 2009, 4:265-270.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
Patel, A.4
Reid, S.5
Bayley, H.6
-
80
-
-
78650483427
-
Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore
-
Chu J., Gonzalez-Lopez M., Cockroft S.L., Amorin M., Ghadiri M.R. Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. Angew Chem Int Ed Engl 2010, 49:10106-10109.
-
(2010)
Angew Chem Int Ed Engl
, vol.49
, pp. 10106-10109
-
-
Chu, J.1
Gonzalez-Lopez, M.2
Cockroft, S.L.3
Amorin, M.4
Ghadiri, M.R.5
-
81
-
-
78650280872
-
Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase
-
Lieberman K.R., Cherf G.M., Doody M.J., Olasagasti F., Kolodji Y., Akeson M. Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 2010, 132:17961-17972.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 17961-17972
-
-
Lieberman, K.R.1
Cherf, G.M.2
Doody, M.J.3
Olasagasti, F.4
Kolodji, Y.5
Akeson, M.6
-
82
-
-
77953303738
-
Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays
-
McNally B., Singer A., Yu Z., Sun Y., Weng Z., Meller A. Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett 2010, 10:2237-2244.
-
(2010)
Nano Lett
, vol.10
, pp. 2237-2244
-
-
McNally, B.1
Singer, A.2
Yu, Z.3
Sun, Y.4
Weng, Z.5
Meller, A.6
-
83
-
-
80054033858
-
Transfer-printing of single DNA molecule arrays on graphene for high-resolution electron imaging and analysis
-
Cerf A., Alava T., Barton R.A., Craighead H.G. Transfer-printing of single DNA molecule arrays on graphene for high-resolution electron imaging and analysis. Nano Lett 2011, 11:4232-4238.
-
(2011)
Nano Lett
, vol.11
, pp. 4232-4238
-
-
Cerf, A.1
Alava, T.2
Barton, R.A.3
Craighead, H.G.4
-
84
-
-
80155134051
-
Single DNA molecule patterning for high-throughput epigenetic mapping
-
Cerf A., Cipriany B.R., Benitez J.J., Craighead H.G. Single DNA molecule patterning for high-throughput epigenetic mapping. Anal Chem 2011, 83:8073-8077.
-
(2011)
Anal Chem
, vol.83
, pp. 8073-8077
-
-
Cerf, A.1
Cipriany, B.R.2
Benitez, J.J.3
Craighead, H.G.4
-
85
-
-
68949191020
-
Partial sequencing of a single DNA molecule with a scanning tunnelling microscope
-
Tanaka H., Kawai T. Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 2009, 4:518-522.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 518-522
-
-
Tanaka, H.1
Kawai, T.2
-
86
-
-
84255209216
-
Cellular dynamics of RNA modification
-
Yi C., Pan T. Cellular dynamics of RNA modification. Acc Chem Res 2011, 44:1380-1388.
-
(2011)
Acc Chem Res
, vol.44
, pp. 1380-1388
-
-
Yi, C.1
Pan, T.2
-
87
-
-
78651335915
-
The RNA modification database, RNAMDB: 2011 update
-
Cantara W.A., Crain P.F., Rozenski J., McCloskey J.A., Harris K.A., Zhang X., Vendeix F.A., Fabris D., Agris P.F. The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res 2011, 39:D195-D201.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cantara, W.A.1
Crain, P.F.2
Rozenski, J.3
McCloskey, J.A.4
Harris, K.A.5
Zhang, X.6
Vendeix, F.A.7
Fabris, D.8
Agris, P.F.9
-
88
-
-
77950476036
-
5-methylcytosine in RNA: detection, enzymatic formation and biological functions
-
Motorin Y., Lyko F., Helm M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 2010, 38:1415-1430.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1415-1430
-
-
Motorin, Y.1
Lyko, F.2
Helm, M.3
-
89
-
-
33751088560
-
A systematic, ligation-based approach to study RNA modifications
-
Saikia M., Dai Q., Decatur W.A., Fournier M.J., Piccirilli J.A., Pan T. A systematic, ligation-based approach to study RNA modifications. RNA 2006, 12:2025-2033.
-
(2006)
RNA
, vol.12
, pp. 2025-2033
-
-
Saikia, M.1
Dai, Q.2
Decatur, W.A.3
Fournier, M.J.4
Piccirilli, J.A.5
Pan, T.6
-
90
-
-
2442643944
-
Detection and quantitation of RNA base modifications
-
Zhao X., Yu Y.T. Detection and quantitation of RNA base modifications. RNA 2004, 10:996-1002.
-
(2004)
RNA
, vol.10
, pp. 996-1002
-
-
Zhao, X.1
Yu, Y.T.2
-
92
-
-
77953752896
-
Sequence based identification of RNA editing sites
-
Eisenberg E., Li J.B., Levanon E.Y. Sequence based identification of RNA editing sites. RNA Biol 2010, 7:248-252.
-
(2010)
RNA Biol
, vol.7
, pp. 248-252
-
-
Eisenberg, E.1
Li, J.B.2
Levanon, E.Y.3
-
93
-
-
84857727947
-
Single-molecule direct RNA sequencing without cDNA synthesis
-
Ozsolak F., Milos P.M. Single-molecule direct RNA sequencing without cDNA synthesis. Wiley Interdiscip Rev RNA 2011, 2:565-570.
-
(2011)
Wiley Interdiscip Rev RNA
, vol.2
, pp. 565-570
-
-
Ozsolak, F.1
Milos, P.M.2
-
94
-
-
79960072102
-
Transcriptome profiling using single-molecule direct RNA sequencing
-
Ozsolak F., Milos P.M. Transcriptome profiling using single-molecule direct RNA sequencing. Methods Mol Biol 2011, 733:51-61.
-
(2011)
Methods Mol Biol
, vol.733
, pp. 51-61
-
-
Ozsolak, F.1
Milos, P.M.2
-
95
-
-
84862623786
-
-
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. RNA, submitted for publication.
-
Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi C, Pan T, Turner SW, Korlach J: Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. RNA 2012, submitted for publication.
-
(2012)
-
-
Vilfan, I.D.1
Tsai, Y.C.2
Clark, T.A.3
Wegener, J.4
Dai, Q.5
Yi, C.6
Pan, T.7
Turner, S.W.8
Korlach, J.9
|