Now showing items 1-20 of 24

    • Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells 

      Luyten, Annouck; Zang, Chongzhi; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Cold Spring Harbor Laboratory Press, 2014)
      Tissues may adopt diverse strategies to establish specific transcriptional programs in daughter lineages. In intestinal crypts, enhancers for genes expressed in both major cell types appear broadly permissive in stem and ...
    • 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 ...
    • 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 ...
    • DiNuP: a systematic approach to identify regions of differential nucleosome positioning 

      Fu, Kai; Tang, Qianzi; Feng, Jianxing; Liu, Xiaole Shirley; Zhang, Yong (Oxford University Press, 2012)
      Motivation: With the rapid development of high-throughput sequencing technologies, the genome-wide profiling of nucleosome positioning has become increasingly affordable. Many future studies will investigate the dynamic ...
    • Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation 

      Hsieh, Chen-Lin; Fei, Teng; Chen, Yiwen; Li, Tiantian; Gao, Yanfei; Wang, Xiaodong; Sun, Tong; Sweeney, Christopher J; Lee, Gwo-Shu Mary; Chen, Shaoyong; Balk, Steven Paul; Liu, Xiaole (Shirley) Shirley; Brown, Myles Avery; Kantoff, Philip Wayne (Proceedings of the National Academy of Sciences, 2014)
      The androgen receptor (AR) is a key factor that regulates the behavior and fate of prostate cancer cells. The AR-regulated network is activated when AR binds enhancer elements and modulates specific enhancer–promoter ...
    • Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes 

      Verzi, M. P.; Shin, H.; Ho, L.-L.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (American Society for Microbiology, 2011)
      Transcription factors that potently induce cell fate often remain expressed in the induced organ throughout life, but their requirements in adults are uncertain and varied. Mechanistically, it is unclear if they activate ...
    • 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 ...
    • Inference of transcriptional regulation in cancers 

      Jiang, Peng; Freedman, Matthew Lawrence; Liu, Jun; Liu, Xiaole (Shirley) Shirley (Proceedings of the National Academy of Sciences, 2015)
      We developed an efficient and accurate computational framework, RABIT (regression analysis with background integration), and comprehensively integrated public transcription factor (TF)-binding profiles with TCGA tumor-profiling ...
    • Integrating regulatory motif discovery and genome-wide expression analysis 

      Conlon, E. M.; Liu, Xiaole (Shirley) Shirley; Lieb, J. D.; Liu, Jun (Proceedings of the National Academy of Sciences, 2003)
      We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression ...
    • An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer 

      Sulahian, R; Casey, F; Shen, J; Qian, Zhirong; Shin, H; Ogino, Shuji; Weir, Barbara Ann; Vazquez, F; Liu, Xiaole (Shirley) Shirley; Hahn, William Chun; Bass, Adam Joel; Chan, Vivian; Shivdasani, Ramesh Arjun (Springer Nature, 2013)
      Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors, but the molecular bases of their oncogenic properties are largely unknown. Because ...
    • Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding 

      Verzi, M. P.; Shin, H.; San Roman, A. K.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (American Society for Microbiology, 2012)
      Tissue-specific gene expression requires modulation of nucleosomes, allowing transcription factors to occupy cis elements that are accessible only in selected tissues. Master transcription factors control cell-specific ...
    • 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 ...
    • Model-Based Analysis of Two-Color Arrays (MA2C) 

      Zhu, Xiaopeng; Zhang, Xinmin; Chen, Runsheng; Manrai, Arjun Kumar; Song, Jun S; Johnson, W. Evan; Li, Wei; Liu, Xiaole Shirley; Liu, Jun (BioMed Central, 2007)
      A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published ...
    • Polycomb-independent activity of EZH2 in castration resistant prostate cancer 

      Xu, Kexin; Wu, Zhenhua; Groner, Anna Claire; He, Housheng H; Cai, Changmeng; Stack, Edward C; Loda, Massimo; Liu, Tao; Morrissey, Colm; Vessella, Robert L; Kantoff, Philip Wayne; Balk, Steven Paul; Liu, Xiaole Shirley; Brown, Myles Avery (BioMed Central, 2013)
    • REST and Stress Resistance in Ageing and Alzheimer’s Disease 

      Lu, Tao; Aron, Liviu; Zullo, Joseph M.; Pan, Ying; Kim, Haeyoung; Chen, Yiwen; Yang, Tun-Hsiang; Kim, Hyun-Min; Drake, Derek Mark; Liu, Xiaole (Shirley) Shirley; Bennett, David A.; Colaiacovo, Monica P.; Yankner, Bruce Albert (Nature Publishing Group, 2014)
      Human neurons are functional over an entire lifetime, yet the mechanisms that preserve function and protect against neurodegeneration during ageing are unknown. Here we show that induction of the repressor element 1-silencing ...
    • 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 ...