-
1
-
-
79960927422
-
Generalized loss of stability of epigenetic domains across cancer types.
-
Hansen KD, Timp W, Corrada Bravo H, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Generalized loss of stability of epigenetic domains across cancer types. Nat Genet 2011, 43:768-775.
-
(2011)
Nat Genet
, vol.43
, pp. 768-775
-
-
Hansen, K.D.1
Timp, W.2
Corrada Bravo, H.3
Sabunciyan, S.4
Langmead, B.5
McDonald, O.G.6
Wen, B.7
Wu, H.8
Liu, Y.9
Diep, D.10
Briem, E.11
Zhang, K.12
Irizarry, R.A.13
Feinberg, A.P.14
-
2
-
-
77249137168
-
Principles and challenges of genome-wide DNA methylation analysis
-
Laird PW. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 2010, 11:191.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 191
-
-
Laird, P.W.1
-
3
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences.
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon GC, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.C.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
Edsall, L.11
Antosiewicz-Bourget, J.12
Stewart, R.13
Ruotti, V.14
Millar, A.H.15
Thomson, J.A.16
Ren, B.17
Ecker, J.R.18
-
4
-
-
83755224300
-
Significance analysis and statistical dissection of variably methylated regions
-
Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics 2012, 13:166-178.
-
(2012)
Biostatistics
, vol.13
, pp. 166-178
-
-
Jaffe, A.E.1
Feinberg, A.P.2
Irizarry, R.A.3
Leek, J.T.4
-
5
-
-
64549096371
-
Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete
-
Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Hors- themke B. Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. Hum Mol Genet 2009, 18:1439-1448.
-
(2009)
Hum Mol Genet
, vol.18
, pp. 1439-1448
-
-
Zeschnigk, M.1
Martin, M.2
Betzl, G.3
Kalbe, A.4
Sirsch, C.5
Buiting, K.6
Gross, S.7
Fritzilas, E.8
Frey, B.9
Rahmann, S.10
Hors-themke, B.11
-
6
-
-
78549291439
-
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
-
Coarfa C, Yu F, Miller C, Chen Z, Harris RA, Milosavljevic A. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics 2010, 11:572.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 572
-
-
Coarfa, C.1
Yu, F.2
Miller, C.3
Chen, Z.4
Harris, R.A.5
Milosavljevic, A.6
-
7
-
-
77949497797
-
BRAT: bisulfite-treated reads analysis tool
-
Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S. BRAT: bisulfite-treated reads analysis tool. Bioinformatics 2010, 26:572-573.
-
(2010)
Bioinformatics
, vol.26
, pp. 572-573
-
-
Harris, E.Y.1
Ponts, N.2
Levchuk, A.3
Roch, K.L.4
Lonardi, S.5
-
9
-
-
68949141599
-
BSMAP: whole genome bisulfite sequence MAPping program
-
Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009, 10:232.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 232
-
-
Xi, Y.1
Li, W.2
-
10
-
-
79957868920
-
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011, 27:1571-1572.
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
11
-
-
79952264847
-
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.
-
Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon GC, Antosiewicz-Bourget J, O'Malley RC, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 2011, 471:68-73.
-
(2011)
Nature
, vol.471
, pp. 68-73
-
-
Lister, R.1
Pelizzola, M.2
Kida, Y.S.3
Hawkins, R.D.4
Nery, J.R.5
Hon, G.C.6
Antosiewicz-Bourget, J.7
O'Malley, R.C.8
Castanon, R.9
Klugman, S.10
Downes, M.11
Yu, R.12
Stewart, R.13
Ren, B.14
Thomson, J.A.15
Evans, R.M.16
Ecker, J.R.17
-
12
-
-
78649969065
-
The DNA methylome of human peripheral blood mononuclear cells
-
Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, Zhang H, Chen Q, Luo R, Chen M, He Y, Jin X, Zhang Q, Yu C, Zhou G, Sun J, Huang Y, Zheng H, Cao H, Zhou X, Guo S, Hu X, Li X, Kristiansen K, Bolund L, Xu J, Wang W, Yang H, Wang J, Li R, Beck S, Wang J, Zhang X. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 2010, 8:e1000533.
-
(2010)
PLoS Biol
, vol.8
-
-
Li, Y.1
Zhu, J.2
Tian, G.3
Li, N.4
Li, Q.5
Ye, M.6
Zheng, H.7
Yu, J.8
Wu, H.9
Sun, J.10
Zhang, H.11
Chen, Q.12
Luo, R.13
Chen, M.14
He, Y.15
Jin, X.16
Zhang, Q.17
Yu, C.18
Zhou, G.19
Sun, J.20
Huang, Y.21
Zheng, H.22
Cao, H.23
Zhou, X.24
Guo, S.25
Hu, X.26
Li, X.27
Kristiansen, K.28
Bolund, L.29
Xu, J.30
Wang, W.31
Yang, H.32
Wang, J.33
Li, R.34
Beck, S.35
Wang, J.36
Zhang, X.37
more..
-
13
-
-
80054718602
-
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.
