-
1
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
10.1101/gad.947102, 11782440
-
Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002, 16:6-21. 10.1101/gad.947102, 11782440.
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
2
-
-
82955207588
-
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation
-
10.1101/gad.179184.111, 3243055, 22156206
-
Wu H, Zhang Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev 2011, 25:2436-2452. 10.1101/gad.179184.111, 3243055, 22156206.
-
(2011)
Genes Dev
, vol.25
, pp. 2436-2452
-
-
Wu, H.1
Zhang, Y.2
-
3
-
-
66149123748
-
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain
-
10.1126/science.1169786, 3263819, 19372393
-
Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930. 10.1126/science.1169786, 3263819, 19372393.
-
(2009)
Science
, vol.324
, pp. 929-930
-
-
Kriaucionis, S.1
Heintz, N.2
-
4
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
10.1126/science.1170116, 2715015, 19372391
-
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935. 10.1126/science.1170116, 2715015, 19372391.
-
(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
Rao, A.11
-
5
-
-
79960626636
-
The discovery of 5-formylcytosine in embryonic stem cell DNA
-
10.1002/anie.201103899, 21721093
-
Pfaffeneder T, Hackner B, Truss M, Munzel M, Muller M, Deiml CA, Hagemeier C, Carell T. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew Chem Int Ed Engl 2011, 50:7008-7012. 10.1002/anie.201103899, 21721093.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, pp. 7008-7012
-
-
Pfaffeneder, T.1
Hackner, B.2
Truss, M.3
Munzel, M.4
Muller, M.5
Deiml, C.A.6
Hagemeier, C.7
Carell, T.8
-
6
-
-
80052495940
-
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
-
10.1126/science.1210944, 3462231, 21817016
-
He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011, 333:1303-1307. 10.1126/science.1210944, 3462231, 21817016.
-
(2011)
Science
, vol.333
, pp. 1303-1307
-
-
He, Y.F.1
Li, B.Z.2
Li, Z.3
Liu, P.4
Wang, Y.5
Tang, Q.6
Ding, J.7
Jia, Y.8
Chen, Z.9
Li, L.10
Sun, Y.11
Li, X.12
Dai, Q.13
Song, C.X.14
Zhang, K.15
He, C.16
Xu, G.L.17
-
7
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
10.1126/science.1210597, 3495246, 21778364
-
Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333:1300-1303. 10.1126/science.1210597, 3495246, 21778364.
-
(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
-
8
-
-
84862776719
-
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA
-
10.1038/nchembio.914, 3307914, 22327402
-
Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu G-L, Luo C, Jiang H, He C. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol 2012, 8:328-330. 10.1038/nchembio.914, 3307914, 22327402.
-
(2012)
Nat Chem Biol
, vol.8
, pp. 328-330
-
-
Zhang, L.1
Lu, X.2
Lu, J.3
Liang, H.4
Dai, Q.5
Xu, G.-L.6
Luo, C.7
Jiang, H.8
He, C.9
-
9
-
-
79959987448
-
5-hydroxymethylcytosine, the sixth base of the genome
-
10.1002/anie.201101547, 21688365
-
Münzel M, Globisch D, Carell T. 5-hydroxymethylcytosine, the sixth base of the genome. Angew Chem Int Ed Engl 2011, 50:6460-6468. 10.1002/anie.201101547, 21688365.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, pp. 6460-6468
-
-
Münzel, M.1
Globisch, D.2
Carell, T.3
-
10
-
-
84871222928
-
The methylomes of six bacteria
-
10.1093/nar/gks891, 3526280, 23034806
-
Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ. The methylomes of six bacteria. Nucleic Acids Res 2012, 40:11450-11462. 10.1093/nar/gks891, 3526280, 23034806.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11450-11462
-
-
Murray, I.A.1
Clark, T.A.2
Morgan, R.D.3
Boitano, M.4
Anton, B.P.5
Luong, K.6
Fomenkov, A.7
Turner, S.W.8
Korlach, J.9
Roberts, R.J.10
-
11
-
-
64349112326
-
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more
-
10.1111/j.1574-6976.2008.00159.x, 2941194, 19175412
-
Marinus MG, Casadesus J. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 2009, 33:488-503. 10.1111/j.1574-6976.2008.00159.x, 2941194, 19175412.
