-
1
-
-
0020699979
-
Hypomethylation distinguishes genes of some human cancers from their normal counterparts
-
6185846
-
Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301:89-92. 10.1038/301089a0, 6185846.
-
(1983)
Nature
, vol.301
, pp. 89-92
-
-
Feinberg, A.P.1
Vogelstein, B.2
-
2
-
-
0024365892
-
Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma
-
2550354
-
Greger V, Passarge E, Hopping W, Messmer E, Horsthemke B. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet 1989, 83:155-158. 10.1007/BF00286709, 2550354.
-
(1989)
Hum Genet
, vol.83
, pp. 155-158
-
-
Greger, V.1
Passarge, E.2
Hopping, W.3
Messmer, E.4
Horsthemke, B.5
-
3
-
-
59149083658
-
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
-
19151716
-
Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 2009, 41:246-250. 10.1038/ng.297, 19151716.
-
(2009)
Nat Genet
, vol.41
, pp. 246-250
-
-
Wen, B.1
Wu, H.2
Shinkai, Y.3
Irizarry, R.A.4
Feinberg, A.P.5
-
4
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
19829295
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, 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. 10.1038/nature08514, 19829295.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.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
-
5
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
21706001
-
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011, 43:768-775. 10.1038/ng.865, 21706001.
-
(2011)
Nat Genet
, vol.43
, pp. 768-775
-
-
Hansen, K.D.1
Timp, W.2
Bravo, H.C.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
-
6
-
-
84655162785
-
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains
-
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2012, 44:40-46. 10.1038/ng.969.
-
(2012)
Nat Genet
, vol.44
, pp. 40-46
-
-
Berman, B.P.1
Weisenberger, D.J.2
Aman, J.F.3
Hinoue, T.4
Ramjan, Z.5
Liu, Y.6
Noushmehr, H.7
Lange, C.P.8
van Dijk, C.M.9
Tollenaar, R.A.10
Van Den Berg, D.11
Laird, P.W.12
-
7
-
-
84856528270
-
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
-
22156296
-
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012, 22:246-258. 10.1101/gr.125872.111, 22156296.
-
(2012)
Genome Res
, vol.22
, pp. 246-258
-
-
Hon, G.C.1
Hawkins, R.D.2
Caballero, O.L.3
Lo, C.4
Lister, R.5
Pelizzola, M.6
Valsesia, A.7
Ye, Z.8
Kuan, S.9
Edsall, L.E.10
Camargo, A.A.11
Stevenson, B.J.12
Ecker, J.R.13
Bafna, V.14
Strausberg, R.L.15
Simpson, A.J.16
Ren, B.17
-
8
-
-
84903516439
-
Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing
-
24847876
-
Hovestadt V, Jones DT, Picelli S, Wang W, Kool M, Northcott PA, Sultan M, Stachurski K, Ryzhova M, Warnatz HJ, Ralser M, Brun S, Bunt J, Jager N, Kleinheinz K, Erkek S, Weber UD, Bartholomae CC, von Kalle C, Lawrenz C, Eils J, Koster J, Versteeg R, Milde T, Witt O, Schmidt S, Wolf S, Pietsch T, Rutkowski S, Scheurlen W, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 2014, 510:537-541. 10.1038/nature13268, 24847876.
-
(2014)
Nature
, vol.510
, pp. 537-541
-
-
Hovestadt, V.1
Jones, D.T.2
Picelli, S.3
Wang, W.4
Kool, M.5
Northcott, P.A.6
Sultan, M.7
Stachurski, K.8
Ryzhova, M.9
Warnatz, H.J.10
Ralser, M.11
Brun, S.12
Bunt, J.13
Jager, N.14
Kleinheinz, K.15
Erkek, S.16
Weber, U.D.17
Bartholomae, C.C.18
von Kalle, C.19
Lawrenz, C.20
Eils, J.21
Koster, J.22
Versteeg, R.23
Milde, T.24
Witt, O.25
Schmidt, S.26
Wolf, S.27
Pietsch, T.28
Rutkowski, S.29
Scheurlen, W.30
more..
-
9
-
-
84893711405
-
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization
-
24068705
-
Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res 2014, 24:177-184. 10.1101/gr.157743.113, 24068705.
