Biologically informed deep neural network for prostate cancer discovery

The DNA methylation landscape of advanced prostate cancer

(2020) Shuang G. Zhao et al.   NATURE GENETICS

Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells

(2020) Brent M. Kuenzi et al.   CANCER CELL

Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer

(2019) William S. Chen et al.   EUROPEAN UROLOGY

MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors

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A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

NOTCH signaling is activated in and contributes to resistance in enzalutamide-resistant prostate cancer cells

(2019) Elia Farah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic correlates of clinical outcome in advanced prostate cancer

(2019) Wassim Abida et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Definitions, methods, and applications in interpretable machine learning

(2019) W. James Murdoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer

(2019) Justin H. Hwang et al.   Cell Reports

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

(2018) David A. Quigley et al.   CELL

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study

(2018) Rahul Aggarwal et al.   JOURNAL OF CLINICAL ONCOLOGY

The long tail of oncogenic drivers in prostate cancer

(2018) Joshua Armenia et al.   NATURE GENETICS

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Overfitting remedy by sparsifying regularization on fully-connected layers of CNNs

(2018) Qi Xu et al.   NEUROCOMPUTING

PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data

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Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer

(2018) Daniel Nava Rodrigues et al.   JOURNAL OF CLINICAL INVESTIGATION

Integrative clinical genomics of metastatic cancer

(2017) Dan R. Robinson et al.   NATURE

Genomic hallmarks of localized, non-indolent prostate cancer

(2017) Michael Fraser et al.   NATURE

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Activation of p53 and destabilization of androgen receptor by combinatorial inhibition of MDM2 and MDMX in prostate cancer cells

(2017) Harman Chopra et al.   Oncotarget

MDM2 Inhibition Sensitizes Prostate Cancer Cells to Androgen Ablation and Radiotherapy in a p53-Dependent Manner

(2016) Felix Y. Feng et al.   NEOPLASIA

Integrative Clinical Genomics of Advanced Prostate Cancer

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Roles of Ubiquitination and SUMOylation on Prostate Cancer: Mechanisms and Clinical Implications

(2015) Zhenbang Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Role of Runx2 phosphorylation in prostate cancer and association with metastatic disease

(2015) C Ge et al.   ONCOGENE

Regulation of p53: a collaboration between Mdm2 and Mdmx

(2015) Dongsheng Pei et al.   Oncotarget

UpSet: Visualization of Intersecting Sets

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Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner

(2014) Päivi Sutinen et al.   NUCLEIC ACIDS RESEARCH

Copy number alteration burden predicts prostate cancer relapse

(2014) H. Hieronymus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization

(2012) B. Graves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDM2 antagonists boost antitumor effect of androgen withdrawal: implications for therapy of prostate cancer

(2011) Christian Tovar et al.   Molecular Cancer

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

The retinoblastoma tumor suppressor controls androgen signaling and human prostate cancer progression

(2010) Ankur Sharma et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical significance of p53 alterations in surgically treated prostate cancers

(2008) Thorsten Schlomm et al.   MODERN PATHOLOGY