X. Liu

发表

Clifford A. Meyer, C. Nusbaum, R. Myers, 2008, Genome Biology.

Evidence against a genomic code for nucleosome positioning Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization”

Kevin Struhl, Yong Zhang, X Shirley Liu, 2010, Nature Structural &Molecular Biology.

Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1

Clifford A. Meyer, P. Silver, Wei Li, 2005, Cell.

Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.

Clifford A. Meyer, Myles A Brown, X. Liu, 2010, Developmental cell.

Differentiation-specific histone modifications reveal dynamic chromatin interactions and alternative partners for the intestinal transcription factor CDX 2

Clifford A. Meyer, X. Liu, Hyunjin Shin, 2011 .

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

Jun S. Liu, J. Aster, X. Liu, 2016, Genome Biology.

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Philipp Kapranov, George Q. Daley, X. Shirley Liu, 2011, Nature.

JARID1B is a luminal lineage-driving oncogene in breast cancer.

Carlos Caldas, Charles J. Vaske, Hanfei Sun, 2014, Cancer cell.

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

X. Shirley Liu, Gert Jan C. Veenstra, Wolfram Tempel, 2012, Cell.

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

Jun S. Liu, Le Cong, R. Irizarry, 2014, Genome Biology.

Target analysis by integration of transcriptome and ChIP-seq data with BETA

Hanfei Sun, Chongzhi Zang, Clifford A. Meyer, 2013, Nature Protocols.

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC

G. Coetzee, X. Liu, L. Macconaill, 2010, Proceedings of the National Academy of Sciences.

A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

Henry W. Long, John G Doench, Guocheng Yuan, 2018, Science.

MYC regulation of a “poor-prognosis” metastatic cancer cell state

Clifford A. Meyer, Ben S. Wittner, B. Wittner, 2010, Proceedings of the National Academy of Sciences.

Differential chromatin marking of introns and expressed exons by H3K36me3

J. Ahringer, T. Down, X. Liu, 2008, Nature Genetics.

CEAS: cis-regulatory element annotation system.

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

Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors.

E. Winer, X. Liu, Kwok-Kin Wong, 2016, Cancer cell.

Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability

James E. Bradner, Donna Neuberg, X. Shirley Liu, 2014, Cell.

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

X. Shirley Liu, Liping Wei, X. Liu, 2006, Nucleic acids research.

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize[W]

X. Liu, Y. Qi, Ning Li, 2009, The Plant Cell Online.

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

X. Liu, G. Freeman, A. Sahu, 2018, Nature Medicine.

A single-cell and spatially resolved atlas of human breast cancers

Stephen R. Williams, N. Weisenfeld, F. Ginhoux, 2021, Nature Genetics.

Large-scale public data reuse to model immunotherapy response and resistance

Peng Jiang, X. Shirley Liu, Changxin Wan, 2020, Genome Medicine.

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

Clifford A. Meyer, Wei Li, Yong Zhang, 2008, Cell.

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.

Clifford A. Meyer, J. Eeckhoute, X. Liu, 2008, Genome research.

of FOXA 1-bound enhancers Cell-type selective chromatin remodeling defines the active subset Material Supplemental

Clifford A. Meyer, J. Eeckhoute, X. Liu, 2009 .

A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress

Henry W. Long, P. Kantoff, Myles A Brown, 2020, bioRxiv.

Targeting the MIF/CXCR7/AKT Signaling Pathway in Castration-Resistant Prostate Cancer

X. Liu, A. Kibel, L. Jia, 2018, Molecular Cancer Research.

Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing

M. Loda, X. Liu, Yiwen Chen, 2017, Proceedings of the National Academy of Sciences.

Integrative analysis and refined design of CRISPR knockout screens

Han Xu, Clifford A. Meyer, Myles Brown, 2017, bioRxiv.

Response and resistance to BET bromodomain inhibitors in triple negative breast cancer

James E. Bradner, Jason S. Carroll, X. Shirley Liu, 2015, Nature.

Computational inference of mRNA stability from histone modification and transcriptome profiles

Clifford A. Meyer, H. Zhao, Yong Zhang, 2012, Nucleic acids research.

Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha

Clifford A. Meyer, Phillip B. Nicol, Jun Liu, 2021, bioRxiv.

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

L. Aravind, R. Ganetzky, X. Liu, 2010, Nature.

Targeting androgen receptor in estrogen receptor-negative breast cancer.

Harvard Medical School, Myles A Brown, X. Liu, 2011, Cancer cell.

ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.

Hongyun Wang, Housheng Hansen He, X Shirley Liu, 2013, The Journal of clinical investigation.

Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.

Jérôme Eeckhoute, Mathieu Lupien, Clifford A. Meyer, 2010, Genes & development.

Genome-wide analysis of estrogen receptor binding sites

Clifford A. Meyer, Jun S. Song, P. Silver, 2006, Nature Genetics.

Model-based analysis of tiling-arrays for ChIP-chip

Clifford A. Meyer, W. Johnson, Wei Li, 2006, Proceedings of the National Academy of Sciences.

Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer

Clifford A. Meyer, M. Loda, P. Kantoff, 2009, Cell.

NOTCH1–RBPJ complexes drive target gene expression through dynamic interactions with superenhancers

Jon C. Aster, Stephen C. Blacklow, X. Shirley Liu, 2013, Proceedings of the National Academy of Sciences.

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2010, Science.

XBP1 Promotes Triple Negative Breast Cancer By Controlling the HIF1 α Pathway

M. Ferrari, D. Iliopoulos, Myles A Brown, 2014, Nature.

BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes

Jun S. Liu, D. Brutlag, X. Liu, 2000, Pacific Symposium on Biocomputing.

Broad chromosomal domains of histone modification patterns in C. elegans.

A. Rechtsteiner, J. Ahringer, J. Lieb, 2011, Genome research.

Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis

Wei Li, X. Liu, J. Carroll, 2009, Proceedings of the National Academy of Sciences.

Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Specific Enhancers That Are Prognostic for Overall Survival

X. Liu, J. Greally, A. Verma, 2014, Clinical Cancer Research.

Biology of Human Tumors Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Speci fi c Enhancers That Are Prognostic for Overall Survival

X. Liu, J. Greally, A. Verma, 2014 .

Transcriptional landscape of the human cell cycle

Clifford A. Meyer, Charles Y. Lin, X. Liu, 2017, Proceedings of the National Academy of Sciences.

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Clifford A. Meyer, Myles A Brown, X. Liu, 2020, Genome Biology.

The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.

Mithat Gönen, Tatiana Nikolskaya, Yuri Nikolsky, 2011, The Journal of clinical investigation.

Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.

Clifford A. Meyer, Ian A. Swinburne, P. Silver, 2006, Genome research.

between pre-mRNA processing and transcription Genomic localization of RNA binding proteins reveals links

Clifford A. Meyer, Ian A. Swinburne, P. Silver, 2006 .

MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

Clifford A. Meyer, Henry W. Long, Myles A Brown, 2021, Nature Methods.

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

Alyssa R. Richman, Brian L. Shaw, A. Regev, 2021, Cell.

Alu elements mediate MYB gene tandem duplication in human T-ALL

Charles Lee, J. Tchinda, L. Chin, 2007, The Journal of experimental medicine.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Marc D. Perry, James B. Brown, Timothy E. Reddy, 2012, Genome research.

Integrative genomic analyses reveal clinically relevant long non-coding RNA in human cancer

Zhen Su, X. Shirley Liu, Yong Zhang, 2013 .

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations.

Henry W. Long, E. Winer, X. Liu, 2018, Cancer cell.

Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells

X. Liu, C. Jin, Kun Lu, 2017, Environmental health perspectives.

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.

Clifford A. Meyer, X. Liu, M. Lupien, 2009, Genome research.

Supplemental Material References Open Access

Clifford A. Meyer, X. Liu, M. Lupien, 2008 .

Chromatin structure analyses identify miRNA promoters

Jun S. Song, Fatih Ozsolak, L. Poling, 2008 .

Chromatin signature of embryonic pluripotency is established during genome activation

Aviv Regev, X. Shirley Liu, Alexander F. Schier, 2010, Nature.

An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine

Myles A Brown, X. Liu, Xiaoqi Zheng, 2016, Scientific Reports.

Snail1-dependent p53 repression regulates expansion and activity of tumour-initiating cells in breast cancer

X. Liu, S. Weiss, Xiao-yan Li, 2016, Nature Cell Biology.

XBP 1 Promotes Triple Negative Breast Cancer By Controlling the HIF 1 α Pathway

Mauro Ferrari, Elgene Lim, Xi Chen, 2014 .

The Role of Notch Receptors in Transcriptional Regulation

J. Aster, X. Liu, C. Zang, 2015, Journal of cellular physiology.

FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance

Henry W. Long, Kristen L Jones, X. Liu, 2021, Nature Cell Biology.

