Xiaole Shirley Liu
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Professor of Biostatistics and Computational Biology at Dana-Farber and Harvard
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Why Is Xiaole Shirley Liu Influential?
(Suggest an Edit or Addition)According to Wikipedia, Xiaole Shirley Liu is computational biologist, cancer researcher, and entrepreneur. She has been a Professor in the Department of Data Sciences at the Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. She is now the co-founder and CEO of GV20 Therapeutics.
Xiaole Shirley Liu's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Model-based Analysis of ChIP-Seq (MACS) (2008) (11787)
- TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. (2017) (3013)
- Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response (2018) (1823)
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012) (1701)
- TIMER2.0 for analysis of tumor-infiltrating immune cells (2020) (1638)
- Genome-wide analysis of estrogen receptor binding sites (2006) (1388)
- Comprehensive analyses of tumor immunity: implications for cancer immunotherapy (2016) (1364)
- Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1 (2005) (1341)
- MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens (2014) (1246)
- Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2 (2010) (1221)
- Identifying ChIP-seq enrichment using MACS (2012) (1205)
- Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project (2010) (931)
- BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes (2000) (928)
- FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription (2008) (924)
- Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer (2009) (891)
- The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. (2011) (820)
- Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells (2011) (762)
- An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments (2002) (752)
- PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. (2008) (725)
- EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent (2012) (724)
- Differential chromatin marking of introns and expressed exons by H3K36me3 (2008) (673)
- Chromatin structure analyses identify miRNA promoters. (2008) (666)
- Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association (2001) (654)
- A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. (2007) (646)
- Cistrome: an integrative platform for transcriptional regulation studies (2011) (621)
- A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism (2011) (620)
- XBP1 Promotes Triple Negative Breast Cancer By Controlling the HIF1 α Pathway (2014) (618)
- REST and Stress Resistance in Aging and Alzheimer’s Disease (2014) (596)
- A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing (2018) (535)
- Chromatin marks identify critical cell types for fine mapping complex trait variants (2012) (522)
- Integrative genomic analyses reveal clinically relevant long non-coding RNA in human cancer (2013) (506)
- Model-based analysis of tiling-arrays for ChIP-chip (2006) (486)
- Sequence determinants of improved CRISPR sgRNA design (2015) (473)
- Nucleosome Dynamics Define Transcriptional Enhancers (2010) (473)
- Response and resistance to BET bromodomain inhibitors in triple negative breast cancer (2015) (437)
- CEAS: cis-regulatory element annotation system (2006) (424)
- Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018) (390)
- Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis (2009) (390)
- Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. (2011) (388)
- Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo (2009) (385)
- Integrating regulatory motif discovery and genome-wide expression analysis (2003) (375)
- 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC (2010) (373)
- Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. (2007) (370)
- Chromatin signature of embryonic pluripotency is established during genome activation (2010) (368)
- High-throughput mapping of the chromatin structure of human promoters (2007) (363)
- Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse (2016) (357)
- Target analysis by integration of transcriptome and ChIP-seq data with BETA (2013) (356)
- GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data (2012) (347)
- Targeting androgen receptor in estrogen receptor-negative breast cancer. (2011) (345)
- Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library (2016) (338)
- TIMER : AWeb Server for Comprehensive Analysis of Tumor-In fi ltrating Immune Cells (2017) (333)
- Comparative analysis of metazoan chromatin organization (2014) (325)
- Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. (2016) (317)
- Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation (2014) (307)
- Large-scale public data reuse to model immunotherapy response and resistance (2020) (306)
- Broad chromosomal domains of histone modification patterns in C. elegans. (2011) (279)
- Identifying and mitigating bias in next-generation sequencing methods for chromatin biology (2014) (272)
- Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize[W] (2009) (271)
- CEAS: cis-regulatory element annotation system (2009) (271)
- Transcriptional role of cyclin D1 in development revealed by a genetic–proteomic screen (2010) (269)
- Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells. (2013) (269)
- Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR (2015) (258)
- Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer (2016) (254)
- Landscape of tumor-infiltrating T cell repertoire of human cancers (2016) (250)
- Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant (2004) (245)
- Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development (2012) (229)
- Topological analysis reveals a PD-L1-associated microenvironmental niche for Reed-Sternberg cells in Hodgkin lymphoma. (2017) (229)
- Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing (2017) (222)
- A single-cell and spatially resolved atlas of human breast cancers (2021) (220)
- Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. (2010) (209)
- Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability (2014) (207)
- NOTCH1–RBPJ complexes drive target gene expression through dynamic interactions with superenhancers (2013) (207)
- ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer. (2013) (205)
- Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species (2006) (183)
- Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics (2012) (179)
- MYC regulation of a “poor-prognosis” metastatic cancer cell state (2010) (173)
- Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. (2010) (172)
- Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute (2019) (168)
- Eukaryotic regulatory element conservation analysis and identification using comparative genomics. (2004) (168)
- Applications of Immunogenomics to Cancer (2017) (168)
- The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. (2012) (163)
- Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations. (2018) (158)
- Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia (2014) (153)
- Systematic evaluation of factors influencing ChIP-seq fidelity (2012) (153)
- Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq (2008) (151)
- DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. (2008) (151)
- JARID1B is a luminal lineage-driving oncogene in breast cancer. (2014) (150)
- Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008) (147)
- Comparative analysis of metazoan chromatin (2014) (137)
- SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. (2014) (136)
- Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model (2015) (136)
- Model-based analysis of two-color arrays (MA2C) (2007) (132)
- Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis (2021) (132)
- Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. (2009) (130)
- A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences (2005) (130)
- A comprehensive view of nuclear receptor cancer cistromes. (2011) (128)
- Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer (2020) (128)
- Estrogen receptor prevents p53-dependent apoptosis in breast cancer (2012) (122)
- VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis (2018) (119)
- Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. (2014) (112)
- Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. (2008) (111)
- Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy (2020) (111)
- Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data (2020) (107)
- Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification (2013) (107)
- Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL−/− clear cell renal carcinoma (2017) (106)
- Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. (2014) (106)
- ARv7 Represses Tumor-Suppressor Genes in Castration-Resistant Prostate Cancer. (2019) (105)
- Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes (2011) (105)
- Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer. (2017) (105)
- Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells (2005) (103)
- Gene Regulatory Networks Mediating Canonical Wnt Signal‐Directed Control of Pluripotency and Differentiation in Embryo Stem Cells (2013) (95)
- Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA. (2005) (95)
- Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium (2011) (95)
- Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective (2004) (94)
