Now showing items 1-20 of 32

    • Advances in Estrogen Receptor Biology: Prospects for Improvements in Targeted Breast Cancer Therapy 

      Shao, Wenlin; Brown, Myles Avery (BioMed Central, 2003)
      Estrogen receptor (ER) has a crucial role in normal breast development and is expressed in the most common breast cancer subtypes. Importantly, its expression is very highly predictive for response to endocrine therapy. ...
    • 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 ...
    • The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis 

      Pomerantz, Mark M.; Li, Fugen; Takeda, David; Lenci, Romina; Chonkar, Apurva; Chabot, Matthew; Cejas, Paloma; Vazquez, Francisca; Cook, Jennifer; Shivdasani, Ramesh A.; Bowden, Michaela; Lis, Rosina; Hahn, William C.; Kantoff, Philip W.; Brown, Myles; Loda, Massimo; Long, Henry W.; Freedman, Matthew L. (2015)
      Master transcription factors interact with DNA to establish cell-type identity and to regulate gene expression in mammalian cells1,2. The genome-wide map of these transcription factor binding sites has been termed the ...
    • 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)
    • Control of androgen receptor action by a novel nuclear receptor binding motif in Bag-1L 

      Cato, Laura; Jehle, Katja; Neeb, Antje; Cato, Andrew CB; Brown, Myles (BioMed Central, 2013)
    • Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L 

      Cato, Laura; Neeb, Antje; Brown, Myles; Cato, Andrew C. B. (Nuclear Receptor Signaling Atlas, 2014)
      Molecular chaperones encompass a group of unrelated proteins that facilitate the correct assembly and disassembly of other macromolecular structures, which they themselves do not remain a part of. They associate with a ...
    • 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 ...
    • Digital Quantification of Gene Expression in Sequential Breast Cancer Biopsies Reveals Activation of an Immune Response 

      Jeselsohn, Rinath M.; Werner, Lillian; Regan, Meredith M.; Fatima, Aquila; Gilmore, Lauren; Collins, Laura C.; Beck, Andrew H.; Bailey, Shannon T.; He, Housheng Hansen; Buchwalter, Gilles; Brown, Myles; Iglehart, J. Dirk; Richardson, Andrea; Come, Steven E. (Public Library of Science, 2013)
      Advancements in molecular biology have unveiled multiple breast cancer promoting pathways and potential therapeutic targets. Large randomized clinical trials remain the ultimate means of validating therapeutic efficacy, ...
    • 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 ...
    • ERG signaling in prostate cancer is driven through PRMT5-dependent methylation of the Androgen Receptor 

      Mounir, Zineb; Korn, Joshua M; Westerling, Thomas; Lin, Fallon; Kirby, Christina A; Schirle, Markus; McAllister, Gregg; Hoffman, Greg; Ramadan, Nadire; Hartung, Anke; Feng, Yan; Kipp, David Randal; Quinn, Christopher; Fodor, Michelle; Baird, Jason; Schoumacher, Marie; Meyer, Ronald; Deeds, James; Buchwalter, Gilles; Stams, Travis; Keen, Nicholas; Sellers, William R; Brown, Myles; Pagliarini, Raymond A (eLife Sciences Publications, Ltd, 2016)
      The TMPRSS2:ERG gene fusion is common in androgen receptor (AR) positive prostate cancers, yet its function remains poorly understood. From a screen for functionally relevant ERG interactors, we identify the arginine ...
    • Estradiol-regulated MicroRNAs Control Estradiol Response in Breast Cancer Cells 

      Bhat-Nakshatri, Poornima; Wang, Guohua; Collins, Nikail R.; Geistlinger, Tim R.; Carroll, Jason S.; Hammond, Scott; Srour, Edward F.; Liu, Yunlong; Nakshatri, Harikrishna; Thomson, Michael J.; Brown, Myles Avery (Oxford University Press, 2009)
      Estradiol (E2) regulates gene expression at the transcriptional level by functioning as a ligand for estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ). E2-inducible proteins c-Myc and E2Fs are required for ...
    • Estrogen Signaling in Breast Tumorigenesis 

      Chi, David (2016-09-09)
      The estrogen receptor (ER) is expressed in approximately 70% of sporadic breast cancers and is believed to activate genes driving tumorigenesis and initial cell proliferation. Therapeutic targeting of the ER signaling ...
    • 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 ...
    • How drug resistance takes shape 

      Jeselsohn, Rinath; Brown, Myles (eLife Sciences Publications, Ltd, 2016)
      Mutations in a hormone receptor can lead to therapeutic resistance by making it less able to bind and respond to hormone blocking drugs and by making it active, even when the hormome is not present.
    • Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer 

      Du, Zhou; Sun, Tong; Hacisuleyman, Ezgi; Fei, Teng; Wang, Xiaodong; Brown, Myles; Rinn, John L.; Lee, Mary Gwo-Shu; Chen, Yiwen; Kantoff, Philip W.; Liu, X. Shirley (Nature Publishing Group, 2016)
      Mounting evidence suggests that long noncoding RNAs (lncRNAs) can function as microRNA sponges and compete for microRNA binding to protein-coding transcripts. However, the prevalence, functional significance and targets ...
    • Integrative genomic analyses reveal clinically relevant long non-coding RNA in human cancer 

      Du, Zhou; Fei, Teng; Verhaak, Roel G.W.; Su, Zhen; Zhang, Yong; Brown, Myles; Chen, Yiwen; Liu, X. Shirley (2013)
      Despite growing appreciations of the importance of long non-coding RNA (lncRNA) in normal physiology and disease, our knowledge of cancer-related lncRNA remains limited. By repurposing microarray probes, we constructed the ...
    • An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine 

      Liu, Yin; Fei, Teng; Zheng, Xiaoqi; Brown, Myles; Zhang, Peng; Liu, X. Shirley; Wang, Haiyun (Nature Publishing Group, 2016)
      An individual tumor harbors multiple molecular alterations that promote cell proliferation and prevent apoptosis and differentiation. Drugs that target specific molecular alterations have been introduced into personalized ...