Now showing items 21-32 of 32

    • MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens 

      Li, Wei; Xu, Han; Xiao, Tengfei; Cong, Le; Love, Michael I; Zhang, Feng; Irizarry, Rafael A; Liu, Jun S; Brown, Myles; Liu, X Shirley (BioMed Central, 2014)
      We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better ...
    • 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)
    • Polymorphic repeat in AIB1 does not alter breast cancer risk 

      Haiman, Christopher A; Hankinson, Susan Elizabeth; Spiegelman, Donna Lynn; Colditz, Graham A.; Willett, Walter C.; Speizer, Frank Erwin; Brown, Myles Avery; Hunter, David J. (BioMed Central, 2000)
      We assessed the association between a glutamine repeat polymorphism in AIB1 and breast cancer risk in a case-control study (464 cases, 624 controls) nested within the Nurses' Health Study cohort. We observed no association ...
    • Primate-specific Evolution of an LDLR Enhancer 

      Wang, Qian-fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M; Chanan, Sumita; Eisen, Michael B; Cheng, Jan-Fang; Rubin, Edward M; Boffelli, Dario; Brown, Myles Avery (BioMed Central, 2006)
      Background: Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. Results: In this study we identified ...
    • Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR 

      Li, Wei; Köster, Johannes; Xu, Han; Chen, Chen-Hao; Xiao, Tengfei; Liu, Jun S.; Brown, Myles; Liu, X. Shirley (BioMed Central, 2015)
      High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines ...
    • 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, ...
    • The Role of Coactivators in Oestrogen Action 

      Brown, Myles Avery; de Mora, J.F. (BioMed Central, 2000)
    • The role of TRIM24 during prostate cancer progression 

      Groner, Anna Claire; Brown, Myles Avery (BioMed Central, 2013)
    • 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 ...
    • TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions 

      Verzi, M. P.; Hatzis, Phillip Evangelos; Sulahian, R.; Philips, J.; Schuijers, J.; Shin, H.; Freed, E.; Lynch, J. P.; Dang, D. T.; Brown, Myles A.; Clevers, H.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Proceedings of the National Academy of Sciences, 2010)
      Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where ...
    • Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts 

      Pfefferle, Adam D; Herschkowitz, Jason I; Usary, Jerry; Harrell, Joshua Chuck; Spike, Benjamin T; Adams, Jessica R; Torres-Arzayus, Maria I; Brown, Myles; Egan, Sean E; Wahl, Geoffrey M; Rosen, Jeffrey M; Perou, Charles M (BioMed Central, 2013)
      Background: Human breast cancer is a heterogeneous disease consisting of multiple molecular subtypes. Genetically engineered mouse models are a useful resource for studying mammary cancers in vivo under genetically controlled ...
    • 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 ...