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.

Jonathan Schug, Christian J Stoeckert, Yong Zhang, 2008, Genes & development.

Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

Han Xu, X. Shirley Liu, Chongzhi Zang, 2013, Nature methods.

A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma

D. Neuberg, M. Shipp, X. Liu, 2020, Nature Medicine.

Mass cytometry of Hodgkin lymphoma reveals a CD4+ regulatory T-cell-rich and exhausted T-effector microenvironment.

D. Neuberg, M. Shipp, X. Liu, 2018, Blood.

Genome-wide Map of Nuclear Protein Degradation Shows NCoR1 Turnover as a Key to Mitochondrial Gene Regulation

X. Liu, D. Scadden, D. Dombkowski, 2013, Cell.

EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent

M. Loda, P. Kantoff, Tao Liu, 2012, Science.

Integrative genomic analyses reveal clinically relevant long non-coding RNA in human cancer

R. Verhaak, Yong Zhang, Zhen Su, 2013, Nature Structural &Molecular Biology.

Amplitude Modulation of Androgen Signaling by C-myc Material Supplemental

X. Liu, Yiwen Chen, Teng Fei, 2013 .

A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin–MLL Inhibition

Francisco J. Sánchez-Rivera, S. Armstrong, S. Lowe, 2022, bioRxiv.

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

Henry W. Long, P. Nelson, Myles A Brown, 2020, Nature Communications.

CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor cells and T cells.

John G Doench, S. Elledge, X. Liu, 2021, Cancer discovery.

Integrin αvβ6-TGFβ-SOX4 Pathway Drives Immune Evasion in Triple-Negative Breast Cancer.

A. Giobbie-Hurder, X. Liu, D. Dillon, 2020, Cancer cell.

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

Clifford A. Meyer, X. Liu, X. Liu, 2014, Nature Reviews Genetics.

Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation

Shourya S. Roy Burman, X. Liu, C. Tokheim, 2021, bioRxiv.

Gene Regulatory Networks Mediating Canonical Wnt Signal‐Directed Control of Pluripotency and Differentiation in Embryo Stem Cells

A. McMahon, X. Liu, Shinsuke Ohba, 2013, Stem cells.

Polycomb-independent activity of EZH2 in castration resistant prostate cancer

Tao Liu, Housheng Hansen He, X Shirley Liu, 2013, Epigenetics & Chromatin.

NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes

Harvard T. H. Chan, X. Liu, R. Shivdasani, 2016, Scientific Reports.

Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells

Chongzhi Zang, X Shirley Liu, X. Liu, 2014, Genes & development.

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

X. Liu, Hyunjin Shin, R. Shivdasani, 2012, Molecular and Cellular Biology.

limited lineage fidelity among specified primary blood cells Active enhancers are delineated de novo during hematopoiesis , with Material

X. Liu, R. Shivdasani, C. Zang, 2014 .

Landscape of B cell immunity and related immune evasion in human cancers

Jun S. Liu, N. Hacohen, Jun Liu, 2018, Nature Genetics.

Landscape of tumor-infiltrating T cell repertoire of human cancers

Jun S. Liu, N. Hacohen, X. Liu, 2016, Nature Genetics.

ARv7 Represses Tumor-Suppressor Genes in Castration-Resistant Prostate Cancer.

Henry W. Long, P. Nelson, B. Trock, 2019, Cancer cell.

Transcriptional role of cyclin D1 in development revealed by a genetic–proteomic screen

Clifford A. Meyer, Joshua E. Elias, Megan F. Cole, 2010, Nature.

TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions

Myles A Brown, X. Liu, H. Clevers, 2010, Proceedings of the National Academy of Sciences.

Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy

M. Dowsett, X. Liu, Han Xu, 2018, Proceedings of the National Academy of Sciences.

Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development

S. Armstrong, X. Liu, R. Koche, 2020, iScience.

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3’-end formation

Kevin Struhl, Yong Zhang, X Shirley Liu, 2010, Proceedings of the National Academy of Sciences.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

Clifford A. Meyer, Jun S. Liu, Armin Schwartzman, 2010, Genome research.

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

G. Freeman, A. Sahu, Shengqing Gu, 2018, Nature Medicine.

In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target

Clifford A. Meyer, Henry W. Long, Y. Zhang, 2021, Cell.

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.

