-
1
-
-
77957279300
-
Next generation sequencing in functional genomics
-
2-s2.0-77957279300 10.1093/bib/bbq018
-
Werner T., Next generation sequencing in functional genomics. Briefings in Bioinformatics 2010 11 5 499 511 2-s2.0-77957279300 10.1093/bib/bbq018
-
(2010)
Briefings in Bioinformatics
, vol.11
, Issue.5
, pp. 499-511
-
-
Werner, T.1
-
2
-
-
72849144434
-
Sequencing technologies the next generation
-
2-s2.0-72849144434 10.1038/nrg2626
-
Metzker M. L., Sequencing technologies the next generation. Nature Reviews Genetics 2010 11 1 31 46 2-s2.0-72849144434 10.1038/nrg2626
-
(2010)
Nature Reviews Genetics
, vol.11
, Issue.1
, pp. 31-46
-
-
Metzker, M.L.1
-
3
-
-
64149123778
-
Next-generation sequencing: From basic research to diagnostics
-
2-s2.0-64149123778 10.1373/clinchem.2008.112789
-
Voelkerding K. V., Dames S. A., Durtschi J. D., Next-generation sequencing: from basic research to diagnostics. Clinical Chemistry 2009 55 4 641 658 2-s2.0-64149123778 10.1373/clinchem.2008.112789
-
(2009)
Clinical Chemistry
, vol.55
, Issue.4
, pp. 641-658
-
-
Voelkerding, K.V.1
Dames, S.A.2
Durtschi, J.D.3
-
4
-
-
84858794353
-
Next generation sequencing in epigenetics: Insights and challenges
-
Meaburn E., Schulz R., Next generation sequencing in epigenetics: insights and challenges. Seminars in Cell & Developmental Biology 2011 23 2 192 199
-
(2011)
Seminars in Cell & Developmental Biology
, vol.23
, Issue.2
, pp. 192-199
-
-
Meaburn, E.1
Schulz, R.2
-
5
-
-
81055157018
-
Studying the epigenome using next generation sequencing
-
2-s2.0-79961115155 10.1136/jmedgenet-2011-100242
-
Ku C. S., Naidoo N., Wu M., Soong R., Studying the epigenome using next generation sequencing. Journal of Medical Genetics 2011 48 721 730 2-s2.0-79961115155 10.1136/jmedgenet-2011-100242
-
(2011)
Journal of Medical Genetics
, vol.48
, pp. 721-730
-
-
Ku, C.S.1
Naidoo, N.2
Wu, M.3
Soong, R.4
-
6
-
-
0022540321
-
CpG-rich islands and the function of DNA methylation
-
Bird A. P., CpG-rich islands and the function of DNA methylation. Nature 1986 321 6067 209 213 2-s2.0-0022540321 (Pubitemid 16016411)
-
(1986)
Nature
, vol.321
, Issue.6067
, pp. 209-213
-
-
Bird, A.P.1
-
7
-
-
0023701018
-
Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases
-
2-s2.0-0023701018
-
Bestor T., Laudano A., Mattaliano R., Ingram V., Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. Journal of Molecular Biology 1988 203 4 971 983 2-s2.0-0023701018
-
(1988)
Journal of Molecular Biology
, vol.203
, Issue.4
, pp. 971-983
-
-
Bestor, T.1
Laudano, A.2
Mattaliano, R.3
Ingram, V.4
-
8
-
-
0026697174
-
Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain
-
2-s2.0-0026697174
-
Bestor T. H., Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain. The EMBO Journal 1992 11 7 2611 2617 2-s2.0-0026697174
-
(1992)
The EMBO Journal
, vol.11
, Issue.7
, pp. 2611-2617
-
-
Bestor, T.H.1
-
9
-
-
15244353967
-
X-inactivation profile reveals extensive variability in X-linked gene expression in females
-
DOI 10.1038/nature03479
-
Carrel L., Willard H. F., X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005 434 7031 400 404 2-s2.0-15244353967 10.1038/nature03479 (Pubitemid 40469185)
-
(2005)
Nature
, vol.434
, Issue.7031
, pp. 400-404
-
-
Carrel, L.1
Willard, H.F.2
-
10
-
-
32044455298
-
Large-scale structure of genomic methylation patterns
-
DOI 10.1101/gr.4362006
-
Rollins R. A., Haghighi F., Edwards J. R., Das R., Zhang M. Q., Ju J., Bestor T. H., Large-scale structure of genomic methylation patterns. Genome Research 2006 16 2 157 163 2-s2.0-32044455298 10.1101/gr.4362006 (Pubitemid 43200263)
-
(2006)
Genome Research
, vol.16
, Issue.2
, pp. 157-163
-
-
Rollins, R.A.1
Haghighi, F.2
Edwards, J.R.3