- Alu elements mediate MYB gene tandem duplication in human T-ALL (2007) (94)
- Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. (2013) (93)
- Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole genome sequencing studies at scale (2020) (93)
- The Role of Notch Receptors in Transcriptional Regulation (2015) (92)
- Landscape of B cell immunity and related immune evasion in human cancers (2018) (88)
- Transcriptional landscape of the human cell cycle (2017) (87)
- Canonical nucleosome organization at promoters forms during genome activation (2014) (87)
- Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3’-end formation (2010) (86)
- Amplitude modulation of androgen signaling by c-MYC. (2013) (85)
- Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome (2009) (80)
- Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. (2013) (80)
- TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions (2010) (80)
- Integrative analyses of single-cell transcriptome and regulome using MAESTRO (2020) (79)
- Improving the bearing fault diagnosis efficiency by the adaptive stochastic resonance in a new nonlinear system (2017) (79)
- Perspectives on ENCODE (2020) (79)
- XBP 1 Promotes Triple Negative Breast Cancer By Controlling the HIF 1 α Pathway (2014) (79)
- Short-Term Effect of Ambient Temperature and the Risk of Stroke: A Systematic Review and Meta-Analysis (2015) (78)
- Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding (2012) (77)
- Targeting epigenetic regulators for cancer therapy (2014) (76)
- Snail1-dependent p53 repression regulates expansion and activity of tumour-initiating cells in breast cancer (2016) (75)
- Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. (2005) (74)
- An integrative ENCODE resource for cancer genomics (2019) (72)
- MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes (2014) (72)
- A boosting approach for motif modeling using ChIP-chip data (2005) (70)
- Mass cytometry of Hodgkin lymphoma reveals a CD4+ regulatory T-cell-rich and exhausted T-effector microenvironment. (2018) (69)
- Inference of transcriptional regulation in cancers (2015) (68)
- Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. (2020) (67)
- Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. (2007) (66)
- Big data mining yields novel insights on cancer (2015) (65)
- Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Specific Enhancers That Are Prognostic for Overall Survival (2014) (63)
- Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. (2006) (63)
- A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma (2020) (63)
- Altered antisense-to-sense transcript ratios in breast cancer (2010) (61)
- Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles (2016) (61)
- Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data (2017) (59)
- modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the (2011) (57)
- Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles (2016) (56)
- EglN2 associates with the NRF1‐PGC1α complex and controls mitochondrial function in breast cancer (2015) (55)
- Getting Started in Tiling Microarray Analysis (2007) (55)
- An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer (2013) (55)
- A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer (2013) (54)
- Integrin αvβ6-TGFβ-SOX4 Pathway Drives Immune Evasion in Triple-Negative Breast Cancer. (2020) (54)
- Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer (2020) (53)
- Mass cytometry of Hodgkin lymphoma reveals a CD 4 + exhausted T-effector and T-regulatory cell rich microenvironment (2018) (53)
- TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data (2021) (50)
- Network analysis of gene essentiality in functional genomics experiments (2015) (50)
- Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks (2019) (49)
- Evidence against a genomic code for nucleosome positioning Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization” (2010) (49)
- Genome-wide Map of Nuclear Protein Degradation Shows NCoR1 Turnover as a Key to Mitochondrial Gene Regulation (2013) (46)
- Gene expression profiling of human breast tissue samples using SAGE-Seq. (2010) (46)
- More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells (2009) (44)
- Development of a quantitative, competitive polymerase chain reaction–enzyme-linked immunosorbent assay for the detection of Wuchereria bancrofti DNA (1999) (44)
- Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila (2011) (44)
- A Flexible and Powerful Bayesian Hierarchical Model for ChIP–Chip Experiments (2008) (43)
- CRISPR-DO for genome-wide CRISPR design and optimization (2016) (42)
- In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target (2020) (41)
- Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. (2008) (41)
- CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse (2013) (40)
- Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells (2012) (40)
- KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells (2016) (39)
- Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy (2018) (38)
- Exploring genetic associations with ceRNA regulation in the human genome (2017) (38)
- Revisit linear regression-based deconvolution methods for tumor gene expression data (2017) (38)
- Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells (2014) (38)
- Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors (2020) (38)
- A suite of web-based programs to search for transcriptional regulatory motifs (2004) (38)
- Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies. (2018) (37)
- High-dimensional genomic data bias correction and data integration using MANCIE (2016) (37)
- Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade. (2021) (36)
- Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase. (2008) (36)
- CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human (2012) (35)
- SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells (2015) (35)
- A high-resolution map of nucleosome positioning on a fission yeast centromere. (2008) (35)
- Computational methodology for ChIP-seq analysis (2013) (34)
- Improved design and analysis of CRISPR knockout screens (2018) (33)
- Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression (2015) (33)
- ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells (2020) (31)
- Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer (2020) (31)
- Association of Exposure to Particular Matter and Carotid Intima-Media Thickness: A Systematic Review and Meta-Analysis (2015) (29)
- Deciphering essential cistromes using genome-wide CRISPR screens (2019) (29)
- BINOCh: binding inference from nucleosome occupancy changes (2011) (28)
- Systematic characterization of mutations altering protein degradation in human cancers. (2021) (28)
- Immune receptor repertoires in pediatric and adult acute myeloid leukemia (2019) (28)
- CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data (2010) (27)
- Association between extreme temperature and acute myocardial infarction hospital admissions in Beijing, China: 2013–2016 (2018) (27)
- Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology* (2006) (26)
- Realizing the empirical mode decomposition by the adaptive stochastic resonance in a new periodical model and its application in bearing fault diagnosis (2017) (26)
- Effects of the short‐term exposure to ambient air pollution on atrial fibrillation (2018) (25)
- NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes (2016) (25)
- The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia (2017) (24)
- Microarray blob-defect removal improves array analysis (2007) (23)
- Determinants of transcription factor regulatory range (2019) (23)
- xMAN: extreme MApping of OligoNucleotides (2008) (23)
- MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data (2011) (23)
- Regulation of Human 3α-Hydroxysteroid Dehydrogenase (AKR1C4) Expression by the Liver X Receptor α (2008) (23)
- Big Data Approaches for Modeling Response and Resistance to Cancer Drugs. (2018) (22)
- Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer. (2022) (22)
- Optimizing the Adaptive Stochastic Resonance and Its Application in Fault Diagnosis (2015) (22)
- Targeting the MIF/CXCR7/AKT Signaling Pathway in Castration-Resistant Prostate Cancer (2018) (20)
- CistromeFinder for ChIP-seq and DNase-seq data reuse (2013) (20)
- Improved Treatment and Utilization of Rice Straw by Coprinopsis cinerea (2018) (20)
- CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor cells and T cells. (2021) (19)
- Computational inference of mRNA stability from histone modification and transcriptome profiles (2012) (19)
- CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments (2017) (18)
- DiNuP: a systematic approach to identify regions of differential nucleosome positioning (2012) (17)
- Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells (2017) (16)
- TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response (2021) (16)
- An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine (2016) (15)
- Inhibition of MAN2A1 Enhances the Immune Response to Anti–PD-L1 in Human Tumors (2020) (15)
- SOX 2 and p 63 colocalize at genetic loci in squamous cell carcinomas (2014) (14)
- CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis (2020) (14)
- Fast alignment and preprocessing of chromatin profiles with Chromap (2021) (13)
- Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation (2021) (13)
