Search Results - "Brown, Myles"

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response by Jiang, Peng, Gu, Shengqing, Pan, Deng, Fu, Jingxin, Sahu, Avinash, Hu, Xihao, Li, Ziyi, Traugh, Nicole, Bu, Xia, Li, Bo, Liu, Jun, Freeman, Gordon J., Brown, Myles A., Wucherpfennig, Kai W., Liu, X. Shirley

“…Cancer treatment by immune checkpoint blockade (ICB) can bring long-lasting clinical benefits, but only a fraction of patients respond to treatment. To predict…”
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ESR1 mutations—a mechanism for acquired endocrine resistance in breast cancer by Jeselsohn, Rinath, Buchwalter, Gilles, De Angelis, Carmine, Brown, Myles, Schiff, Rachel

“…Key Points Over the past 18 months, recurrent activating mutations within the oestrogen receptor α (ER) LBD have been detected in 15–20% of patients with…”
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Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis by Zheng, Rongbin, Wan, Changxin, Mei, Shenglin, Qin, Qian, Wu, Qiu, Sun, Hanfei, Chen, Chen-Hao, Brown, Myles, Zhang, Xiaoyan, Meyer, Clifford A, Liu, X Shirley

“…Abstract The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin…”
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Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse by 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

“…Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide…”
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Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library by Zhu, Shiyou, Li, Wei, Liu, Jingze, Chen, Chen-Hao, Liao, Qi, Xu, Ping, Xu, Han, Xiao, Tengfei, Cao, Zhongzheng, Peng, Jingyu, Yuan, Pengfei, Brown, Myles, Liu, Xiaole Shirley, Wei, Wensheng

“…Long non-coding RNAs are identified using a high-throughput paired-guide RNA genomic deletion screen. CRISPR–Cas9 screens have been widely adopted to analyze…”
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Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data by Qin, Qian, Fan, Jingyu, Zheng, Rongbin, Wan, Changxin, Mei, Shenglin, Wu, Qiu, Sun, Hanfei, Brown, Myles, Zhang, Jing, Meyer, Clifford A, Liu, X Shirley

“…We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on…”
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Role of steroid receptor and coregulator mutations in hormone-dependent cancers by Groner, Anna C, Brown, Myles

“…Steroid hormones mediate critical lineage-specific developmental and physiologic responses. They function by binding their cognate receptors, which are…”
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Sequence determinants of improved CRISPR sgRNA design by Xu, Han, Xiao, Tengfei, Chen, Chen-Hao, Li, Wei, Meyer, Clifford A, Wu, Qiu, Wu, Di, Cong, Le, Zhang, Feng, Liu, Jun S, Brown, Myles, Liu, X Shirley

“…The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9…”
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Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer by 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

“…Mounting evidence suggests that long noncoding RNAs (lncRNAs) can function as microRNA sponges and compete for microRNA binding to protein-coding transcripts…”
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Transcriptional Regulation in Prostate Cancer by Labbé, David P, Brown, Myles

“…Prostate cancer development involves corruption of the normal prostate transcriptional network, following deregulated expression or mutation of key…”
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Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute by Wang, Binbin, Wang, Mei, Zhang, Wubing, Xiao, Tengfei, Chen, Chen-Hao, Wu, Alexander, Wu, Feizhen, Traugh, Nicole, Wang, Xiaoqing, Li, Ziyi, Mei, Shenglin, Cui, Yingbo, Shi, Sailing, Lipp, Jesse Jonathan, Hinterndorfer, Matthias, Zuber, Johannes, Brown, Myles, Li, Wei, Liu, X. Shirley

