Search Results - "Liu, X. Shirley"

TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells by Li, Taiwen, Fan, Jingyu, Wang, Binbin, Traugh, Nicole, Chen, Qianming, Liu, Jun S, Li, Bo, Liu, X Shirley

“…Recent clinical successes of cancer immunotherapy necessitate the investigation of the interaction between malignant cells and the host immune system. However,…”
Get full text

TIMER2.0 for analysis of tumor-infiltrating immune cells by Li, Taiwen, Fu, Jingxin, Zeng, Zexian, Cohen, David, Li, Jing, Chen, Qianming, Li, Bo, Liu, X Shirley

“…Abstract Tumor progression and the efficacy of immunotherapy are strongly influenced by the composition and abundance of immune cells in the tumor…”
Get full text

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…”
Get full text

Large-scale public data reuse to model immunotherapy response and resistance by Fu, Jingxin, Li, Karen, Zhang, Wubing, Wan, Changxin, Zhang, Jing, Jiang, Peng, Liu, X Shirley

“…Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response…”
Get full text

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…”
Get full text

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy by Li, Bo, Severson, Eric, Pignon, Jean-Christophe, Zhao, Haoquan, Li, Taiwen, Novak, Jesse, Jiang, Peng, Shen, Hui, Aster, Jon C, Rodig, Scott, Signoretti, Sabina, Liu, Jun S, Liu, X Shirley

“…Understanding the interactions between tumor and the host immune system is critical to finding prognostic biomarkers, reducing drug resistance, and developing…”
Get full text

CEAS: cis-regulatory element annotation system by Shin, Hyunjin, Liu, Tao, Manrai, Arjun K., Liu, X. Shirley

“…We present a tool designed to characterize genome-wide protein–DNA interaction patterns from ChIP-chip and ChIP-Seq data. This stand-alone extension of our web…”
Get full text

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…”
Get full text

Targeting Androgen Receptor in Estrogen Receptor-Negative Breast Cancer by Ni, Min, Chen, Yiwen, Lim, Elgene, Wimberly, Hallie, Bailey, Shannon T., Imai, Yuuki, Rimm, David L., Shirley Liu, X., Brown, Myles

“…Endocrine therapies for breast cancer that target the estrogen receptor (ER) are ineffective in the 25%–30% of cases that are ER negative (ER–). Androgen…”
Get full text

Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy by Gao, Yang, Nihira, Naoe Taira, Bu, Xia, Chu, Chen, Zhang, Jinfang, Kolodziejczyk, Aleksandra, Fan, Yizeng, Chan, Ngai Ting, Ma, Leina, Liu, Jing, Wang, Dong, Dai, Xiaoming, Liu, Huadong, Ono, Masaya, Nakanishi, Akira, Inuzuka, Hiroyuki, North, Brian J., Huang, Yu-Han, Sharma, Samanta, Geng, Yan, Xu, Wei, Liu, X. Shirley, Li, Lei, Miki, Yoshio, Sicinski, Piotr, Freeman, Gordon J., Wei, Wenyi

“…Immunotherapies that target programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4 (CTLA4) have…”
Get full text

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR by Li, Wei, Köster, Johannes, Xu, Han, Chen, Chen-Hao, Xiao, Tengfei, Liu, Jun S, Brown, Myles, Liu, X Shirley

“…High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and…”
Get full text

A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing by Pan, Deng, Kobayashi, Aya, Jiang, Peng, Ferrari de Andrade, Lucas, Tay, Rong En, Luoma, Adrienne M, Tsoucas, Daphne, Qiu, Xintao, Lim, Klothilda, Rao, Prakash, Long, Henry W, Yuan, Guo-Cheng, Doench, John, Brown, Myles, Liu, X Shirley, Wucherpfennig, Kai W

“…Many human cancers are resistant to immunotherapy, for reasons that are poorly understood. We used a genome-scale CRISPR-Cas9 screen to identify mechanisms of…”
Get full text

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model by Zhang, Naiqian, Wang, Haiyun, Fang, Yun, Wang, Jun, Zheng, Xiaoqi, Liu, X Shirley

“…The ability to predict the response of a cancer patient to a therapeutic agent is a major goal in modern oncology that should ultimately lead to personalized…”
Get full text

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…”
Get full text

Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism by Feng, Dan, Liu, Tao, Sun, Zheng, Bugge, Anne, Mullican, Shannon E, Alenghat, Theresa, Liu, X. Shirley, Lazar, Mitchell A

“…Disruption of the circadian clock exacerbates metabolic diseases, including obesity and diabetes. We show that histone deacetylase 3 (HDAC3) recruitment to the…”
Get full text

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data by JIANXING FENG, MEYER, Clififord A, QIAN WANG, LIU, Jun S, SHIRLEY LIU, X, YONG ZHANG

“…RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost…”
Get full text

Chromatin marks identify critical cell types for fine mapping complex trait variants by Trynka, Gosia, Sandor, Cynthia, Han, Buhm, Xu, Han, Stranger, Barbara E, Liu, X Shirley, Raychaudhuri, Soumya

“…Soumya Raychaudhuri and colleagues report a broadly applicable method that uses chromatin marks, specifically H3K4me3, to identify critical cell types to fine…”
Get full text

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…”
Get full text

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…”
Get full text

A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases by Hirsch, Heather A., Iliopoulos, Dimitrios, Joshi, Amita, Zhang, Yong, Jaeger, Savina A., Bulyk, Martha, Tsichlis, Philip N., Shirley Liu, X., Struhl, Kevin

“…Transcriptional profiling of two isogenic models of transformation identifies a gene signature linking cancer with inflammatory and metabolic diseases. In…”
Get full text