- Analysis of Acoustic Wave Frequency Spectrum Characters of Rock Mass under Blasting Damage Based on the HHT Method (2018) (13)
- Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. (2011) (12)
- PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression (2014) (12)
- FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance (2021) (11)
- Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress (2022) (11)
- Statistical models for biological sequence motif discovery (2002) (11)
- Effect of different directions of attentional shift on inhibition of return in three-dimensional space (2014) (11)
- Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data. (2020) (11)
- Addendum: REST and stress resistance in ageing and Alzheimer’s disease (2016) (11)
- Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. (2012) (11)
- Effects of Ambient Temperature on Acute Exacerbations of Chronic Obstructive Pulmonary Disease: Results from a Time-Series Analysis of 143318 Hospitalizations (2020) (10)
- 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). (2010) (10)
- Effects of Repetition Suppression on Sound Induced Flash Illusion With Aging (2020) (9)
- Clonal tracing reveals diverse patterns of response to immune checkpoint blockade (2020) (9)
- Analysis of Hospital Charges of Inpatients with Acute Ischemic Stroke in Beijing, China, 2012–2015 (2018) (9)
- adjacent binding on a genome-wide scale and C / EBP factors orchestrate adipocyte biology via γ PPAR Material Supplemental (2008) (8)
- The effect of actuator and its coupling conditions on eardrum-stimulated middle ear implants: A numerical analysis (2016) (8)
- Associations between ambient temperature and adult asthma hospitalizations in Beijing, China: a time-stratified case-crossover study (2022) (8)
- Regulation of human 3 alpha-hydroxysteroid dehydrogenase (AKR1C4) expression by the liver X receptor alpha. (2008) (8)
- Distribution and predictors of hospital charges for haemorrhagic stroke patients in Beijing, China, March 2012 to February 2015: a retrospective study (2018) (7)
- Checkpoint blockade-induced CD8+ T cell differentiation in head and neck cancer responders (2022) (7)
- Phase II study of cetuximab in combination with modified FOLFIRI in patients with advanced gastric cancer who failed first-line chemotherapy (EFFI study). (2010) (7)
- Reply to Evidence against a genomic code for nucleosome positioning (2010) (7)
- Short-term effects of cold spells on hospitalisations for acute exacerbation of chronic obstructive pulmonary disease: a time-series study in Beijing, China (2021) (7)
- Large-scale public data reuse to model immunotherapy response and resistance (2020) (7)
- Evaluation of immune repertoire inference methods from RNA-seq data (2018) (7)
- Impaired Hydroxylation of 5-Methylcytosine In TET2 mutated Patients with Myeloid Malignancies (2010) (6)
- Genetic fusions favor tumorigenesis through degron loss in oncogenes (2021) (6)
- A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin–MLL Inhibition (2022) (6)
- MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells (2021) (6)
- Tropospheric ozone column retrieval from the Ozone Monitoring Instrument by means of a neural network algorithm (2011) (6)
- Increased Risk of Hospital Admission for Asthma in Children From Short-Term Exposure to Air Pollution: Case-Crossover Evidence From Northern China (2021) (5)
- Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation (2021) (5)
- Increased hospital admissions for asthma from short-term exposure to cold spells in Beijing, China. (2021) (5)
- Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development (2020) (5)
- A Bayesian model for single cell transcript expression analysis on MERFISH data (2018) (5)
- Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response (2018) (5)
- Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays (2009) (5)
- The degradation and saccharification of microcrystalline cellulose in aqueous acetone solution with low severity dilute sulfuric acid (2018) (5)
- Differentiation-specific histone modifications reveal dynamic chromatin interactions and alternative partners for the intestinal transcription factor CDX 2 (2011) (4)
- machinery coordinate regulation of core components of the gene regulation Elucidation of the ELK 1 target gene network reveals a role in the Material (2009) (4)
- A Bayesian model for single cell transcript expression analysis on MERFISH data (2018) (4)
- Zirconia-supported 12-tungstophosphoric acid: Characterization and catalytic behavior in degradation of alkali lignin (2018) (4)
- Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC) (2021) (4)
- Inhibition of return at different eccentricities in visual field under three-dimensional (3D) world (2017) (4)
