Now showing items 1-8 of 8

    • 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 ...
    • ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline 

      Qin, Qian; Mei, Shenglin; Wu, Qiu; Sun, Hanfei; Li, Lewyn; Taing, Len; Chen, Sujun; Li, Fugen; Liu, Tao; Zang, Chongzhi; Xu, Han; Chen, Yiwen; Meyer, Clifford A.; Zhang, Yong; Brown, Myles; Long, Henry W.; Liu, X. Shirley (BioMed Central, 2016)
      Background: Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard ...
    • Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse 

      Mei, Shenglin; Qin, Qian; Wu, Qiu; Sun, Hanfei; Zheng, Rongbin; Zang, Chongzhi; Zhu, Muyuan; Wu, Jiaxin; Shi, Xiaohui; Taing, Len; Liu, Tao; Brown, Myles; Meyer, Clifford A.; Liu, X. Shirley (Oxford University Press, 2017)
      Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and ...
    • High-dimensional genomic data bias correction and data integration using MANCIE 

      Zang, Chongzhi; Wang, Tao; Deng, Ke; Li, Bo; Hu, Sheng'en; Qin, Qian; Xiao, Tengfei; Zhang, Shihua; Meyer, Clifford A.; He, Housheng Hansen; Brown, Myles; Liu, Jun S.; Xie, Yang; Liu, X. Shirley (Nature Publishing Group, 2016)
      High-dimensional genomic data analysis is challenging due to noises and biases in high-throughput experiments. We present a computational method matrix analysis and normalization by concordant information enhancement ...
    • 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 ...
    • Network analysis of gene essentiality in functional genomics experiments 

      Jiang, Peng; Wang, Hongfang; Li, Wei; Zang, Chongzhi; Li, Bo; Wong, Yinling J.; Meyer, Cliff; Liu, Jun S.; Aster, Jon C.; Liu, X. Shirley (BioMed Central, 2015)
      Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated with gene ...
    • NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes 

      Zang, Chongzhi; Luyten, Annouck; Chen, Justina; Liu, X. Shirley; Shivdasani, Ramesh A. (Nature Publishing Group, 2016)
      Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome-wide chromatin dynamics and ChIP-seq to determine these transcription factors’ (TFs) activities in terminal megakaryocyte (MK) ...
    • Partitioning heritability by functional annotation using genome-wide association summary statistics 

      Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R.; Consortium, ReproGen; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R. B.; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark; Patterson, Nick; Neale, Benjamin M.; Price, Alkes L. (2015)
      Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here, we analyze a broad set of functional elements, including cell-type-specific ...