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 488-503
-
-
Marinus, M.G.1
Casadesus, J.2
-
12
-
-
0035189042
-
Roles of DNA adenine methylation in regulating bacterial gene expression and virulence
-
10.1128/IAI.69.12.7197-7204.2001, 98802, 11705888
-
Low DA, Weyand NJ, Mahan MJ. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun 2001, 69:7197-7204. 10.1128/IAI.69.12.7197-7204.2001, 98802, 11705888.
-
(2001)
Infect Immun
, vol.69
, pp. 7197-7204
-
-
Low, D.A.1
Weyand, N.J.2
Mahan, M.J.3
-
13
-
-
77749277177
-
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
-
10.1371/journal.pone.0008888, 2811190, 20126651
-
Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PloS One 2010, 5:e8888. 10.1371/journal.pone.0008888, 2811190, 20126651.
-
(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
-
14
-
-
84861990517
-
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome
-
10.1016/j.cell.2012.04.027, 22608086
-
Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380. 10.1016/j.cell.2012.04.027, 22608086.
-
(2012)
Cell
, vol.149
, pp. 1368-1380
-
-
Yu, M.1
Hon, G.C.2
Szulwach, K.E.3
Song, C.X.4
Zhang, L.5
Kim, A.6
Li, X.7
Dai, Q.8
Shen, Y.9
Park, B.10
Min, J.H.11
Jin, P.12
Ren, B.13
He, C.14
-
15
-
-
84861221693
-
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
-
10.1126/science.1220671, 22539555
-
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012, 336:934-937. 10.1126/science.1220671, 22539555.
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
Branco, M.R.2
Ficz, G.3
Oxley, D.4
Krueger, F.5
Reik, W.6
Balasubramanian, S.7
-
16
-
-
84857877933
-
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
-
10.1093/nar/gkr1146, 3287169, 22156058
-
Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, Boitano M, Fomenkov A, Roberts RJ, Korlach J. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 2012, 40:e29. 10.1093/nar/gkr1146, 3287169, 22156058.
-
(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
Boitano, M.6
Fomenkov, A.7
Roberts, R.J.8
Korlach, J.9
-
17
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
10.1038/nmeth.1459, 2879396, 20453866
-
Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7:461-465. 10.1038/nmeth.1459, 2879396, 20453866.
-
(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
-
18
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
10.1126/science.1162986, 19023044
-
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138. 10.1126/science.1162986, 19023044.
-
(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
Bibillo, A.11
Bjornson, K.12
Chaudhuri, B.13
Christians, F.14
Cicero, R.15
Clark, S.16
Dalal, R.17
Dewinter, A.18
Dixon, J.19
Foquet, M.20
Gaertner, A.21
Hardenbol, P.22
Heiner, C.23
Hester, K.24
Holden, D.25
Kearns, G.26
Kong, X.27
Kuse, R.28
Lacroix, Y.29
Lin, S.30
Lundquist, P.31
more..
-
19
-
-
77957051540
-
Real-time DNA sequencing from single polymerase molecules
-
Korlach J, Bjornson KP, Chaudhuri BP, Cicero RL, Flusberg BA, Gray JJ, Holden D, Saxena R, Wegener J, Turner SW. 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
-
20
-
-
84861802222
-
Direct detection and sequencing of damaged DNA bases
-
10.1186/2041-9414-2-10, 3264494, 22185597
-
Clark TA, Spittle KE, Turner SW, Korlach J. Direct detection and sequencing of damaged DNA bases. Genome Integr 2011, 2:10. 10.1186/2041-9414-2-10, 3264494, 22185597.
-
(2011)
Genome Integr
, vol.2
, pp. 10
-
-
Clark, T.A.1
Spittle, K.E.2
Turner, S.W.3
Korlach, J.4
-
21
-
-
84856453032
-
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine
-
Song CX, Clark TA, Lu XY, Kislyuk A, Dai Q, Turner SW, He C, Korlach J. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods 2012, 9:75-77.
-
(2012)
Nat Methods
, vol.9
, pp. 75-77
-
-
Song, C.X.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
-
22
-
-
8844274078
-
Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29
-
10.1016/j.molcel.2004.10.019, 15546620
-
Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol Cell 2004, 16:609-618. 10.1016/j.molcel.2004.10.019, 15546620.
-
(2004)
Mol Cell
, vol.16
, pp. 609-618
-
-
Kamtekar, S.1
Berman, A.J.2
Wang, J.3
Lazaro, J.M.4
de Vega, M.5
Blanco, L.6
Salas, M.7
Steitz, T.A.8
-
23
-
-
0026338873
-
Restriction and modification systems
-
10.1146/annurev.ge.25.120191.003101, 1812816
-
Wilson GG, Murray NE. Restriction and modification systems. Ann Rev Genet 1991, 25:585-627. 10.1146/annurev.ge.25.120191.003101, 1812816.