Das, R.4
Zhang, M.Q.5
Ju, J.6
Bestor, T.H.7
-
11
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
DOI 10.1038/nrg2341, PII NRG2341
-
Suzuki M. M., Bird A., DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics 2008 9 6 465 476 2-s2.0-43749098985 10.1038/nrg2341 (Pubitemid 351693975)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.6
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
12
-
-
53449100282
-
Quantitative analysis of human tissue-specific differences in methylation
-
2-s2.0-53449100282 10.1016/j.bbrc.2008.09.044
-
Igarashi J., Muroi S., Kawashima H., Wang X., Shinojima Y., Kitamura E., Oinuma T., Nemoto N., Song F., Ghosh S., Held W. A., Nagase H., Quantitative analysis of human tissue-specific differences in methylation. Biochemical and Biophysical Research Communications 2008 376 4 658 664 2-s2.0-53449100282 10.1016/j.bbrc.2008.09.044
-
(2008)
Biochemical and Biophysical Research Communications
, vol.376
, Issue.4
, pp. 658-664
-
-
Igarashi, J.1
Muroi, S.2
Kawashima, H.3
Wang, X.4
Shinojima, Y.5
Kitamura, E.6
Oinuma, T.7
Nemoto, N.8
Song, F.9
Ghosh, S.10
Held, W.A.11
Nagase, H.12
-
13
-
-
84868520898
-
Monozygotic twins: Genes are not the destiny?
-
Chatterjee A., Morison I. M., Monozygotic twins: genes are not the destiny? Bioinformation 2011 7 7 369 370
-
(2011)
Bioinformation
, vol.7
, Issue.7
, pp. 369-370
-
-
Chatterjee, A.1
Morison, I.M.2
-
14
-
-
0036561649
-
Altered methylation patterns in cancer cell genomes: Cause or consequence?
-
DOI 10.1016/S1535-6108(02)00061-2
-
Baylin S., Bestor T. H., Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 2002 1 4 299 305 2-s2.0-0036561649 10.1016/S1535-6108(02)00061-2 (Pubitemid 41039130)
-
(2002)
Cancer Cell
, vol.1
, Issue.4
, pp. 299-305
-
-
Baylin, S.1
Bestor, T.H.2
-
15
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
2-s2.0-49649125042 10.1038/nature07107
-
Meissner A., Mikkelsen T. S., Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein B. E., Nusbaum C., Jaffe D. B., Gnirke A., Jaenisch R., Lander E. S., Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008 454 7205 766 770 2-s2.0-49649125042 10.1038/nature07107
-
(2008)
Nature
, vol.454
, Issue.7205
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
Gnirke, A.11
Jaenisch, R.12
Lander, E.S.13
-
16
-
-
84856568045
-
RRBSMAP: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
-
Xi Y., Bock C., Muller F., RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 2012 28 3 430 432
-
(2012)
Bioinformatics
, vol.28
, Issue.3
, pp. 430-432
-
-
Xi, Y.1
Bock, C.2
Muller, F.3
-
17
-
-
77951836633
-
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis
-
2-s2.0-77951836633 10.1038/nature08990
-
Baranzini S. E., Mudge J., Van Velkinburgh J. C., Khankhanian P., Khrebtukova I., Miller N. A., Zhang L., Farmer A. D., Bell C. J., Kim R. W., May G. D., Woodward J. E., Caillier S. J., McElroy J. P., Gomez R., Pando M. J., Clendenen L. E., Ganusova E. E., Schilkey F. D., Ramaraj T., Khan O. A., Huntley J. J., Luo S., Kwok P. Y., Wu T. D., Schroth G. P., Oksenberg J. R., Hauser S. L., Kingsmore S. F., Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 2010 464 7293 1351 1356 2-s2.0-77951836633 10.1038/nature08990
-
(2010)
Nature
, vol.464
, Issue.7293
, pp. 1351-1356
-
-
Baranzini, S.E.1
Mudge, J.2
Van Velkinburgh, J.C.3
Khankhanian, P.4
Khrebtukova, I.5
Miller, N.A.6
Zhang, L.7
Farmer, A.D.8
Bell, C.J.9
Kim, R.W.10
May, G.D.11
Woodward, J.E.12
Caillier, S.J.13
McElroy, J.P.14
Gomez, R.15
Pando, M.J.16
Clendenen, L.E.17
Ganusova, E.E.18
Schilkey, F.D.19
Ramaraj, T.20
Khan, O.A.21
Huntley, J.J.22
Luo, S.23
Kwok, P.Y.24
Wu, T.D.25
Schroth, G.P.26
Oksenberg, J.R.27
Hauser, S.L.28
Kingsmore, S.F.29
more..