-
(2014)
Genome Res
, vol.24
, pp. 177-184
-
-
Hansen, K.D.1
Sabunciyan, S.2
Langmead, B.3
Nagy, N.4
Curley, R.5
Klein, G.6
Klein, E.7
Salamon, D.8
Feinberg, A.P.9
-
10
-
-
80053493397
-
Large-scale methylation domains mark a functional subset of neuronally expressed genes
-
21784875
-
Schroeder DI, Lott P, Korf I, LaSalle JM. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res 2011, 21:1583-1591. 10.1101/gr.119131.110, 21784875.
-
(2011)
Genome Res
, vol.21
, pp. 1583-1591
-
-
Schroeder, D.I.1
Lott, P.2
Korf, I.3
LaSalle, J.M.4
-
11
-
-
84858828509
-
Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation
-
22453031
-
Teschendorff AE, Jones A, Fiegl H, Sargent A, Zhuang JJ, Kitchener HC, Widschwendter M. Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. Genome Med 2012, 4:24. 10.1186/gm323, 22453031.
-
(2012)
Genome Med
, vol.4
, pp. 24
-
-
Teschendorff, A.E.1
Jones, A.2
Fiegl, H.3
Sargent, A.4
Zhuang, J.J.5
Kitchener, H.C.6
Widschwendter, M.7
-
12
-
-
84898746948
-
Age-related epigenetic drift in the pathogenesis of MDS and AML
-
24414704
-
Maegawa S, Gough SM, Watanabe-Okochi N, Lu Y, Zhang N, Castoro RJ, Estecio MR, Jelinek J, Liang S, Kitamura T, Aplan PD, Issa JP. Age-related epigenetic drift in the pathogenesis of MDS and AML. Genome Res 2014, 24:580-591. 10.1101/gr.157529.113, 24414704.
-
(2014)
Genome Res
, vol.24
, pp. 580-591
-
-
Maegawa, S.1
Gough, S.M.2
Watanabe-Okochi, N.3
Lu, Y.4
Zhang, N.5
Castoro, R.J.6
Estecio, M.R.7
Jelinek, J.8
Liang, S.9
Kitamura, T.10
Aplan, P.D.11
Issa, J.P.12
-
13
-
-
84896501999
-
Molecular rules governing de novo methylation in cancer
-
24453003
-
Nejman D, Straussman R, Steinfeld I, Ruvolo M, Roberts D, Yakhini Z, Cedar H. Molecular rules governing de novo methylation in cancer. Cancer Res 2014, 74:1475-1483. 10.1158/0008-5472.CAN-13-3042, 24453003.
-
(2014)
Cancer Res
, vol.74
, pp. 1475-1483
-
-
Nejman, D.1
Straussman, R.2
Steinfeld, I.3
Ruvolo, M.4
Roberts, D.5
Yakhini, Z.6
Cedar, H.7
-
14
-
-
84921690954
-
-
Epiviz: interactive visual analytics for functional genomics data. Nat Methods 2014, [epub ahead of print]
-
Chelaru F, Smith L, Goldstein N, Chelaru F, Smith L, Goldstein N, Bravo HC: Epiviz: interactive visual analytics for functional genomics data. Nat Methods 2014, [epub ahead of print] doi:10.1038/nmeth.3038.
-
-
-
Chelaru, F.1
Smith, L.2
Goldstein, N.3
Chelaru, F.4
Smith, L.5
Goldstein, N.6
Bravo, H.C.7
-
15
-
-
84897548625
-
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
-
24478339
-
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 2014, 30:1363-1369. 10.1093/bioinformatics/btu049, 24478339.
-
(2014)
Bioinformatics
, vol.30
, pp. 1363-1369
-
-
Aryee, M.J.1
Jaffe, A.E.2
Corrada-Bravo, H.3
Ladd-Acosta, C.4
Feinberg, A.P.5
Hansen, K.D.6
Irizarry, R.A.7
-
16
-
-
84863386102
-
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
-
22422453
-
Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012, 41:200-209. 10.1093/ije/dyr238, 22422453.
-
(2012)
Int J Epidemiol
, vol.41
, pp. 200-209
-
-
Jaffe, A.E.1
Murakami, P.2
Lee, H.3
Leek, J.T.4
Fallin, M.D.5
Feinberg, A.P.6
Irizarry, R.A.7
-
17
-
-
77749291770
-
Frozen robust multiarray analysis (fRMA)
-
20097884
-
McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics 2010, 11:242-253. 10.1093/biostatistics/kxp059, 20097884.