“…Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR–Cas9) is a powerful technology for the systematic evaluation of gene function…”
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In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target by Wang, Xiaoqing, Tokheim, Collin, Gu, Shengqing Stan, Wang, Binbin, Tang, Qin, Li, Yihao, Traugh, Nicole, Zeng, Zexian, Zhang, Yi, Li, Ziyi, Zhang, Boning, Fu, Jingxin, Xiao, Tengfei, Li, Wei, Meyer, Clifford A., Chu, Jun, Jiang, Peng, Cejas, Paloma, Lim, Klothilda, Long, Henry, Brown, Myles, Liu, X. Shirley

“…Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain…”
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Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing by Fei, Teng, Chen, Yiwen, Xiao, Tengfei, Li, Wei, Cato, Laura, Zhang, Peng, Cotter, Maura B., Bowden, Michaela, Lis, Rosina T., Zhao, Shuang G., Wu, Qiu, Feng, Felix Y., Loda, Massimo, He, Housheng Hansen, Liu, X. Shirley, Brown, Myles

“…Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we…”
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Integrative analyses of single-cell transcriptome and regulome using MAESTRO by Wang, Chenfei, Sun, Dongqing, Huang, Xin, Wan, Changxin, Li, Ziyi, Han, Ya, Qin, Qian, Fan, Jingyu, Qiu, Xintao, Xie, Yingtian, Meyer, Clifford A, Brown, Myles, Tang, Ming, Long, Henry, Liu, Tao, Liu, X Shirley

“…We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (…”
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The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis by Pomerantz, Mark M, Li, Fugen, Takeda, David Y, 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

“…Matthew Freedman and colleagues show that androgen receptor (AR) binding sites undergo extensive reprogramming during prostate epithelial transformation. They…”
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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis by Cornwell, MacIntosh, Vangala, Mahesh, Taing, Len, Herbert, Zachary, Köster, Johannes, Li, Bo, Sun, Hanfei, Li, Taiwen, Zhang, Jian, Qiu, Xintao, Pun, Matthew, Jeselsohn, Rinath, Brown, Myles, Liu, X Shirley, Long, Henry W

“…RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and…”
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The Evolving Role of the Estrogen Receptor Mutations in Endocrine Therapy-Resistant Breast Cancer by Jeselsohn, Rinath, De Angelis, Carmine, Brown, Myles, Schiff, Rachel

“…Recurrent ligand-binding domain ESR1 mutations have recently been detected in a substantial number of patients with metastatic ER+ breast cancer and evolve…”
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Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations by Jeselsohn, Rinath, Bergholz, Johann S., Pun, Matthew, Cornwell, MacIntosh, Liu, Weihan, Nardone, Agostina, Xiao, Tengfei, Li, Wei, Qiu, Xintao, Buchwalter, Gilles, Feiglin, Ariel, Abell-Hart, Kayley, Fei, Teng, Rao, Prakash, Long, Henry, Kwiatkowski, Nicholas, Zhang, Tinghu, Gray, Nathanael, Melchers, Diane, Houtman, Rene, Liu, X. Shirley, Cohen, Ofir, Wagle, Nikhil, Winer, Eric P., Zhao, Jean, Brown, Myles

“…Estrogen receptor α (ER) ligand-binding domain (LBD) mutations are found in a substantial number of endocrine treatment-resistant metastatic ER-positive (ER+)…”
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Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer by Mei, Shenglin, Meyer, Clifford A, Zheng, Rongbin, Qin, Qian, Wu, Qiu, Jiang, Peng, Li, Bo, Shi, Xiaohui, Wang, Binbin, Fan, Jingyu, Shih, Celina, Brown, Myles, Zang, Chongzhi, Liu, X Shirley

“…Cancer results from a breakdown of normal gene expression control, so the study of gene regulation is critical to cancer research. To gain insight into the…”
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Estrogen receptor prevents p53-dependent apoptosis in breast cancer by Bailey, Shannon T, Shin, Hyunjin, Westerling, Thomas, Liu, Xiaole Shirley, Brown, Myles

“…More than two-thirds of breast cancers express the estrogen receptor (ER) and depend on estrogen for growth and survival. Therapies targeting ER function,…”
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