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DNA Methylation Analysis:
- Steven D. Sheridan, Kraig M. Theriault, Surya A. Reis, Fen Zhou, Jon M. Madison, Laurence Daheron, Jeanne F. Loring, Stephen J. Haggarty: Epigenetic Characterization of the FMR1 Gene and Aberrant Neurodevelopment in Human Induced Pluripotent Stem Cell Models of Fragile X Syndrome. PLoS One. 2011;6(10) e26203
- Matthias Stadtfeld, Effie Apostolou, Hidenori Akutsu, Atsushi Fukuda, Patricia Follett, Sridaran Natesan, Tomohiro Kono,
Toshi Shioda, and Konrad Hochedlinger: Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells: Nature. 2010 May 13;465(7295):175-81
- Achia Urbach, Ori Bar-Nur George Q. Daley, and Nissim Benvenisty Differential Modeling of Fragile X Syndrome by Human Embryonic Stem Cells and Induced Pluripotent Stem Cells. Cell Stem Cell 6, May 7, 2010: 407 – 411
- Ye Zheng, Steven Josefowicz, Ashutosh Chaudhry, Xiao P. Peng, Katherine Forbush, and Alexander Y. Rudensky: Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature. 2010 February 11; 463(7282): 808-812
- England RPM, Pyro-QCpG: Quantitative analysis of methylation in multiple CpG sites by Pyrosequencing(R). Nature Method: 2005;2:12.
- Kang SW, Shih PA, Mathew RO, Mahata M, Biswas N, Rao F, Yan L, Bouchard J, Malhotra R, Tolwani A, Khandrika S, Mehta RL, O'Connor DT.
Renal kallikrein excretion and epigenetics in human acute kidney injury: Expression, mechanisms and consequences. BMC Nephrology 2011, 12(1):27
- Chung M Wong, Douglas L Anderton, Sallie Smith-Schneider, Megan A Wing, Melissa C Greven, and Kathleen F Arcaro. Quantitative analysis of promoter methylation in exfoliated epithelial cells isolated from breast milk of healthy women. Epigenetics. 2010 October 1; 5(7): 645–655.
- W. E. Harrington, T. K. Mutabingwa, A. Muehlenbachs, B. Sorensen, M. C. Bolla, M. Fried, and P. E. Duffy. Competitive facilitation of drug-resistant Plasmodium falciparum malaria parasites in pregnant women who receive preventive treatment. Proc Natl Acad Sci U S A. 2009 June 2; 106(22): 9027–9032.
- Ronald M Adkins, Fridtjof Thomas, Frances A Tylavsky, and Julia Krushkal. Parental ages and levels of DNA methylation in the newborn are correlated. BMC Med Genet. 2011; 12: 47.
- P M Das, A D Thor, S M Edgerton, S K Barry, D F Chen, and F E Jones. Reactivation of epigenetically silenced HER4/ERBB4 results in apoptosis of breast tumor cells. Oncogene. 2010 September 16; 29(37): 5214–5219. Published online 2010 July 5.
- Sucheta M. Vaingankar, Ying Li, Angelo Corti, Nilima Biswas, Jiaur Gayen, Daniel T. O'Connor, and Sushil K. Mahata. Long human CHGA flanking chromosome 14 sequence required for optimal BAC transgenic “rescue” of disease phenotypes in the mouse Chga knockout. Physiol Genomics. 2010 March; 41(1): 91–101.
- Shengfa Liu, Jianbing Mu, Hongying Jiang, and Xin-zhuan Su. Effects of Plasmodium falciparum Mixed Infections on in Vitro Antimalarial Drug Tests and Genotyping. Am J Trop Med Hyg. Am J Trop Med Hyg. 2008 August; 79 (2) : 178–184.
- Katsuhiko Nosho, Takako Kawasaki, Mutsuko Ohnishi, Yuko Suemoto, Gregory J Kirkner, Dimity Zepf, Liying Yan, Janina A Longtine, Charles S Fuchs, and Shuji Ogino. PIK3CA Mutation in Colorectal Cancer: Relationship with Genetic and Epigenetic Alterations Neoplasia. 2008 June; 10(6): 534–541.
- Diana E. Pankevich, Sarah L. Teegarden, Andrew D. Hedin, Catherine L. Jensen, and Tracy L. Bale. Caloric restriction experience reprograms stress and orexegenic pathways and promotes binge-eating. J Neurosci. 2010 December 1; 30 (48) : 16399–16407.
- Coren A. Milbury, Jin Li, and G. Mike Makrigiorgos. Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations Nucleic Acids Res. 2011 January; 39(1): e2.
