X. Liu

发表

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

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

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

An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

Jun S. Liu, X. Liu, D. Brutlag, 2002, Nature Biotechnology.

Big data mining yields novel insights on cancer

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

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.

Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.

X. Liu, Xin Yi, Wenying Xu, 2013, Molecular plant.

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

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

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

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

Chromatin structure analyses identify miRNA promoters

Jun S. Song, X. Liu, Fatih Ozsolak, 2008 .

High-throughput mapping of the chromatin structure of human promoters

Jun S. Song, X. Liu, Fatih Ozsolak, 2007, Nature Biotechnology.

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

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

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

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

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

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

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.

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

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

Cistrome: an integrative platform for transcriptional regulation studies

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

Differential chromatin marking of introns and expressed exons by H3K36me3

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

Sequence determinants of improved CRISPR sgRNA design

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

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.

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

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

Exploring genetic associations with ceRNA regulation in the human genome

Pak Chung Sham, Jean-Pierre A. Kocher, Mulin Jun Li, 2017, Nucleic acids research.

Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

Jun S. Song, Hyunjin, Yong Zhang, 2008, BMC Genomics.

Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles

Joaquim Bellmunt, Shirley X. Liu, Paloma Cejas, 2016, Nature Medicine.

Genome-wide analysis of estrogen receptor binding sites

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

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

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

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

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

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

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

A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer

Clifford A. Meyer, X. Liu, Hai-Yang Wang, 2013, BMC Genomics.

Chromatin signature of embryonic pluripotency is established during genome activation

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

Systematic evaluation of factors influencing ChIP-seq fidelity

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

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

K. Struhl, M. Snyder, Z. Moqtaderi, 2009, Nature Structural &Molecular Biology.

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..

Model-based analysis of two-color arrays (MA2C)

Wei Li, Runsheng Chen, Jun S. Liu, 2007, Genome Biology.

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

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

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Clifford A. Meyer, Henry W. Long, Tao Liu, 2020, Genome Biology.

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

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

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

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

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR

Jun S. Liu, Myles A Brown, X. Liu, 2015, Genome Biology.

Deciphering essential cistromes using genome-wide CRISPR screens

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

Integrating regulatory motif discovery and genome-wide expression analysis

Jun S. Liu, Erin M. Conlon, J. Lieb, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

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

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.

Landscape of tumor-infiltrating T cell repertoire of human cancers

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

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

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

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.

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

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

TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.

Jun S. Liu, X. Liu, Bo Li, 2017, Cancer research.

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.

A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

Tao Liu, X. Shirley Liu, Tao Liu, 2011, Science.

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

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

Chromatin marks identify critical cell types for fine mapping complex trait variants

Buhm Han, Han Xu, Soumya Raychaudhuri, 2012 .

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.

Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole genome sequencing studies at scale

Ivana V. Yang, Andrew D. Johnson, Ryan D. Hernandez, 2020, Nature Genetics.

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

Clifford A. Meyer, Jun S. Liu, X. Liu, 2010 .

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

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

Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data.

Jun S. Liu, X. Liu, Taiwen Li, 2020, Methods in molecular biology.

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

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

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

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

Big Data Approaches for Modeling Response and Resistance to Cancer Drugs.

W. Sellers, X. Liu, Peng Jiang, 2018, Annual review of biomedical data science.

Determinants of transcription factor regulatory range

Clifford A. Meyer, Jun S. Liu, Myles A Brown, 2020, Nature Communications.

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

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

Computational inference of mRNA stability from histone modification and transcriptome profiles

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

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

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

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

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

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

Shirley X. Liu, Henry W. Long, Myles A Brown, 2015, Molecular Cancer Research.

Targeting androgen receptor in estrogen receptor-negative breast cancer.

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

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.

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.

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.

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.

In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target

Clifford A. Meyer, Henry W. Long, Y. Zhang, 2020, bioRxiv.

Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer

X. Liu, E. Lam, A. Forrest, 2020, bioRxiv.

Immune receptor repertoires in pediatric and adult acute myeloid leukemia

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

adjacent binding on a genome-wide scale and C / EBP factors orchestrate adipocyte biology via γ PPAR Material Supplemental

J. Schug, Yong Zhang, X. Liu, 2008 .

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 .

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.

Parity and BRCA1/2-associated breast cancer risk linked to hormone-responsive p27 + luminal epithelial progenitors

Stuart, Pedram, Gedge, 2018 .

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

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

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

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

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

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

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

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

Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1.

P. Nelson, Myles A Brown, X. Liu, 2011, Cancer cell.

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

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

MetaTiME: Meta-components of the Tumor Immune Microenvironment

Clifford A. Meyer, Myles A Brown, X. Liu, 2022, bioRxiv.

Topical therapy for regression and melanoma prevention of congenital giant nevi

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

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

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

Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer.

Clifford A. Meyer, Myles A Brown, X. Liu, 2017, Cancer research.

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

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

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.

KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells

X. Liu, Peng Zhang, Liang Tang, 2016, Oncotarget.

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.

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

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

MetaTiME: Meta-components of the Tumor Immune Microenvironment

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

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

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

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.

Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer

X. Liu, A. Forrest, S. O'toole, 2020, The EMBO journal.

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.

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.

