Xiaole Shirley Liu

发表

Comparative analysis of metazoan chromatin

William Stafford Noble, Stephen C. J. Parker, Maxwell W. Libbrecht, 2014 .

Identifying ChIP-seq enrichment using MACS

Yong Zhang, Jianxing Feng, T. Liu, 2012, Nature Protocols.

Nucleosome Dynamics Define Transcriptional Enhancers

Clifford A. Meyer, J. Lieb, K. Zhao, 2010, Nature Genetics.

Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA.

Jie Yan, Jun S. Liu, Jun S Liu, 2005, Molecular cell.

Inference of transcriptional regulation in cancers

Jun S. Liu, M. Freedman, Xiaole Shirley Liu, 2015, Proceedings of the National Academy of Sciences.

Tropospheric ozone column retrieval from the Ozone Monitoring Instrument by means of a neural network algorithm

Kelly Chance, Bojan Bojkov, F. Del Frate, 2011 .

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

Zhongzheng Cao, Han Xu, Pengfei Yuan, 2016, Nature Biotechnology.

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

Clifford A. Meyer, Ian A. Swinburne, P. Silver, 2005, Genome Biology.

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

P. Kantoff, Myles A Brown, Yiwen Chen, 2014, Proceedings of the National Academy of Sciences.

MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes

Han Xu, Yong Hou, Hua-Jun Wu, 2014, Genome Biology.

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

David Botstein, Patrick O. Brown, D. Botstein, 2001, Nature Genetics.

A comprehensive view of nuclear receptor cancer cistromes.

Qian Wang, Tao Liu, Mathieu Lupien, 2011, Cancer research.

Annals of the New York Academy of Sciences Targeting Epigenetic Regulators for Cancer Therapy

Robert A Copeland, Scott A Armstrong, S. Armstrong, 2022 .

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

Tao Liu, Clifford A. Meyer, Jun S. Liu, 2011, Genome Biology.

Sensitivity study of ozone retrieval from UV measurements on geostationary platforms

Michael J. Newchurch, Xiaole Shirley Liu, Jae H. Kim, 2012 .

Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells.

Elgene Lim, Xi Chen, Wenjun Guo, 2013, Cancer cell.

An optimal-estimation-based aerosol retrieval algorithm using OMI near-UV observations

Ukkyo Jeong, Robert J. D. Spurr, Pawan K. Bhartia, 2016 .

Preliminary results of randomized phase III study comparing efficacy and safety of first-line erlotinib versus carboplatin (CBDCA) plus gemcitabine (GEM) in Chinese advanced non-small cell lung cancer (NSCLC) patients (pts) with EGFR-activating mutations (OPTIMAL).

Yi-long Wu, Xiaole Shirley Liu, C. Zhou, 2010 .

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

Qian Wang, Jianxing Feng, Clifford A. Meyer, 2012, Bioinform..

Evaluation of immune repertoire inference methods from RNA-seq data

Jun S. Liu, Xiaole Shirley Liu, Xihao Hu, 2018, Nature Biotechnology.

Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation

Emily M. Thrash, Emma S. Hathaway, Shuqiang Li, 2021, Blood.

Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data

Jun S. Liu, S. Signoretti, T. Choueiri, 2016, bioRxiv.

Genome analysis CRISPR-DO for genome-wide CRISPR design and optimization

Xiaole Shirley Liu, Wei Li, Qi Liu, 2016 .

Estrogen receptor prevents p53-dependent apoptosis in breast cancer

Hyunjin Shin, Xiaole Shirley Liu, S. Bailey, 2012, Proceedings of the National Academy of Sciences.

A boosting approach for motif modeling using ChIP-chip data

Qing Zhou, Xin Lu, Pengyu Hong, 2005, Bioinform..

BINOCh: binding inference from nucleosome occupancy changes

Myles Brown, Clifford A. Meyer, Xiaole Shirley Liu, 2011, Bioinform..

Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity.

Jun S. Song, Jun S Song, Myles Brown, 2008, Cancer research.

xMAN: extreme MApping of OligoNucleotides

Myles Brown, Jason S. Carroll, Xiaole Shirley Liu, 2008, BMC Genomics.

Getting Started in Tiling Microarray Analysis

Xiaole Shirley Liu, Xiaole Shirley Liu, 2007, PLoS Comput. Biol..

TIMER2.0 for analysis of tumor-infiltrating immune cells

Xiaole Shirley Liu, Taiwen Li, Qianming Chen, 2020, Nucleic Acids Res..

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF-inhibitor Resistant Melanoma

Myles Brown, Nicole Traugh, Sailing Shi, 2019, bioRxiv.

CEAS: cis-regulatory element annotation system

Jun Song, Xiaole Shirley Liu, Liping Wei, 2006, Nucleic Acids Res..

CEAS: cis-regulatory element annotation system

Tao Liu, Xiaole Shirley Liu, Hyunjin Shin, 2009, Bioinform..

Comparative analysis of metazoan chromatin organization

Moritz Herrmann, Manolis Kellis, Stephen C. J. Parker, 2014, Nature.

Statistical models for biological sequence motif discovery

Xiaole Liu, Mayetri Gupta, Charles E. Lawrence, 2002 .

A Bayesian model for single cell transcript expression analysis on MERFISH data

Myles Brown, Johannes Köster, Xiaole Shirley Liu, 2018, Bioinform..

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

Xiaoyan Zhang, Myles Brown, Shenglin Mei, 2018, Nucleic Acids Res..

Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia

J. Schug, J. Aster, B. Bernstein, 2014, Proceedings of the National Academy of Sciences.

Topological analysis reveals a PD-L1-associated microenvironmental niche for Reed-Sternberg cells in Hodgkin lymphoma.