- Quantitative comparison of surface properties of enzymatic hydrolysis lignin before and after degradation (2018) (4)
- CRISPR Screens Identify Essential Cell Growth Mediators in BRAF-inhibitor Resistant Melanoma (2019) (4)
- IKAROS and MENIN Coordinate Therapeutically Actionable Leukaemogenic Gene Expression in MLL-r Acute Myeloid Leukaemia (2022) (4)
- chromatin dynamics Differential DNase I hypersensitivity reveals factor-dependent Material Supplemental (2012) (4)
- Topical therapy for regression and melanoma prevention of congenital giant nevi (2022) (4)
- Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers (2019) (3)
- Air Quality Observations from the Ozone Monitoring Instrument on EOS/Aura - HCHO and CHO-CHO (2008) (3)
- KDM 1 A promotes tumor cell invasion by silencing TIMP 3 in non-small cell lung cancer cells (2016) (3)
- Polycomb-independent activity of EZH2 in castration resistant prostate cancer (2013) (3)
- A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer (2013) (3)
- Abstract IA11: Dependency of prostate cancer on HNRNPL and its associated RNAs (2016) (3)
- Evaluation of Round Window Stimulation Performance in Otosclerosis Using Finite Element Modeling (2016) (3)
- Integrative analysis and refined design of CRISPR knockout screens (2017) (3)
- Integrin avb6–TGFb–SOX4 Pathway Drives Immune Evasion in Triple-Negative Breast Cancer (2020) (3)
- ChIP-Chip: algorithms for calling binding sites. (2009) (3)
- Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network (2020) (3)
- Inhibition of MAN2A1 enhances tumor response to anti-PD-L1. (2020) (3)
- Cells Is Polycomb-Independent EZH 2 Oncogenic Activity in Castration-Resistant Prostate Cancer (2013) (3)
- Critical Assessment of TOMS-derived Tropospheric Ozone: Comparisons with Other Measurements and Model Evaluation of Controlling Processes (2001) (3)
- Airborne, Ground-based, and Satellite Measurements of BrO during ARCTAS and ARCPAC (2008) (2)
- centromeren map of nucleosome positioning on a fission yeast (2008) (2)
- modENCODE and ENCODE resources for analysis of metazoan chromatin organization (2013) (2)
- of FOXA 1-bound enhancers Cell-type selective chromatin remodeling defines the active subset Material Supplemental (2009) (2)
- H3PW12O40/ZrO2 and 1-Butyl-3-methylimidazolium Chloride: A Double-Effect Catalyst for the Degradation of Alkali Lignin (2019) (2)
- Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data (2016) (2)
- Reward reduces the fission illusion in the sound-induced flash illusion (2022) (2)
- Monitoring of Tropospheric Ozone from Backscattered Ultraviolet Measurements on Geostationary Platforms (2009) (2)
- Association of Exposure to Particular Matter and Carotid Intima-MediaThickness: A Systematic Review and Meta-Analysis (2015) (2)
- Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer (2020) (2)
- between pre-mRNA processing and transcription Genomic localization of RNA binding proteins reveals links (2006) (2)
- Hippo signaling pathway regulates cancer cell-intrinsic MHC-II expression. (2022) (2)
- Systematic evaluation of variability in ChIP-chip experiments using data (2008) (2)
- Polycomb-independent activity of EZH2 in castration resistant prostate cancer (2013) (1)
- genome activation Canonical nucleosome organization at promoters forms during Material (2014) (1)
- Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response (2022) (1)
- Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data (2020) (1)
- CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data (2021) (1)
- Biology of Human Tumors Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Speci fi c Enhancers That Are Prognostic for Overall Survival (2014) (1)
- Ozone Profile and Tropospheric Ozone Retrieval from SCIAMACHY Nadir Measurements (2005) (1)
- Abstract P108: In vivo CRISPR screens identify E3 ligase COP1 as a modulator of macrophage infiltration and cancer immunotherapy target (2021) (1)
- Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR 1 Activating Mutations Graphical Abstract Highlights (2018) (1)
- demonstrating tissue-specific gene expression methylated regions ( T-DMRs ) in mouse promoter regions DNA methylation profile of tissue-dependent and differentially Material Supplemental (2008) (1)
- Analysis of ChIP-chip Data on Genome Tiling Microarrays (2009) (1)
- A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress (2020) (1)
- MAESTRO (Model-based AnalysEs of Single-cell Transcriptome and RegulOme) (2020) (1)
- Comprehensive characterizations of immune receptor repertoire in tumors and cancer immunotherapy studies. (2022) (1)
- modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental (2012) (1)
