ChromHMM: automating chromatin-state discovery and characterization.
作者信息
Ernst Jason, Kellis Manolis
出版信息
Nat Methods. 2012 Feb 28;9(3):215-6. doi: 10.1038/nmeth.1906.
Abstract
摘要
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1
Mapping and analysis of chromatin state dynamics in nine human cell types.绘制和分析九种人类细胞类型中的染色质状态动态。
Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.
2
Identification of functional elements and regulatory circuits by Drosophila modENCODE.通过 Drosophila modENCODE 鉴定功能元件和调控回路。
Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.
3
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.系统蛋白质定位图谱揭示了果蝇细胞中的五种主要染色质类型。
Cell. 2010 Oct 15;143(2):212-24. doi: 10.1016/j.cell.2010.09.009. Epub 2010 Sep 30.
4
Discovery and characterization of chromatin states for systematic annotation of the human genome.发现和描述染色质状态，用于系统注释人类基因组。
Nat Biotechnol. 2010 Aug;28(8):817-25. doi: 10.1038/nbt.1662. Epub 2010 Jul 25.
5
Unsupervised segmentation of continuous genomic data.连续基因组数据的无监督分割
Bioinformatics. 2007 Jun 1;23(11):1424-6. doi: 10.1093/bioinformatics/btm096. Epub 2007 Mar 23.
6
The human genome browser at UCSC.加州大学圣克鲁兹分校的人类基因组浏览器。
Genome Res. 2002 Jun;12(6):996-1006. doi: 10.1101/gr.229102.
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