D. Neuberg, M. Shipp, G. Freeman, 2017, Blood.

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

Clifford A. Meyer, Xiaole Shirley Liu, Changxin Wan, 2019, Nucleic Acids Res..

The histone H 3 Lys 27 demethylase JMJD 3 regulates gene expression by impacting transcriptional elongation

S. Gygi, J. Villén, Xiaole Shirley Liu, 2012 .

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Tao Liu, Xiaohui Shi, Myles Brown, 2016, Nucleic Acids Res..

SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells

Yong Zhang, P. Atadja, E. Li, 2015, Genome research.

Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network

P. A. Futreal, Daoud M. Meerzaman, S. Gabriel, 2020, Clinical Cancer Research.

EglN2 associates with the NRF1‐PGC1α complex and controls mitochondrial function in breast cancer

Xi Chen, C. Fan, W. Kaelin, 2015, The EMBO journal.

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Bo Li, Jian Zhang, Myles Brown, 2018, BMC Bioinformatics.

Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC)

E. Cerami, I. Wistuba, Catherine J. Wu, 2021, Clinical Cancer Research.

Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL−/− clear cell renal carcinoma

W. Kaelin, Xiaole Shirley Liu, Wei Li, 2017, Proceedings of the National Academy of Sciences.

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences

Clifford A. Meyer, Xiaole Shirley Liu, Wei Li, 2005, ISMB.

Title Comparative analysis of metazoan chromatin organization Permalink

William Stafford Noble, Stephen C. J. Parker, Maxwell W. Libbrecht, 2014 .

modENCODE and ENCODE resources for analysis of metazoan chromatin organization

Park, Stephen C. J. Parker, Maxwell W. Libbrecht, 2013 .

Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant

G. Schoolnik, Xiaole Shirley Liu, F. Yildiz, 2004, Molecular microbiology.

CistromeFinder for ChIP-seq and DNase-seq data reuse

Tao Liu, Jing Liu, Bo Qin, 2013, Bioinform..

A suite of web-based programs to search for transcriptional regulatory motifs

Serafim Batzoglou, Douglas L. Brutlag, Xiaole Shirley Liu, 2004, Nucleic Acids Res..

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

Tao Liu, Qian Wang, Bo Qin, 2012, Bioinform..

DiNuP: a systematic approach to identify regions of differential nucleosome positioning

Jianxing Feng, Xiaole Shirley Liu, Kai Fu, 2012, Bioinform..

Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer

Henry W. Long, R. Berkowitz, C. Feltmate, 2020, Cancer Research.

Improved design and analysis of CRISPR knockout screens

Peng Jiang, Han Xu, Myles Brown, 2018, Bioinform..

The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia

J. Aster, S. Blacklow, W. Pear, 2017, PloS one.

Reply to Evidence against a genomic code for nucleosome positioning

K. Struhl, M. Snyder, Z. Moqtaderi, 2010 .

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model

Jun Wang, Yun Fang, Xiaoqi Zheng, 2015, PLoS Comput. Biol..

Regulation of Human 3α-Hydroxysteroid Dehydrogenase (AKR1C4) Expression by the Liver X Receptor α

Xiaole Shirley Liu, R. Savkur, S. Nagpal, 2008, Molecular Pharmacology.

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Jing Liu, Qian Wang, Juan Wang, 2013, Nucleic Acids Res..

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data

Zhi Chen, Cheng Li, Meng Zhou, 2010, Nucleic Acids Res..

Critical Assessment of TOMS-derived Tropospheric Ozone: Comparisons with Other Measurements and Model Evaluation of Controlling Processes

D. Jacob, G. Brasseur, L. Horowitz, 2001 .

Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer

Henry W. Long, Pandya, R. Berkowitz, 2020, Cancer Research.

CEAS: cis-regulatory element annotation system.

Jun S. Song, Liping Wei, Xiaole Shirley Liu, 2006, Nucleic acids research.

Applying whole-genome studies of epigenetic regulation to study human disease

S. Henikoff, M. Bulyk, J. Lieb, 2006, Cytogenetic and Genome Research.

Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila

X. Shirley Liu, Xiangfeng Wang, X. Liu, 2011, Front. Gene..

An integrative ENCODE resource for cancer genomics

Jie Xu, Lucas Lochovsky, Donghoon Lee, 2019, Nature Communications.

CRISPR-DO for genome-wide CRISPR design and optimization

Wei Li, Qi Liu, Jian Ma, 2016, Bioinform..

The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation.

S. Gygi, Xiaole Shirley Liu, Honghui Ma, 2012, Genes & development.

Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes

X. Shirley Liu, Hyunjin Shin, Ramesh A. Shivdasani, 2011, Molecular and Cellular Biology.

Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies.

Jun S. Liu, J. Aster, X. Liu, 2018, Cell systems.

Inhibition of MAN2A1 Enhances the Immune Response to Anti–PD-L1 in Human Tumors

Shengqing Gu, Xiaole Shirley Liu, K. Wucherpfennig, 2020, Clinical Cancer Research.

Identifying ChIP-seq enrichment using MACS

Yong Zhang, Jianxing Feng, T. Liu, 2012, Nature Protocols.

Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells.

R. Weinberg, B. Lim, W. Tam, 2013, Cancer cell.

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

Clifford A. Meyer, Xiaole Shirley Liu, Chenhao Chen, 2018, Nucleic Acids Res..

Topological analysis reveals a PD-L1-associated microenvironmental niche for Reed-Sternberg cells in Hodgkin lymphoma.

D. Neuberg, M. Shipp, F. Hodi, 2017, Blood.

Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data

S. Signoretti, T. Choueiri, Xiaole Shirley Liu, 2016, bioRxiv.

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Henry W. Long, Xiaole Shirley Liu, Len Taing, 2018, BMC Bioinformatics.