2011


• Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu M, Stewart R, Ren B, Thomson JA, Evans RM, and Ecker JR. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. Mar 2011. 471:68–73. PMID: 21289626
2010


• Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farmham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 2010 29(10):1045-104. PMID: 20944595
  
  
• Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single nucleotide resolution. Nat Methods 2010 7(2): 133-136. PMID: 20062050
  
  
• Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010 28(10):1097-1105. PMID: 20852635
  
  
• Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010 28(10):1106-1114. PMID: 20852634
  
  
• Deal RB, Henikoff JG, Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science. 2010 May 28;328(5982):1161-4. PMID: 20508129
  
  
• Varley KE, Mitra RD. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res. 2010 Sep;20(9):1279-87. Epub 2010 Jul 13. PMID: 20627893
  
  
• Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD. Single molecule epigenetic analysis in a nanofluidic channel. Cipriany Anal Chem. 2010 Mar 15;82(6):2480-7. PMID: 20184350
  
  
• Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD, Skalka AM, Katz RA. Identification of a functional network of human epigenetic silencing factors. J Biol Chem. 2010 Jan 1; 285 (1):422-33. PMID: 19880521
  
  
• Zhang, J., Chen, Y., Zhang, Z., Xing, G., Wysocka, J. and Zhao, Y., MS/MS/MS reveals false positive identification of histone serine methylation. J Proteome Res, 2010. 9(1): p. 585-94. PMCID: PMC2801770
  
  
• Zhang K, Chen Y, Zhang Z, Tao S, Zhu H, Zhao Y. Unrestrictive Identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. Proteomics, 2010. 10(5): p. 896-903. PMID: 20049863
  
  
• Ji Y, Tulin AV. The roles of PARP1 in gene control and cell differentiation. Current Opinion in Genetics & Development. 2010. PMID: 20591646
  
  
2009


• Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-B 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(7271):315-322. PMID: 19829295
  
  
• Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009 Apr;27(4):353-60. Epub 2009 Mar 29. PMID: 19330000
  
  
• Bua DJ, Kuo AJ, Cheung P, Liu CL, Migliori V, Espejo A, Casadio F, Bassi C, Amati B, Bedford MT, Guccione E, Gozani O. Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. PLoS One.et al. 2009 Aug 26;4(8):e6789. PMID: 19956676
  
  
• Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell. 2009 Dec 24;139(7):1290-302. PMID: 20064375

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