- Clonal tracing reveals diverse patterns of response to immune checkpoint blockade (2020) (1)
- Association of extreme precipitation with hospitalizations for acute myocardial infarction in Beijing, China: A time-series study (2022) (1)
- Research of Cities’ Gas Load Predicting Model Based on Wavelet Neural Network (2011) (1)
- DeepBCR: Deep learning framework for cancer-type classification and binding affinity estimation using B cell receptor repertoires (2019) (1)
- A closer look into DNase I hypersensitivity (2013) (1)
- ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells (2020) (1)
- Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha (2022) (1)
- Landscape of B cell immunity and related immune evasion in human cancers (2019) (1)
- Exploring functional variation affecting ceRNA regulation in humans (2015) (1)
- MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens (2014) (1)
- COMPOSITIONS AND METHODS FOR MAKING AND DECODING PAIRED-GUIDE RNA LIBRARIES AND USES THEREOF (2019) (0)
- Abstract B24: High-dimensional genomic data integration and bias correction using MANCIE (2016) (0)
- Neural network architecture search with AMBER (2021) (0)
- Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines. (2023) (0)
- Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha (2021) (0)
- Genome-Wide Analysis of NOTCH1, ETS Family Factors, and RUNX1 Binding in Human T Lymphoblastic Leukemia Cells Reveals Distinct Regulatory Elements (2012) (0)
- Overcoming Therapeutic R esistance in HER 2-Positive Breast Cancers with CDK 4 / 6 Inhibitors Highlights (2016) (0)
- The Lysine Histone Methyltransferase SETD2 Is Required for Appropriate Immunoglobulin VDJ Recombination (2018) (0)
- Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop) (2014) (0)
- Eyjafjallajökull Eruptions: direct SO2 plume height estimation and enhanced ash detection with OMI (2010) (0)
- An Integrated Modeling and Observing System with Near Real-Time Applications (2010) (0)
- Abstract 941: Targeting androgen receptor in estrogen receptor-negative breast cancer (2011) (0)
- Abstract 3779: Clonal tracing reveals different mechanisms of resistance to immune checkpoint blockade (2019) (0)
- Integrative analyses of single-cell transcriptome and regulome using MAESTRO (2020) (0)
- Abstract A22: Functional long noncoding RNAs in castration-resistant prostate cancer (2016) (0)
- Long non-coding RNA-mediated PTEN regulation in prostate cancer. (2015) (0)
- Alternative Super-Enhancer States Determine MYC Sensitivity to Notch and Brd4 Inhibitors in T Lymphoblastic Leukemia/Lymphoma (2014) (0)
- Abstract A077: Microenvironmental factors shape resistance patterns to immune checkpoint blockade (2019) (0)
- Abstract A12: Identification of resistance to immune checkpoint blockade (2018) (0)
- Title Comparative analysis of metazoan chromatin organization Permalink (2014) (0)
- Abstract LB-74: The estrogen receptor regulates the transcription of p53 target genes in breast cancer cells (2012) (0)
- Therapeutic Mechanism of BET Bromodomain Inhibitor in Breast Cancer (2014) (0)
- QB-13006-XSL 54..70 (2013) (0)
- Revisit linear regression-based deconvolution methods for tumor gene expression data (2017) (0)
- Gibbs sampling and bioinformatics (2005) (0)
- Abstract 1822: An integrated approach to identify clinically relevant long non-coding RNAs (lncRNAs) in cancer. (2013) (0)
- Joint Xena-Trinity-Cistrome-Cravat/MuPIT Collaboration (2014) (0)
- He centromere A high-resolution map of nucleosome positioning on a fission yeast data (2008) (0)
- Effects of remote ischemic preconditioning on occurrence of postoperative delirium in elderly patients undergoing radical mastectomy (2019) (0)
- Private and Public Incentives for Hospitals to Improve the Quality and Reduce the Cost of Care (2020) (0)
- Abstract 1391: SOX2-p63 interaction and genomic co-localization in squamous cell carcinomas (2014) (0)
- Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR (2015) (0)
- Effects of Ambient Temperature on Acute Exacerbations of Chronic Obstructive Pulmonary Disease: Results from a Time-Series Analysis of 143318 Hospitalizations [Corrigendum] (2021) (0)
- Neural Network Algorithms for Height Resolved Ozone Retrievals from OMI Level 1b Data (2009) (0)
- Simulating selected hormonal pathways during a 24 hour period and the implications for aging research (2017) (0)
- Butorphanol for preoperative analgesia in patients with Stanford type A aortic dissection (2019) (0)
- Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes (2022) (0)
- MetaTiME: Meta-components of the Tumor Immune Microenvironment (2023) (0)
- ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline (2016) (0)