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

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

Fast alignment and preprocessing of chromatin profiles with Chromap

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

Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence.

Runsheng Chen, X Shirley Liu, Michael P Washburn, 2007, Molecular cell.

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.

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.

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

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

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade

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

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

X. Liu, Shengqing Gu, K. Wucherpfennig, 2020, Clinical Cancer Research.

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

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

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

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

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

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

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

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

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

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

Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.

X. Liu, H. He, R. Schüle, 2014, Cell reports.

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

Clifford A. Meyer, X. Liu, H. He, 2012 .

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles

Shenglin Mei, Qian Qin, Chongzhi Zang, 2016, Genome research.

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

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

Computational methodology for ChIP-seq analysis

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

R EVIEW Computational methodology for ChIP-seq analysis

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

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

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

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 .

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

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

Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome

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

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.

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

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

ChIP-Chip: algorithms for calling binding sites.

Clifford A. Meyer, X. Liu, X. Liu, 2009, Methods in molecular biology.

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

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

Systematic evaluation of variability in ChIP-chip experiments using data

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

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

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

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Clifford A. Meyer, Henry W. Long, Tao Liu, 2020, Genome Biology.

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

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

Transcriptional landscape of the human cell cycle

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

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

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

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.

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 .

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

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

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.

Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma Discovery of Biomarkers Predictive of GSI Response in

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

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

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

Overcoming Therapeutic R esistance in HER 2-Positive Breast Cancers with CDK 4 / 6 Inhibitors Highlights

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

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.

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.

High-dimensional genomic data bias correction and data integration using MANCIE

Ke Deng, Yang Xie, Chongzhi Zang, 2016, Nature Communications.

Amplitude Modulation of Androgen Signaling by C-myc Material Supplemental

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

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

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

Canonical nucleosome organization at promoters forms during genome activation

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

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

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

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

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

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.

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.

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.

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

Robert, Redd, D. Neuberg, 2018 .

Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

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

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

Clifford A. Meyer, X. Liu, Qiu Wu, 2020, Genome Biology.

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

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

Applications of Immunogenomics to Cancer

Elaine R. Mardis, X. Shirley Liu, E. Mardis, 2017, Cell.

Checkpoint blockade-induced CD8+ T cell differentiation in head and neck cancer responders

Katie M. Campbell, O. Griffith, X. Liu, 2022, Journal for ImmunoTherapy of Cancer.

Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

X. Liu, E. V. Van Allen, S. Signoretti, 2020, Cancer Immunology Research.

Systematic characterization of mutations altering protein degradation in human cancers.

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

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.

Cells Is Polycomb-Independent EZH 2 Oncogenic Activity in Castration-Resistant Prostate Cancer

M. Loda, P. Kantoff, Tao Liu, 2013 .

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

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

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.

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

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

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

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

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.

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.

Genetic fusions favor tumorigenesis through degron loss in oncogenes

P. Pandolfi, X. Liu, C. Tokheim, 2021, Nature Communications.

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.

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

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

Network analysis of gene essentiality in functional genomics experiments

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

Immune receptor repertoires in pediatric and adult acute myeloid leukemia

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

Integrative analysis and refined design of CRISPR knockout screens

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

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.

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

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

An integrative ENCODE resource for cancer genomics

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

CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

Len Taing, Xintao Qiu, Avery S. Feit, 2020, bioRxiv.

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.

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

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

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 .

Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade.

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

Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.

Wei Zhou, Geir Skogerbø, Runsheng Chen, 2007, Genome research.

modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2011 .

Altered antisense-to-sense transcript ratios in breast cancer

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

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

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

Perspectives on ENCODE

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

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

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

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

Mauro Ferrari, Elgene Lim, Xi Chen, 2014 .

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

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

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.

Target Gene-specific Regulation of Androgen Receptor Activity by P42/p44 Mitogen-activated Protein Kinase

X. Liu, Wei Li, Qianben Wang, 2008 .

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.

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

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

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.

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade

Clifford A. Meyer, Henry W. Long, X. Liu, 2020, Genome Biology.

The Role of Notch Receptors in Transcriptional Regulation

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

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.

Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute

Alexander P. Wu, X. Liu, J. Zuber, 2019, Nature Protocols.

Polycomb-independent activity of EZH2 in castration resistant prostate cancer

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

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.

Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective

Shane T. Jensen, Jun S. Liu, X. Shirley Liu, 2004 .

TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response

X. Liu, G. Freeman, K. Yates, 2021, Nucleic Acids Res..

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

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

DeepBCR: Deep learning framework for cancer-type classification and binding affinity estimation using B cell receptor repertoires

X. Liu, Xihao Hu, 2019, bioRxiv.

KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells

X. Liu, Peng Zhang, Liang Tang, 2016, Oncotarget.

Hippo signaling pathway regulates cancer cell-intrinsic MHC-II expression.

X. Liu, F. Hodi, S. Rodig, 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.

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.

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

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

genome activation Canonical nucleosome organization at promoters forms during Material

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

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

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

Revisit linear regression-based deconvolution methods for tumor gene expression data

X. Shirley Liu, Jun S. Liu, Bo Li, 2017, Genome Biology.

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.

CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data

Clifford A. Meyer, Henry W. Long, X. Liu, 2021, bioRxiv.

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.

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

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

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

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