-
18
-
-
79551677421
-
Reference maps of human es and ips cell variation enable high-throughput characterization of pluripotent cell lines
-
2-s2.0-79551677421 10.1016/j.cell.2010.12.032
-
Bock C., Kiskinis E., Verstappen G., Gu H., Boulting G., Smith Z. D., Ziller M., Croft G. F., Amoroso M. W., Oakley D. H., Gnirke A., Eggan K., Meissner A., Reference maps of human es and ips cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011 144 3 439 452 2-s2.0-79551677421 10.1016/j.cell.2010.12.032
-
(2011)
Cell
, vol.144
, Issue.3
, pp. 439-452
-
-
Bock, C.1
Kiskinis, E.2
Verstappen, G.3
Gu, H.4
Boulting, G.5
Smith, Z.D.6
Ziller, M.7
Croft, G.F.8
Amoroso, M.W.9
Oakley, D.H.10
Gnirke, A.11
Eggan, K.12
Meissner, A.13
-
19
-
-
80052306947
-
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
-
e1002228
-
Gertz J., Varley K. E., Reddy T. E., Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genetics 2011 7 8 e1002228
-
(2011)
PLoS Genetics
, vol.7
, Issue.8
-
-
Gertz, J.1
Varley, K.E.2
Reddy, T.E.3
-
20
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
2-s2.0-77449153454 10.1038/nmeth.1414
-
Gu H., Bock C., Mikkelsen T. S., Jäger N., Smith Z. D., Tomazou E., Gnirke A., Lander E. S., Meissner A., Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods 2010 7 2 133 136 2-s2.0-77449153454 10.1038/nmeth.1414
-
(2010)
Nature Methods
, vol.7
, Issue.2
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
Jäger, N.4
Smith, Z.D.5
Tomazou, E.6
Gnirke, A.7
Lander, E.S.8
Meissner, A.9
-
21
-
-
79960926264
-
Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
-
2-s2.0-79960926264 10.1038/ng.864
-
Smallwood S. A., Tomizawa S. I., Krueger F., Ruf N., Carli N., Segonds-Pichon A., Sato S., Hata K., Andrews S. R., Kelsey G., Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nature Genetics 2011 43 8 811 814 2-s2.0-79960926264 10.1038/ng.864
-
(2011)
Nature Genetics
, vol.43
, Issue.8
, pp. 811-814
-
-
Smallwood, S.A.1
Tomizawa, S.I.2
Krueger, F.3
Ruf, N.4
Carli, N.5
Segonds-Pichon, A.6
Sato, S.7
Hata, K.8
Andrews, S.R.9
Kelsey, G.10
-
22
-
-
79955510962
-
Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer
-
2-s2.0-79955510962 10.1172/JCI43169
-
Steine E. J., Ehrich M., Bell G. W., Raj A., Reddy S., Van Oudenaarden A., Jaenisch R., Linhart H. G., Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. The Journal of Clinical Investigation 2011 121 5 1748 1752 2-s2.0-79955510962 10.1172/JCI43169
-
(2011)
The Journal of Clinical Investigation
, vol.121
, Issue.5
, pp. 1748-1752
-
-
Steine, E.J.1
Ehrich, M.2
Bell, G.W.3
Raj, A.4
Reddy, S.5
Van Oudenaarden, A.6
Jaenisch, R.7
Linhart, H.G.8
-
23
-
-
68949141599
-
BSMAP: Whole genome bisulfite sequence MAPping program
-
2-s2.0-68949141599 10.1186/1471-2105-10-232article 232
-
Xi Y., Li W., BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009 10, article 232 2-s2.0-68949141599 10.1186/1471-2105-10-232
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Xi, Y.1
Li, W.2
-
24
-
-
84861563688
-
Comparison of alignment software for genome-wide bisulphite sequence data
-
Article E79
-
