Now showing items 1-6 of 6

    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity 

      Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Kim, Tae-Kyung; Zieba, Jennifer; Ruan, Yijun; Bickel, Peter J.; Wold, Barbara J.; Lieb, Jason D.; Chen, Yiwen; Liu, Tao; Zhang, Yong; He, Housheng H; Myers, Richard M.; White, Kevin P.; Liu, Xiaole Shirley (Nature Publishing Group, 2012)
      We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila ...
    • XBP1 Promotes Triple Negative Breast Cancer By Controlling the HIF1 α Pathway 

      Chen, Xi; Iliopoulos, Dimitrios; Zhang, Qing; Tang, Qianzi; Greenblatt, Matthew B.; Hatziapostolou, Maria; Lim, Elgene; Tam, Wai Leong; Ni, Min; Chen, Yiwen; Mai, Junhua; Shen, Haifa; Hu, Dorothy Z.; Adoro, Stanley; Hu, Bella; Song, Minkyung; Tan, Chen; Landis, Melissa D.; Ferrari, Mauro; Shin, Sandra J.; Brown, Myles; Chang, Jenny C.; Liu, X. Shirley; Glimcher, Laurie H. (2014)
      Cancer cells induce a set of adaptive response pathways to survive in the face of stressors due to inadequate vascularization1. One such adaptive pathway is the unfolded protein (UPR) or endoplasmic reticulum (ER) stress ...