- Kristi Kerkel, Nicole Schupf, Kota Hatta, Deborah Pang, Martha Salas, Alexander Kratz, Mark Minden, Vundavalli Murty, Warren B. Zigman, Richard P. Mayeux, Edmund C. Jenkins, Ali Torkamani, Nicholas J. Schork, Wayne Silverman, B. Anne Croy, and Benjamin Tycko. Altered DNA Methylation in Leukocytes with Trisomy 21 PLoS Genet. 2010 November; 6(11): e1001212.
- Mechanisms of transcriptional regulation and prognostic significance of activated leukocyte cell adhesion molecule in cancer Judy A King, Fang Tan, Flaubert Mbeunkui, Zachariah Chambers, Sarah Cantrell, Hairu Chen, Diego Alvarez, Lalita A Shevde, and Solomon F Ofori-Acquah Mol Cancer. 2010; 9: 266. Published online 2010 October 7. doi: 10.1186/1476-4598-9-266 PMCID: PMC2958981
- Carlos Guerrero-Bosagna, Matthew Settles, Ben Lucker, and Michael K. Skinner. Epigenetic Transgenerational Actions of Vinclozolin on Promoter Regions of the Sperm Epigenome. PLoS One. 2010; 5(9): e13100.
- Maren Godmann, Erin May, and Sarah Kimmins. Epigenetic Mechanisms Regulate Stem Cell Expressed Genes Pou5f1 and Gfra1 in a Male Germ Cell Line. PLoS One. 2010; 5(9): e12727.
- Bethany L. Wienholz, Michael S. Kareta, Amir H. Moarefi, Catherine A. Gordon, Paul A. Ginno, and Frédéric Chédin. DNMT3L Modulates Significant and Distinct Flanking Sequence Preference for DNA Methylation by DNMT3A and DNMT3B In Vivo. PLoS Genet. 2010 September; 6(9): e1001106.
- Lisa Mirabello, Sharon A Savage, Larissa Korde, Shahinaz M Gadalla, and Mark H Greene. LINE-1 methylation is inherited in familial testicular cancer kindreds. BMC Med Genet. 2010; 11: 77.
- Bermans J. Iskandar, Elias Rizk, Brenton Meier, Nithya Hariharan, Teodoro Bottiglieri, Richard H. Finnell, David F. Jarrard, Ruma V. Banerjee, J.H. Pate Skene, Aaron Nelson, Nirav Patel, Carmen Gherasim, Kathleen Simon, Thomas D. Cook, and Kirk J. Hogan. Folate regulation of axonal regeneration in the rodent central nervous system through DNA methylation. J Clin Invest. 2010 May 3; 120(5): 1603–1616.
- Jenne M. Westberry, Amanda L. Trout, and Melinda E. Wilson. Epigenetic Regulation of Estrogen Receptor α Gene Expression in the Mouse Cortex during Early Postnatal Development. Endocrinology. 2010 February; 151(2): 731–740.
- Jason E. Fish, Matthew S. Yan, Charles C. Matouk, Rosanne St. Bernard, J. J. David Ho, Anna Gavryushova, Deepak Srivastava, and Philip A. Marsden. Hypoxic Repression of Endothelial Nitric-oxide Synthase Transcription Is Coupled with Eviction of Promoter Histones. J Biol Chem. 2010 January 8; 285(2): 810–826.
- Jin Li, Coren A. Milbury, Cheng Li, and G. Mike Makrigiorgos. Two-round COLD-PCR-based Sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma. Hum Mutat. Hum Mutat. 2009 November; 30 (11) : 1583–1590.
- Mario Dandrea, Massimo Donadelli, Chiara Costanzo, Aldo Scarpa, and Marta Palmieri. MeCP2/H3meK9 are involved in IL-6 gene silencing in pancreatic adenocarcinoma cell lines. Nucleic Acids Res. 2009 November; 37(20): 6681–6690.
- Gregory A. Dunn and Tracy L. Bale. Maternal High-Fat Diet Promotes Body Length Increases and Insulin Insensitivity in Second-Generation Mice. Endocrinology. 2009 November; 150(11): 4999–5009.
- Akio Kuroda, Tibor A. Rauch, Ivan Todorov, Hsun Teresa Ku, Ismail H. Al-Abdullah, Fouad Kandeel, Yoko Mullen, Gerd P. Pfeifer, and Kevin Ferreri. Insulin Gene Expression Is Regulated by DNA Methylation. PLoS One. 2009; 4(9): e6953.
- Josefa González, J. Michael Macpherson, and Dmitri A. Petrov. A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster. Mol Biol Evol. 2009 September; 26(9): 1949–1961.
- Rietschel P, Wolchok JD, Krown S, Gerst S, Jungbluth AA, Busam K, Smith K, Orlow I, Panageas K, Chapman PB Phase II study of extended-dose temozolomide in patients with melanoma. J Clin Oncol. 2008 May 10;26(14):2299-304.