-
(2010)
Biostatistics
, vol.11
, pp. 242-253
-
-
McCall, M.N.1
Bolstad, B.M.2
Irizarry, R.A.3
-
18
-
-
84867637986
-
Gene expression anti-profiles as a basis for accurate universal cancer signatures
-
23088656
-
Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics 2012, 13:272. 10.1186/1471-2105-13-272, 23088656.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 272
-
-
Bravo, H.C.1
Pihur, V.2
McCall, M.3
Irizarry, R.A.4
Leek, J.T.5
-
19
-
-
84898957989
-
Determinants of expression variability
-
24435799
-
Alemu EY, Carl JW, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Res 2014, 42:3503-3514. 10.1093/nar/gkt1364, 24435799.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 3503-3514
-
-
Alemu, E.Y.1
Carl, J.W.2
Corrada Bravo, H.3
Hannenhalli, S.4
-
20
-
-
35748952199
-
A gene expression bar code for microarray data
-
17906632
-
Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nat Methods 2007, 4:911-913. 10.1038/nmeth1102, 17906632.
-
(2007)
Nat Methods
, vol.4
, pp. 911-913
-
-
Zilliox, M.J.1
Irizarry, R.A.2
-
21
-
-
78651271261
-
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes
-
21177656
-
McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res 2011, 39:D1011-1015. 10.1093/nar/gkq1259, 21177656.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1011-1015
-
-
McCall, M.N.1
Uppal, K.2
Jaffee, H.A.3
Zilliox, M.J.4
Irizarry, R.A.5
-
22
-
-
70449730819
-
The Bethesda System For Reporting Thyroid Cytopathology
-
19846805
-
Cibas ES, Ali SZ. The Bethesda System For Reporting Thyroid Cytopathology. Am J Clin Pathol 2009, 132:658-665. 10.1309/AJCPPHLWMI3JV4LA, 19846805.
-
(2009)
Am J Clin Pathol
, vol.132
, pp. 658-665
-
-
Cibas, E.S.1
Ali, S.Z.2
-
23
-
-
45149084413
-
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
-
18463634
-
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008, 453:948-951. 10.1038/nature06947, 18463634.
-
(2008)
Nature
, vol.453
, pp. 948-951
-
-
Guelen, L.1
Pagie, L.2
Brasset, E.3
Meuleman, W.4
Faza, M.B.5
Talhout, W.6
Eussen, B.H.7
de Klein, A.8
Wessels, L.9
de Laat, W.10
van Steensel, B.11
-
24
-
-
79961023271
-
Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition
-
21725293
-
McDonald OG, Wu H, Timp W, Doi A, Feinberg AP. Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. Nat Struct Mol Biol 2011, 18:867-874. 10.1038/nsmb.2084, 21725293.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 867-874
-
-
McDonald, O.G.1
Wu, H.2
Timp, W.3
Doi, A.4
Feinberg, A.P.5
-
25
-
-
77649271805
-
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
-
20173741
-
Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD, Clark SJ. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 2010, 12:235-246. 20173741.
-
(2010)
Nat Cell Biol
, vol.12
, pp. 235-246
-
-
Coolen, M.W.1
Stirzaker, C.2
Song, J.Z.3
Statham, A.L.4
Kassir, Z.5
Moreno, C.S.6
Young, A.N.7
Varma, V.8
Speed, T.P.9
Cowley, M.10
Lacaze, P.11
Kaplan, W.12
Robinson, M.D.13
Clark, S.J.14
-
26
-
-
84875745673
-
Interplay between the cancer genome and epigenome
-
23540689
-
Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell 2013, 153:38-55. 10.1016/j.cell.2013.03.008, 23540689.
-
(2013)
Cell
, vol.153
, pp. 38-55
-
-
Shen, H.1
Laird, P.W.2
-
27
-
-
84889573275
-
Histone lysine demethylases as targets for anticancer therapy
-
24232376
-
Hojfeldt JW, Agger K, Helin K. Histone lysine demethylases as targets for anticancer therapy. Nat Rev Drug Discov 2013, 12:917-930. 10.1038/nrd4154, 24232376.
-
(2013)
Nat Rev Drug Discov
, vol.12
, pp. 917-930
-
-
Hojfeldt, J.W.1
Agger, K.2
Helin, K.3
|