-
Becker C, Hagmann J, MÄuller J, Koenig D, Stegle O, Borgwardt K, Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 2011, 480:245-249.
-
(2011)
Nature
, vol.480
, pp. 245-249
-
-
Becker, C.1
Hagmann, J.2
MÄuller, J.3
Koenig, D.4
Stegle, O.5
Borgwardt, K.6
Weigel, D.7
-
14
-
-
77649267695
-
Dynamic changes in the human methylome during differentiation.
-
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL. Dynamic changes in the human methylome during differentiation. Genome Res 2010, 20:320-331.
-
(2010)
Genome Res
, vol.20
, pp. 320-331
-
-
Laurent, L.1
Wong, E.2
Li, G.3
Huynh, T.4
Tsirigos, A.5
Ong, C.T.6
Low, H.M.7
Kin Sung, K.W.8
Rigoutsos, I.9
Loring, J.10
Wei, C.L.11
-
15
-
-
80052918929
-
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.
-
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell 2011, 44:17-28.
-
(2011)
Mol Cell
, vol.44
, pp. 17-28
-
-
Hodges, E.1
Molaro, A.2
Dos Santos, C.O.3
Thekkat, P.4
Song, Q.5
Uren, P.J.6
Park, J.7
Butler, J.8
Rafii, S.9
McCombie, W.R.10
Smith, A.D.11
Hannon, G.J.12
-
16
-
-
84860130525
-
Social environment is associated with gene regulatory variation in the rhesus macaque immune system.
-
Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, Gilad Y. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proc Natl Acad Sci USA 2012, 109:6490-6495.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 6490-6495
-
-
Tung, J.1
Barreiro, L.B.2
Johnson, Z.P.3
Hansen, K.D.4
Michopoulos, V.5
Toufexis, D.6
Michelini, K.7
Wilson, M.E.8
Gilad, Y.9
-
17
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
-
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
18
-
-
84856576667
-
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data
-
Kreck B, Marnellos G, Richter J, Krueger F, Siebert R, Franke A. B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. Bioinformatics 2012, 28:428-429.
-
(2012)
Bioinformatics
, vol.28
, pp. 428-429
-
-
Kreck, B.1
Marnellos, G.2
Richter, J.3
Krueger, F.4
Siebert, R.5
Franke, A.6
-
19
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
20
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2.
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
21
-
-
68549104404
-
The sequence alignment/map format and SAMtools.
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
22
-
-
78751682536
-
Overcoming bias and systematic errors in next generation sequencing data
-
Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Med 2010, 2:87.
-
(2010)
Genome Med
, vol.2
, pp. 87
-
-
Taub, M.A.1
Corrada Bravo, H.2
Irizarry, R.A.3
-
23
-
-
77956837921
-
Model-based quality assessment and base-calling for second-generation sequencing data
-
Corrada Bravo H, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics 2010, 66:665-674.
-
(2010)
Biometrics
, vol.66
, pp. 665-674
-
-
Corrada Bravo, H.1
Irizarry, R.A.2
-
24
-
-
33751505540
-
DNA methylation profiling of human chromosomes 6, 20 and 22.
-
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006, 38:1378-1385.
-
(2006)
Nat Genet
, vol.38
, pp. 1378-1385
-
-
Eckhardt, F.1
Lewin, J.2
Cortese, R.3
Rakyan, V.K.4
Attwood, J.5
Burger, M.6
Burton, J.7
Cox, T.V.8
Davies, R.9
Down, T.A.10
Haefliger, C.11
Horton, R.12
Howe, K.13
Jackson, D.K.14
Kunde, J.15
Koenig, C.16
Liddle, J.17
Niblett, D.18
Otto, T.19
Pettett, R.20
Seemann, S.21
Thompson, C.22
West, T.23
Rogers, J.24
Olek, A.25
Berlin, K.26
Beck, S.27
more..
-
25
-
-
43149098062
-
Comprehensive high-throughput arrays for relative methylation (CHARM).
-
Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 2008, 18:780-790.
-
(2008)
Genome Res
, vol.18
, pp. 780-790
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Carvalho, B.3
Wu, H.4
Brandenburg, S.A.5
Jeddeloh, J.A.6
Wen, B.7
Feinberg, A.P.8
-
26
-
-
0037372003
-
Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
-
Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003, 33:245-254.
-
(2003)
Nat Genet
, vol.33
, pp. 245-254
-
-
Jaenisch, R.1
Bird, A.2
-
27
-
-
59149084538
-
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
-
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009, 41:178-186.
-
(2009)
Nat Genet
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Wen, B.3
Wu, Z.4
Montano, C.5
Onyango, P.6
Cui, H.7
Gabo, K.8
Rongione, M.9
Webster, M.10
Ji, H.11
Potash, J.B.12
Sabunciyan, S.13
Feinberg, A.P.14
-
29
-
-
84878072314
-
The Human DNA Methylome
-
The Human DNA Methylome. , http://neomorph.salk.edu/human_methylome/data.html
-
-
-
-
30
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
31
-
-
84878075208
-
BSmooth
-
BSmooth. , http://rafalab.jhsph.edu/bsmooth
-
-
-
|