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Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.

Andrews J, Kennette W, Pilon J, Hodgson A, Tuck AB, Chambers AF, Rodenhiser DI.

PLoS One. 2010 Jan 13;5(1):e8665. doi: 10.1371/journal.pone.0008665.


Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context.

Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Padbury JF, Bueno R, Sugarbaker DJ, Yeh RF, Wiencke JK, Kelsey KT.

PLoS Genet. 2009 Aug;5(8):e1000602. doi: 10.1371/journal.pgen.1000602. Epub 2009 Aug 14.


Oncogenic activating mutations are associated with local copy gain.

Modrek B, Ge L, Pandita A, Lin E, Mohan S, Yue P, Guerrero S, Lin WM, Pham T, Modrusan Z, Seshagiri S, Stern HM, Waring P, Garraway LA, Chant J, Stokoe D, Cavet G.

Mol Cancer Res. 2009 Aug;7(8):1244-52. doi: 10.1158/1541-7786.MCR-08-0532. Epub 2009 Aug 11.


Copy number variation has little impact on bead-array-based measures of DNA methylation.

Houseman EA, Christensen BC, Karagas MR, Wrensch MR, Nelson HH, Wiemels JL, Zheng S, Wiencke JK, Kelsey KT, Marsit CJ.

Bioinformatics. 2009 Aug 15;25(16):1999-2005. doi: 10.1093/bioinformatics/btp364. Epub 2009 Jun 19.


Cancer statistics, 2009.

Jemal A, Siegel R, Ward E, Hao Y, Xu J, Thun MJ.

CA Cancer J Clin. 2009 Jul-Aug;59(4):225-49. doi: 10.3322/caac.20006. Epub 2009 May 27.


High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.

Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM.

Nucleic Acids Res. 2009 Jul;37(12):3829-39. doi: 10.1093/nar/gkp260. Epub 2009 Apr 22.


Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability.

Richards KL, Zhang B, Baggerly KA, Colella S, Lang JC, Schuller DE, Krahe R.

PLoS One. 2009;4(3):e4941. doi: 10.1371/journal.pone.0004941. Epub 2009 Mar 18.


Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling.

Sadikovic B, Yoshimoto M, Chilton-MacNeill S, Thorner P, Squire JA, Zielenska M.

Hum Mol Genet. 2009 Jun 1;18(11):1962-75. doi: 10.1093/hmg/ddp117. Epub 2009 Mar 13.


Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression.

Li X, Galipeau PC, Sanchez CA, Blount PL, Maley CC, Arnaudo J, Peiffer DA, Pokholok D, Gunderson KL, Reid BJ.

Cancer Prev Res (Phila). 2008 Nov;1(6):413-23. doi: 10.1158/1940-6207.CAPR-08-0121.


Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma.

Marsit CJ, Christensen BC, Houseman EA, Karagas MR, Wrensch MR, Yeh RF, Nelson HH, Wiemels JL, Zheng S, Posner MR, McClean MD, Wiencke JK, Kelsey KT.

Carcinogenesis. 2009 Mar;30(3):416-22. doi: 10.1093/carcin/bgp006. Epub 2009 Jan 6.


Epigenetic profiles distinguish pleural mesothelioma from normal pleura and predict lung asbestos burden and clinical outcome.

Christensen BC, Houseman EA, Godleski JJ, Marsit CJ, Longacker JL, Roelofs CR, Karagas MR, Wrensch MR, Yeh RF, Nelson HH, Wiemels JL, Zheng S, Wiencke JK, Bueno R, Sugarbaker DJ, Kelsey KT.

Cancer Res. 2009 Jan 1;69(1):227-34. doi: 10.1158/0008-5472.CAN-08-2586.


Alterations of p16 and p14ARF genes and their 9p21 locus in oral squamous cell carcinoma.

Ohta S, Uemura H, Matsui Y, Ishiguro H, Fujinami K, Kondo K, Miyamoto H, Yazawa T, Danenberg K, Danenberg PV, Tohnai I, Kubota Y.

Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2009 Jan;107(1):81-91. doi: 10.1016/j.tripleo.2008.08.027.


Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific.

Jun P, Hong C, Lal A, Wong JM, McDermott MW, Bollen AW, Plass C, Held WA, Smiraglia DJ, Costello JF.

Neuro Oncol. 2009 Aug;11(4):414-22. doi: 10.1215/15228517-2008-096. Epub 2008 Nov 11.


Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.

Costello JF, Hong C, Plass C, Smiraglia DJ.

Methods Mol Biol. 2009;507:131-48. doi: 10.1007/978-1-59745-522-0_11.


Chromosomal changes characterize head and neck cancer with poor prognosis.

Bauer VL, Braselmann H, Henke M, Mattern D, Walch A, Unger K, Baudis M, Lassmann S, Huber R, Wienberg J, Werner M, Zitzelsberger HF.

J Mol Med (Berl). 2008 Dec;86(12):1353-65. doi: 10.1007/s00109-008-0397-0. Epub 2008 Sep 23.


Integrated analysis of copy number alterations and loss of heterozygosity in human pancreatic cancer using a high-resolution, single nucleotide polymorphism array.

Lin LJ, Asaoka Y, Tada M, Sanada M, Nannya Y, Tanaka Y, Tateishi K, Ohta M, Seto M, Sasahira N, Tada M, Kawabe T, Zheng CQ, Kanai F, Ogawa S, Omata M.

Oncology. 2008;75(1-2):102-12. doi: 10.1159/000155813. Epub 2008 Sep 12.


Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions.

Houseman EA, Christensen BC, Yeh RF, Marsit CJ, Karagas MR, Wrensch M, Nelson HH, Wiemels J, Zheng S, Wiencke JK, Kelsey KT.

BMC Bioinformatics. 2008 Sep 9;9:365. doi: 10.1186/1471-2105-9-365.


Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Cancer Genome Atlas Research Network.

Nature. 2008 Oct 23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4. Erratum in: Nature. 2013 Feb 28;494(7438):506.


Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.

Science. 2008 Sep 26;321(5897):1801-6. doi: 10.1126/science.1164368. Epub 2008 Sep 4.


Hypermethylation of E-cadherin is an independent predictor of improved survival in head and neck squamous cell carcinoma.

Marsit CJ, Posner MR, McClean MD, Kelsey KT.

Cancer. 2008 Oct 1;113(7):1566-71. doi: 10.1002/cncr.23770.

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