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HIF1A Employs CDK8-Mediator to Stimulate RNAPII Elongation in Response to Hypoxia

Cell, 2013-06, Vol.153 (6), p.1327-1339

2013

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

Nature methods, 2022-09, Vol.19 (9), p.1097

2022

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Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway

Cancer cell, 2020-01, Vol.37 (1), p.104-122.e12

2020

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The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

Nature genetics, 2015-11, Vol.47 (11), p.1346-1351

2015

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A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer

Cell, 2018-07, Vol.174 (2), p.422-432.e13

2018

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

BMC bioinformatics, 2018-04, Vol.19 (1), p.135-135, Article 135

2018

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

Science (American Association for the Advancement of Science), 2018-02, Vol.359 (6377), p.770-775

2018

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Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance

Science (American Association for the Advancement of Science), 2017-01, Vol.355 (6320), p.78-83

2017

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High-Resolution ATAC-Seq Analysis of Frozen Clinical Tissues

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2458, p.259

2022

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Prostate cancer reactivates developmental epigenomic programs during metastatic progression

Nature genetics, 2020-08, Vol.52 (8), p.790-799

2020

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Principles and methods of integrative chromatin analysis in primary tissues and tumors

Biochimica et biophysica acta. Reviews on cancer, 2020-01, Vol.1873 (1), p.188333-188333, Article 188333

2020

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Parametric techno-economic studies of coal/biomass co-gasification for IGCC plants with carbon capture using various coal ranks, fuel-feeding schemes, and syngas cooling methods

International journal of energy research, 2016-03, Vol.40 (4), p.473-496

2016

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A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)

Clinical cancer research, 2019-07, Vol.25 (14), p.4480-4492

2019

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Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

eLife, 2017-09, Vol.6

2017

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ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

BMC bioinformatics, 2016-10, Vol.17 (1), p.404-404, Article 404

2016

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

Nature protocols, 2023-08, Vol.18 (8), p.2404-2414

2023

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Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade

Cancer discovery, 2021-06, Vol.11 (6), p.1524-1541

2021

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Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

Cell reports (Cambridge), 2017-03, Vol.18 (10), p.2359-2372

2017

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MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

Nature communications, 2022-05, Vol.13 (1), p.2559-17, Article 2559

2022

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Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Genome Biology, 2020-08, Vol.21 (1), p.198-198, Article 198

2020

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

Cell, 2021-10, Vol.184 (21), p.5357-5374.e22

2021

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Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

Nature (London), 2014-02, Vol.506 (7489), p.511-515

2014

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HIF1A Employs CDK8-Mediator to Stimulate RNAPII Elongation in Response to Hypoxia

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

Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer

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

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

Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance

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

High-Resolution ATAC-Seq Analysis of Frozen Clinical Tissues

Prostate cancer reactivates developmental epigenomic programs during metastatic progression

Principles and methods of integrative chromatin analysis in primary tissues and tumors

Parametric techno-economic studies of coal/biomass co-gasification for IGCC plants with carbon capture using various coal ranks, fuel-feeding schemes, and syngas cooling methods

A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)

Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

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

Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade

Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

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

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

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