'Leveling' the playing field for analyses of single-base resolution DNA methylomes.
作者信息
Schultz Matthew D, Schmitz Robert J, Ecker Joseph R
出版信息
Trends Genet. 2012 Dec;28(12):583-5. doi: 10.1016/j.tig.2012.10.012. Epub 2012 Nov 3.
Abstract
摘要
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2
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3
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Cell. 2008 May 2;133(3):523-36. doi: 10.1016/j.cell.2008.03.029.
4
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Nature. 2008 Mar 13;452(7184):215-9. doi: 10.1038/nature06745. Epub 2008 Feb 17.
5
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Nucleic Acids Res. 1994 Aug 11;22(15):2990-7. doi: 10.1093/nar/22.15.2990.
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