- Realizing the empirical mode decomposition by the adaptive stochastic resonance in a new periodical model and its application in bearing fault diagnosis (2017) (0)
- Abstract 1849: Androgen receptor transcriptionally represses genes mediating DNA synthesis and repair in prostate cancer (2015) (0)
- limited lineage fidelity among specified primary blood cells Active enhancers are delineated de novo during hematopoiesis , with Material (2014) (0)
- Parity and BRCA1/2-associated breast cancer risk linked to hormone-responsive p27 + luminal epithelial progenitors (2018) (0)
- VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis (2018) (0)
- Targeting theMIF / CXCR 7 / AKTSignalingPathway in Castration-Resistant Prostate Cancer (2018) (0)
- Abstract A146: Systematic discovery of immune regulatory mechanisms in tumor cells (2019) (0)
- Design of Control System for the Intelligent Auxiliary Medicine Taking Device (2016) (0)
- Erratum: “Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells” (2018) (0)
- Compensation Mechanisms May Not Always Account for Enhanced Multisensory Illusion in Older Adults: Evidence from Sound-Induced Flash Illusion (2022) (0)
- Global Pollution Monitoring from Geostationary Orbit: Instrumental and Spectroscopic requirements (2008) (0)
- Effect of different directions of attentional shift on inhibition of return in three-dimensional space (2016) (0)
- The Memory Project: "Knocking on Memory’s Door with a Video Camera" (2016) (0)
- Genome analysis CRISPR-DO for genome-wide CRISPR design and optimization (2016) (0)
- Abstract 5238: Integrative analysis of functional long noncoding RNAs during prostate cancer progression (2014) (0)
- Science Accomplishments from a Decade of Aura OMI/MLS Tropospheric Ozone Measurements (2014) (0)
- Comprehensive analyses of tumor immunity: implications for cancer immunotherapy (2016) (0)
- Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma Discovery of Biomarkers Predictive of GSI Response in (2014) (0)
- Studies on Using Azolla for O2-Supplementation and Its Test (2004) (0)
- Abstract 4966: Characteristics of immune repertoires in early lung cancer patients (2019) (0)
- Integrating sequencing and microarray data to identify novel functions of epigenetic regulators in cancer (2013) (0)
- Abstract 65: Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade (2021) (0)
- Author Correction: Perspectives on ENCODE (2022) (0)
- Abstract 5118: TIDE-E: an online evaluator of tumor immune-suppressive function of gene sets (2019) (0)
- ARv 7 Represses Tumor-Su ppressor Genes in Castration-Resistant Prostate Cancer Graphical (2019) (0)
- Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute (2019) (0)
- Abstract B12: LSD1 mediates global AR transcription suppression in prostate cancer cells (2012) (0)
- Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers (2019) (0)
- Determinants of transcription factor regulatory range (2020) (0)
- Immune receptor repertoires in pediatric and adult acute myeloid leukemia (2019) (0)
- Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data (2017) (0)
- SAGE-Seq Gene expression profiling of human breast tissue samples using Material (2010) (0)
- Network analysis of gene essentiality in functional genomics experiments (2015) (0)
- Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation. (2020) (0)
- Title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer (2020) (0)
- MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes (2014) (0)
- An eight-year record of ozone profiles and tropospheric column ozone from GOME (2006) (0)
- Local and Systemic Effects of Immune Checkpoint Blockade on Relapsed Myeloid Malignancies Following Allogeneic Hematopoietic Stem Cell Transplantation (2020) (0)
- Abstract B162: Comprehensive analyses of tumor immunity with implications to cancer immunotherapies (2016) (0)
- A closer look into DNase I hypersensitivity (2013) (0)
- Abstract 5675: Single-cell mass cytometry of classical Hodgkin lymphoma defines an exhausted and immunosuppressive microenvironment (2018) (0)
- Genome-wide analysis of HIF-1 binding with chromatin immunoprecipitation and tiled microarray (2007) (0)
- An Integrated Modeling and Observing System for Hazards and Regional Climate Simulations (2010) (0)
- Erratum for Verzi et al., Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding (2014) (0)
- Abstract A19: Network analysis of gene essentiality in CRISPR screens (2015) (0)
- T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data (2022) (0)
- Abstract LB098: Integrative approaches to modulate antigen presentation and boost cancer immune response (2022) (0)
- Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale (2020) (0)
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