-
(1991)
Ann Rev Genet
, vol.25
, pp. 585-627
-
-
Wilson, G.G.1
Murray, N.E.2
-
24
-
-
75549086595
-
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
-
10.1093/nar/gkp874, 2808884, 19846593
-
Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010, 38:D234-236. 10.1093/nar/gkp874, 2808884, 19846593.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
25
-
-
84863664355
-
A hybrid approach for the automated finishing of bacterial genomes
-
Bashir A, Klammer AA, Robins WP, Chin C-S, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotech 2012, 30:701-707.
-
(2012)
Nat Biotech
, vol.30
, pp. 701-707
-
-
Bashir, A.1
Klammer, A.A.2
Robins, W.P.3
Chin, C.-S.4
Webster, D.5
Paxinos, E.6
Hsu, D.7
Ashby, M.8
Wang, S.9
Peluso, P.10
Sebra, R.11
Sorenson, J.12
Bullard, J.13
Yen, J.14
Valdovino, M.15
Mollova, E.16
Luong, K.17
Lin, S.18
LaMay, B.19
Joshi, A.20
Rowe, L.21
Frace, M.22
Tarr, C.L.23
Turnsek, M.24
Davis, B.M.25
Kasarskis, A.26
Mekalanos, J.J.27
Waldor, M.K.28
Schadt, E.E.29
more..
-
26
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotech 2012, 30:6.93-700.
-
(2012)
Nat Biotech
, vol.30
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
Wang, Z.7
Rasko, D.A.8
McCombie, W.R.9
Jarvis, E.D.10
Phillippy, A.M.11
-
27
-
-
84870880581
-
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
-
Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature Biotechnol 2012, 30:1232-1239.
-
(2012)
Nature Biotechnol
, vol.30
, pp. 1232-1239
-
-
Fang, G.1
Munera, D.2
Friedman, D.I.3
Mandlik, A.4
Chao, M.C.5
Banerjee, O.6
Feng, Z.7
Losic, B.8
Mahajan, M.C.9
Jabado, O.J.10
Deikus, G.11
Clark, T.A.12
Luong, K.13
Murray, I.A.14
Davis, B.M.15
Keren-Paz, A.16
Chess, A.17
Roberts, R.J.18
Korlach, J.19
Turner, S.W.20
Kumar, V.21
Waldor, M.K.22
Schadt, E.E.23
more..
-
28
-
-
84870939871
-
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
-
3530673, 23093720
-
Schadt E, Banerjee O, Fang G, Feng Z, Wong W, Zhang X, Kislyuk A, Clark T, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res 2012, 23:129-141. 3530673, 23093720.
-
(2012)
Genome Res
, vol.23
, pp. 129-141
-
-
Schadt, E.1
Banerjee, O.2
Fang, G.3
Feng, Z.4
Wong, W.5
Zhang, X.6
Kislyuk, A.7
Clark, T.8
Luong, K.9
Keren-Paz, A.10
Chess, A.11
Kumar, V.12
Chen-Plotkin, A.13
Sondheimer, N.14
Korlach, J.15
Kasarskis, A.16
-
29
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
10.1093/nar/gkq543, 2926623, 20571086
-
Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010, 38:e159. 10.1093/nar/gkq543, 2926623, 20571086.
-
(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
-
30
-
-
84874696797
-
BLASR
-
BLASR. , http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR
-
-
-
-
31
-
-
84874668916
-
SMRT Analysis
-
SMRT Analysis. , http://www.smrtcommunity.com/SMRT-Analysis/Software/SMRT-Analysis
-
-
-
-
32
-
-
84874748102
-
Detecting DNA Base Modifications
-
Detecting DNA Base Modifications. , http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf
-
-
-
-
33
-
-
79958117256
-
MEME-ChIP: motif analysis of large DNA datasets
-
10.1093/bioinformatics/btr189, 3106185, 21486936
-
Machanick P, Bailey TL. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 2011, 27:1696-1697. 10.1093/bioinformatics/btr189, 3106185, 21486936.
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.L.2
-
34
-
-
69649109364
-
Circos: an information aesthetic for comparative genomics
-
10.1101/gr.092759.109, 2752132, 19541911
-
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
|