Now showing items 1-16 of 16

    • 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 ...
    • Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers 

      Eeckhoute, J.; Lupien, M.; Meyer, Clifford; Verzi, M. P.; Shivdasani, Ramesh Arjun; Liu, Xiaole (Shirley) Shirley; Brown, Myles A. (Cold Spring Harbor Laboratory Press, 2008)
      Selective activity of a specific set of enhancers defines tissue-specific gene transcription. The pioneer factor FOXA1 has been shown to induce functional enhancer competency through chromatin openings. We have previously ...
    • 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 ...
    • A closer look into DNase I hypersensitivity 

      He, Housheng H; Meyer, Clifford; Long, Henry W; Liu, Xiaole Shirley; Brown, Myles Avery (BioMed Central, 2013)
    • 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 ...
    • Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2 

      Verzi, Michael P.; Shin, Hyunjin; He, H. Hansen; Sulahian, Rita; Meyer, Clifford; Montgomery, Robert K.; Fleet, James C.; Brown, Myles A.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Elsevier BV, 2010)
      Cell differentiation requires remodeling of tissue-specific gene loci and activities of key transcriptional regulators, which are recognized for their dominant control over cellular programs. Using epigenomic methods, we ...
    • Exon expression profiling reveals stimulus-mediated exon use in neural cells 

      McKee, Adrienne E; Neretti, Nicola; Carvalho, Luis E; Brodsky, Alexander S; Meyer, Clifford; Meyer, Clifford; Fox, Edward Alvin; Silver, Pamela A. (BioMed Central, 2007)
      Background: Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both the abundance and architecture of specific mRNAs. Although calcium-induced transcription and transcript variation have ...
    • Gene expression profiling of human breast tissue samples using SAGE-Seq 

      Wu, Z. J.; Meyer, Clifford; Choudhury, S.; Shipitsin, M.; Maruyama, R.; Bessarabova, M.; Nikolskaya, T.; Sukumar, S.; Schwartzman, A.; Liu, Jun; Polyak, Kornelia; Liu, Xiaole (Shirley) Shirley (Cold Spring Harbor Laboratory Press, 2010)
      We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow ...
    • Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells 

      Brodsky, Alexander S; Meyer, Clifford; Swinburne, Ian A; Hall, Giles; Keenan, Benjamin J; Liu, Xiaole Shirley; Fox, Edward Alvin; Silver, Pamela A. (BioMed Central, 2005)
      Background: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be ...
    • 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 ...
    • MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data 

      Chen, Yiwen; Meyer, Clifford; Liu, Tao; Li, Wei; Liu, Jun; Liu, Xiaole (Shirley) Shirley (Springer Science + Business Media, 2011)
      The ChIP-chip and ChIP-seq techniques enable genome-wide mapping of in vivo protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison and integration ...
    • Response and resistance to BET bromodomain inhibitors in triple negative breast cancer 

      Shu, Shaokun; Lin, Charles Y.; He, Housheng Hansen; Witwicki, Robert M.; Tabassum, Doris P.; Roberts, Justin M.; Janiszewska, Michalina; Huh, Sung Jin; Liang, Yi; Ryan, Jeremy; Doherty, Ernest; Mohammed, Hisham; Guo, Hao; Stover, Daniel G.; Ekram, Muhammad B.; Brown, Jonathan; D'Santos, Clive; Krop, Ian E.; Dillon, Deborah; McKeown, Michael; Ott, Christopher; Qi, Jun; Ni, Min; Rao, Prakash K.; Duarte, Melissa; Wu, Shwu-Yuan; Chiang, Cheng-Ming; Anders, Lars; Young, Richard A.; Winer, Eric; Letai, Antony; Barry, William T.; Carroll, Jason S.; Long, Henry; Brown, Myles; Liu, X. Shirley; Meyer, Clifford A.; Bradner, James E.; Polyak, Kornelia (2015)
      Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy1-3. BET bromodomain inhibitors, which have shown efficacy in several models of cancer4-6, ...
    • Sequence determinants of improved CRISPR sgRNA design 

      Xu, Han; Xiao, Tengfei; Chen, Chen-Hao; Li, Wei; Meyer, Clifford; Wu, Qiu; Wu, Di; Cong, Le; Zhang, Feng; Liu, Jun; Brown, Myles A.; Liu, Xiaole (Shirley) Shirley (Cold Spring Harbor Laboratory Press, 2015)
      The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques ...
    • A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer 

      Wang, Haiyun; Meyer, Clifford A; Fei, Teng; Wang, Gang; Zhang, Fan; Liu, X Shirley (BioMed Central, 2013)
      Background: The epithelial-to-mesenchymal transition is an important mechanism in cancer metastasis. Although transcription factors including SNAIL, SLUG, and TWIST1 regulate the epithelial-to-mesenchymal transition, other ...