K. Struhl, S. Jaeger, M. Bulyk, 2010, Cancer cell.

Genome-wide and Organ-specific Landscapes of Epigenetic Modifications and Their Relationships to Mrna and Small Rna Transcriptomes in Maize

Y. Qi, Ning Li, Xueyong Li, 2022 .

Systematic characterization of mutations altering protein degradation in human cancers.

S. Elledge, X. Liu, C. Tokheim, 2021, Molecular cell.

Chromatin structure analyses identify miRNA promoters.

Jun S. Song, Fatih Ozsolak, L. Poling, 2008, Genes & development.

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

H. Lähdesmäki, L. Aravind, X. Liu, 2012, Proceedings of the National Academy of Sciences.

A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.

K. Pienta, A. Chinnaiyan, Myles A Brown, 2007, Molecular cell.

Network analysis of gene essentiality in functional genomics experiments

Jon C. Aster, X. Shirley Liu, Chongzhi Zang, 2015, Genome Biology.

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.

Angela N. Brooks, M. Meyerson, D. DeLuca, 2014, The Journal of clinical investigation.

Altered antisense-to-sense transcript ratios in breast cancer

A. Protopopov, Jun Yao, X. Liu, 2010, Proceedings of the National Academy of Sciences.

Computational methodology for ChIP-seq analysis

Tao Liu, X. Shirley Liu, Hyunjin Shin, 2013, Quantitative Biology.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Mark Gerstein, Kevin Struhl, Zhiping Weng, 2008, Genome research.

Systematic evaluation of variability in ChIP-chip experiments using data

Jun S. Song, Xiaoqin, Xiao-qin, 2008 .

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer

J. Rinn, P. Kantoff, Myles A Brown, 2016, Nature Communications.

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

Jun S. Liu, Jun S Liu, X Shirley Liu, 2017, Nature Genetics.

Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma.

C. Moskaluk, J. Aster, B. Bernstein, 2014, Cancer discovery.

BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes

D. Brutlag, X. Liu, Jun S. Liu, 2000, Pacific Symposium on Biocomputing.

More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells

Gang Pei, X Shirley Liu, Dangsheng Li, 2009, Cell Research.

Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

Serafim Batzoglou, Russ B Altman, Liping Wei, 2004, Genome research.

Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.

Tao Liu, X Shirley Liu, Xiangfeng Wang, 2011, Genomics.

TIMER : AWeb Server for Comprehensive Analysis of Tumor-In fi ltrating Immune Cells

Jun S. Liu, X. Liu, Taiwen Li, 2017 .

PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression

Qian Wang, X. Liu, Su Wang, 2014, Scientific Reports.

Topical therapy for regression and melanoma prevention of congenital giant nevi

Clifford A. Meyer, Y. Zhang, M. Mihm, 2022, Cell.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Response and resistance to BET bromodomain inhibitors in triple negative breast cancer

Clifford A. Meyer, Henry W. Long, Christopher J. Ott, 2015, Nature.

Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy

Aleksandra A. Kolodziejczyk, X. Liu, G. Freeman, 2020, Nature Cell Biology.

MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment

Clifford A. Meyer, X. Liu, Chenfei Wang, 2023, Nature communications.

MetaTiME: Meta-components of the Tumor Immune Microenvironment

Clifford A. Meyer, Myles A Brown, X. Liu, 2023, bioRxiv.

Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade.

Clifford A. Meyer, Henry W. Long, X. Liu, 2021, Cancer discovery.

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

Clifford A. Meyer, Myles A Brown, X. Liu, 2012, Genome research.

Mass cytometry of Hodgkin lymphoma reveals a CD 4 + exhausted T-effector and T-regulatory cell rich microenvironment

Robert, Redd, D. Neuberg, 2018 .

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade

Clifford A. Meyer, Henry W. Long, Y. Zhang, 2020, Genome biology.

Cistrome: an integrative platform for transcriptional regulation studies

Clifford A. Meyer, Yong Zhang, Myles A Brown, 2011, Genome Biology.

He centromere A high-resolution map of nucleosome positioning on a fission yeast data

Jun S. Song, Xiangwei He, Xingkun Liu, 2008 .

centromeren map of nucleosome positioning on a fission yeast

Jun S. Song, Xiangwei He, Xingkun Liu, 2008 .

Canonical nucleosome organization at promoters forms during genome activation

Yong Zhang, Paul van Hummelen, X Shirley Liu, 2014, Genome research.

Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

Henry W. Long, X. Liu, C. Tokheim, 2023, Nature Protocols.