- Kim HR, Hwang KA, Kim KC, Kang I. Down-regulation of IL-7Ralpha expression in human T cells via DNA methylation J Immunol. 2007 May 1;178(9):5473-9
- Dejeux E, Audard V, Cavard C, Gut IG, Terris B, Tost J. Rapid identification of promoter hypermethylation in hepatocellular
carcinoma by pyrosequencing of etiologically homogeneous sample pools. J Mol Diagn. 2007 Sep;9(4):510-20. Epub 2007 Aug 9
- Pasquali L, Bedeir A, Ringquist S, Styche A, Bhargava R, Trucco G. Quantification of CpG island methylation in progressive breast lesions from normal to invasive carcinoma. Cancer Lett. 2007 Nov 8;257(1):136-44. Epub 2007 Aug 15
- Estécio MRH, Gharibyan V, Shen L, Ibrahim AEF, Doshi K, He R, Jelinek J, Yang AS, Yan PS, Huang TM, Tajara EH, and Issa JP. LINE-1 Hypomethylation in Cancer Is Highly Variable and Inversely Correlated with Microsatellite Instability PLoS ONE. 2007; 2(5): e399. Published online 2007 May 2. doi: 10.1371/journal.pone.0000399. PMCID: 1851990
- Liu T, Zhang X, So CK, Wang S, Wang P, Yan L, Myers R, Chen Z, Patterson AP, Yang CS, Chen X. Regulation of Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human esophageal epithelial. Cell Carcinogenesis, 2007 Feb; 28(2): 488-96
- Brakensiek K, Wingen LU, Langer F, Kreipe H, Lehmann U. Quantitative high-resolution CpG island mapping with Pyrosequencing reveals disease-specific methylation patterns of the CDKN2B gene in myelodysplastic syndrome and myeloid leukemia. Clin Chem. 2007 Jan;53(1):17-23. Epub 2006 Nov 9
- Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J Mol Diagn 2006;8:582-588.
- Schernhammer ES, Giovannucci EL, Fuchs CS, Ogino S. A prospective study of dietary folate and vitamin B and colon cancer according to MSI and KRAS mutational status. Cancer Epidemiol Biomarkers Prev 2008;17:2895-2898.
- Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Meyerhardt JA, Loda M, Giovannucci EL, Fuchs CS. CpG island methylator phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut 2009;58:90-96.
- Pop R, Shearstone JR, Shen Q, Liu Y, Hallstrom K, Koulnis M, Gribnau J, Socolovsky M: A Key Commitment Step in Erythropoiesis Is Synchronized with the Cell Cycle Clock through Mutual Inhibition between PU.1 and S-phase Progression PLoS Biology September 2010 | Volume 8 | Issue 9 | e1000484
- Paul W. Hollenbach, Aaron N. Nguyen, Helen Brady, Michelle Williams, Yuhong Ning1, Normand Richard, Leslie Krushel,
Sharon L. Aukerman, Carla Heise1, Kyle J. MacBeth: A Comparison of Azacitidine and Decitabine Activities in Acute Myeloid Leukemia Cell Lines. PLoS ONE February 2010 , Volume 5, Issue 2, e9001
- Lisa Mirabello, Sharon A Savage, Larissa Korde, Shahinaz M Gadalla, and Mark H Greene: RLeIsNearEch- a1rt icmle ethylation is inherited in familial testicular cancer kindreds. BMC Medical Genetics 2010, 11:77
- Jinming Liu, Manisha Ballaney, Umaima Al-alem, Chunli Quan, Ximei Jin, Frederica Perera, Lung-Chi Chen, and Rachel L. Miller: Combined Inhaled Diesel Exhaust Particles and Allergen Exposure Alter Methylation of T Helper Genes and IgE Production In Vivo. TOXICOLOGICAL SCIENCES 102(1), 76-81 (2008).
- Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010 Nov 5;7(5):618-30. Epub 2010 Sep 30
- Reed K, Poulin ML, Yan L, Parissenti AM. Comparison of bisulfite sequencing PCR with pyrosequencing for measuring differences in DNA methylation. Anal Biochem. 2010 Feb 1;397(1):96-106. Epub 2009 Oct 14.
- Sepulveda AR, Jones D, Ogino S, Samowitz W, Gulley ML, Edwards R, Levenson V, Pratt VM, Yang B, Nafa K, Yan L, Vitazka P. CpG methylation analysis--current status of clinical assays and potential applications in molecular diagnostics: a report of the Association for Molecular Pathology. J Mol Diagn. 2009 Jul;11(4):266-78. Epub 2009 Jun 18..
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