Chatterjee A., Stockwell P. A., Rodger E. J., Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research 2012 40 10, article e79
-
(2012)
Nucleic Acids Research
, vol.40
, Issue.10
-
-
Chatterjee, A.1
Stockwell, P.A.2
Rodger, E.J.3
-
25
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
2-s2.0-79957868920 10.1093/bioinformatics/btr167
-
Krueger F., Andrews S. R., Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011 27 11 1571 1572 2-s2.0-79957868920 10.1093/bioinformatics/btr167
-
(2011)
Bioinformatics
, vol.27
, Issue.11
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
26
-
-
67649854923
-
High-throughput bisulfite sequencing in mammalian genomes
-
2-s2.0-67649854923 10.1016/j.ymeth.2009.05.003
-
Smith Z. D., Gu H., Bock C., Gnirke A., Meissner A., High-throughput bisulfite sequencing in mammalian genomes. Methods 2009 48 3 226 232 2-s2.0-67649854923 10.1016/j.ymeth.2009.05.003
-
(2009)
Methods
, vol.48
, Issue.3
, pp. 226-232
-
-
Smith, Z.D.1
Gu, H.2
Bock, C.3
Gnirke, A.4
Meissner, A.5
-
27
-
-
79952788617
-
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
-
2-s2.0-79952788617 10.1038/nprot.2010.190
-
Gu H., Smith Z. D., Bock C., Boyle P., Gnirke A., Meissner A., Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 2011 6 4 468 481 2-s2.0-79952788617 10.1038/nprot.2010.190
-
(2011)
Nature Protocols
, vol.6
, Issue.4
, pp. 468-481
-
-
Gu, H.1
Smith, Z.D.2
Bock, C.3
Boyle, P.4
Gnirke, A.5
Meissner, A.6
-
28
-
-
0036311202
-
Identification and resolution of artifacts in bisulfite sequencing
-
DOI 10.1016/S1046-2023(02)00060-9, PII S1046202302000609
-
Warnecke P. M., Stirzaker C., Song J., Grunau C., Melki J. R., Clark S. J., Identification and resolution of artifacts in bisulfite sequencing. Methods 2002 27 2 101 107 2-s2.0-0036311202 10.1016/S1046-2023(02)00060-9 (Pubitemid 34757119)
-
(2002)
Methods
, vol.27
, Issue.2
, pp. 101-107
-
-
Warnecke, P.M.1
Stirzaker, C.2
Song, J.3
Grunau, C.4
Melki, J.R.5
Clark, S.J.6
-
30
-
-
0014682668
-
Structure of subtilisin B P N ′ at 2.5 Å resolution
-
2-s2.0-0014682668 10.1038/221235a0
-
Wright C. S., Alden R. A., Kraut J., Structure of subtilisin B P N ′ at 2.5 Å resolution. Nature 1969 221 5177 235 242 2-s2.0-0014682668 10.1038/221235a0
-
(1969)
Nature
, vol.221
, Issue.5177
, pp. 235-242
-
-
Wright, C.S.1
Alden, R.A.2
Kraut, J.3
-
31
-
-
77951226627
-
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
-
2-s2.0-77951226627 10.1093/nar/gkp1137
-
Cock P. J. A., Fields C. J., Goto N., Heuer M. L., Rice P. M., The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2009 38 6 1767 1771 2-s2.0-77951226627 10.1093/nar/gkp1137
-
(2009)
Nucleic Acids Research
, vol.38
, Issue.6
, pp. 1767-1771
-
-
Cock, P.J.A.1
Fields, C.J.2
Goto, N.3
Heuer, M.L.4
Rice, P.M.5
-
32
-
-
77957151956
-
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
-
2-s2.0-77957151956 10.1186/1471-2105-11-485 article 485
-
Cox M. P., Peterson D. A., Biggs P. J., SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010 11, article 485 2-s2.0-77957151956 10.1186/1471-2105-11-485
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
|