SOX 2 and p 63 colocalize at genetic loci in squamous cell carcinomas

Angela N. Brooks, M. Meyerson, D. DeLuca, 2014 .

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

X. Liu, Xihao Hu, Zhangyi Ouyang, 2021, Nature Methods.

Immune receptor repertoires in pediatric and adult acute myeloid leukemia

N. Hacohen, X. Liu, A. Sahu, 2019, Genome Medicine.

Comprehensive characterizations of immune receptor repertoire in tumors and cancer immunotherapy studies.

K. Livak, Heng Li, Bo Li, 2022, Cancer immunology research.

Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology*

X. Liu, D. Frank, E. Nelson, 2006, Journal of Biological Chemistry.

A Flexible and Powerful Bayesian Hierarchical Model for ChIP–Chip Experiments

Raphael Gottardo, Wei Li, X Shirley Liu, 2008, Biometrics.

Fast alignment and preprocessing of chromatin profiles with Chromap

Clifford A. Meyer, Heng Li, Tao Liu, 2021, Nature Communications.

Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response

Myles A Brown, X. Liu, Zexian Zeng, 2022, Science advances.

Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer.

X. Liu, A. Califano, C. Drake, 2022, Clinical cancer research : an official journal of the American Association for Cancer Research.

genome activation Canonical nucleosome organization at promoters forms during Material

A. Schier, Yong Zhang, X. Liu, 2014 .

Sequence determinants of improved CRISPR sgRNA design

Clifford A. Meyer, Jun S. Liu, Le Cong, 2015, Genome research.

An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer

X. Shirley Liu, Hyunjin Shin, Shuji Ogino, 2013, Oncogene.

CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis

Henry W. Long, Len Taing, P. Cejas, 2021, Genom. Proteom. Bioinform..

Deciphering essential cistromes using genome-wide CRISPR screens

Alexander P. Wu, Myles A Brown, X. Liu, 2019, Proceedings of the National Academy of Sciences.

Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.

Gedge D. Rosson, M. Pike, I. Haviv, 2013, Cell stem cell.

Targeting theMIF / CXCR 7 / AKTSignalingPathway in Castration-Resistant Prostate Cancer

A. Kibel, L. Jia, B. Gui, 2018 .

Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.

Clifford A. Meyer, X. Liu, Q. Tang, 2012, Molecular endocrinology.

modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental

James B. Brown, Timothy E. Reddy, P. Bickel, 2012 .

IKAROS and MENIN Coordinate Therapeutically Actionable Leukaemogenic Gene Expression in MLL-r Acute Myeloid Leukaemia

S. Armstrong, A. Letai, X. Liu, 2022, Nature Cancer.

Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer.

Jacob D. Jaffe, Henry W. Long, Thomas O. McDonald, 2020, Molecular cell.

Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress

Henry W. Long, P. Kantoff, X. Liu, 2022, Proceedings of the National Academy of Sciences.

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.

Adam A. Margolin, Richard A Young, Teresa Palomero, 2005, Blood.

Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome

Clifford A. Meyer, J. Eeckhoute, X. Liu, 2009, Molecular and Cellular Biology.

Systematic evaluation of factors influencing ChIP-seq fidelity

P. Bickel, B. Wold, R. Myers, 2012, Nature Methods.

R EVIEW Computational methodology for ChIP-seq analysis

Yong Zhang, X. Liu, T. Liu, 2013 .

ARv 7 Represses Tumor-Su ppressor Genes in Castration-Resistant Prostate Cancer Graphical

Henry W. Long, P. Nelson, B. Trock, 2019 .

chromatin dynamics Differential DNase I hypersensitivity reveals factor-dependent Material Supplemental

Clifford A. Meyer, H. He, V. Jordan, 2012 .

Big data mining yields novel insights on cancer

X. Liu, P. Jiang, Peng Jiang, 2015, Nature Genetics.

Integrin avb6–TGFb–SOX4 Pathway Drives Immune Evasion in Triple-Negative Breast Cancer

A. Giobbie-Hurder, X. Liu, D. Dillon, 2020 .

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR 1 Activating Mutations Graphical Abstract Highlights

Henry W. Long, E. Winer, N. Gray, 2018 .

Neural network architecture search with AMBER

X. Shirley Liu, Yi Zhang, Yang Liu, 2021, Nature Machine Intelligence.

Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

I. Haviv, X. Liu, T. Nikolskaya, 2011, PLoS genetics.

DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression.

X. Liu, S. Yagi, K. Hirabayashi, 2008, Genome research.