Now showing items 1-4 of 4

    • Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification 

      He, Housheng Hansen; Meyer, Clifford A.; Hu, Sheng'en Shawn; Chen, Mei-Wei; Zang, Chongzhi; Liu, Yin; Rao, Prakash K.; Fei, Teng; Xu, Han; Long, Henry; Liu, X. Shirley; Brown, Myles (2014)
      DNase-seq is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize the performance of DNase-seq. We found that sequencing short 50-100bp ...
    • Computational inference of mRNA stability from histone modification and transcriptome profiles 

      Wang, Chengyang; Tian, Rui; Zhao, Qian; Xu, Han; Meyer, Clifford; Li, Cheng; Zhang, Yong; Liu, Xiaole Shirley (Oxford University Press, 2012)
      Histone modifications play important roles in regulating eukaryotic gene expression and have been used to model expression levels. Here, we present a regression model to systematically infer mRNA stability by comparing ...
    • MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens 

      Li, Wei; Xu, Han; Xiao, Tengfei; Cong, Le; Love, Michael I; Zhang, Feng; Irizarry, Rafael A; Liu, Jun S; Brown, Myles; Liu, X Shirley (BioMed Central, 2014)
      We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better ...
    • MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes 

      Zheng, Xiaoqi; Zhao, Qian; Wu, Hua-Jun; Li, Wei; Wang, Haiyun; Meyer, Clifford A; Qin, Qian Alvin; Xu, Han; Zang, Chongzhi; Jiang, Peng; Li, Fuqiang; Hou, Yong; He, Jianxing; Wang, Jun; Zhang, Peng; Zhang, Yong; Liu, Xiaole Shirley (BioMed Central, 2014)
      We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated ...