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Items: 1 to 20 of 41

1.

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG.

Genome Res. 2012 Jun;22(6):1128-38. doi: 10.1101/gr.133728.111. Epub 2012 Mar 30.

2.

A DNA hypermethylation module for the stem/progenitor cell signature of cancer.

Easwaran H, Johnstone SE, Van Neste L, Ohm J, Mosbruger T, Wang Q, Aryee MJ, Joyce P, Ahuja N, Weisenberger D, Collisson E, Zhu J, Yegnasubramanian S, Matsui W, Baylin SB.

Genome Res. 2012 May;22(5):837-49. doi: 10.1101/gr.131169.111. Epub 2012 Mar 5.

3.

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers.

Xu Y, Hu B, Choi AJ, Gopalan B, Lee BH, Kalady MF, Church JM, Ting AH.

Genome Res. 2012 Feb;22(2):283-91. doi: 10.1101/gr.122788.111. Epub 2011 Oct 11.

4.

Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers.

Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M.

Cancer Res. 2011 Oct 15;71(20):6320-6. doi: 10.1158/0008-5472.CAN-11-1021. Epub 2011 Aug 23. Erratum in: Cancer Res. 2012 Feb 15;72(4):1039.

5.

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.

Shu W, Chen H, Bo X, Wang S.

Nucleic Acids Res. 2011 Sep 1;39(17):7428-43. doi: 10.1093/nar/gkr443. Epub 2011 Jun 17.

6.

Genome-scale analysis of aberrant DNA methylation in colorectal cancer.

Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D, Malik S, Pan F, Noushmehr H, van Dijk CM, Tollenaar RA, Laird PW.

Genome Res. 2012 Feb;22(2):271-82. doi: 10.1101/gr.117523.110. Epub 2011 Jun 9.

7.

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis.

Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ.

Genome Res. 2011 Aug;21(8):1313-27. doi: 10.1101/gr.114843.110. Epub 2011 Jun 2.

8.

A DNA methylation fingerprint of 1628 human samples.

Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Graña O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M.

Genome Res. 2012 Feb;22(2):407-19. doi: 10.1101/gr.119867.110. Epub 2011 May 25.

9.

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.

10.

Methyl-CpG binding column-based identification of nine genes hypermethylated in colorectal cancer.

Kober P, Bujko M, Olędzki J, Tysarowski A, Siedlecki JA.

Mol Carcinog. 2011 Nov;50(11):846-56. doi: 10.1002/mc.20763. Epub 2011 Mar 22.

PMID:
21438024
11.

Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas.

Oster B, Thorsen K, Lamy P, Wojdacz TK, Hansen LL, Birkenkamp-Demtröder K, Sørensen KD, Laurberg S, Orntoft TF, Andersen CL.

Int J Cancer. 2011 Dec 15;129(12):2855-66. doi: 10.1002/ijc.25951. Epub 2011 Apr 1.

12.

Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer.

Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH.

Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4364-9. doi: 10.1073/pnas.1013224108. Epub 2011 Feb 28.

13.

Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008.

Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM.

Int J Cancer. 2010 Dec 15;127(12):2893-917. doi: 10.1002/ijc.25516.

14.

Quantitative comparison of genome-wide DNA methylation mapping technologies.

Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A.

Nat Biotechnol. 2010 Oct;28(10):1106-14. doi: 10.1038/nbt.1681. Epub 2010 Sep 19.

15.

Regularization Paths for Generalized Linear Models via Coordinate Descent.

Friedman J, Hastie T, Tibshirani R.

J Stat Softw. 2010;33(1):1-22.

16.

Whole-genome DNA methylation profiling using MethylCap-seq.

Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG.

Methods. 2010 Nov;52(3):232-6. doi: 10.1016/j.ymeth.2010.06.012. Epub 2010 Jun 11.

PMID:
20542119
17.

Expression and prognostic role of syndecan-2 in prostate cancer.

Popović A, Demirović A, Spajić B, Stimac G, Kruslin B, Tomas D.

Prostate Cancer Prostatic Dis. 2010 Mar;13(1):78-82. doi: 10.1038/pcan.2009.43. Epub 2009 Sep 29.

PMID:
19786981
18.

Prognostic significance of altered expression of SDC2 and CYR61 in esophageal squamous cell carcinoma.

Huang X, Xiao DW, Xu LY, Zhong HJ, Liao LD, Xie ZF, Li EM.

Oncol Rep. 2009 Apr;21(4):1123-9.

PMID:
19288017
19.

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.

Nat Genet. 2009 Feb;41(2):178-86. doi: 10.1038/ng.298. Epub 2009 Jan 18.

20.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

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