Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

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

(2021) Xintao Qiu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate

(2020) Abbie S. Ireland et al.   CANCER CELL

Author Correction: Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis

(2020) Donglim Esther Park et al.   NATURE CELL BIOLOGY

Regulation of CEACAM5 and Therapeutic Efficacy of an Anti-CEACAM5–SN38 Antibody–drug Conjugate in Neuroendocrine Prostate Cancer

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Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies

(2019) Nikolas G. Balanis et al.   CANCER CELL

MCPyV Large T antigen induced atonal homolog 1 (ATOH1) is a lineage-dependency oncogene in Merkel cell carcinoma

(2019) Kaiji Fan et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

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

(2018) MacIntosh Cornwell et al.   BMC BIOINFORMATICS

Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC)

(2018) Jonathan Welti et al.   CLINICAL CANCER RESEARCH

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

A phase 1b/2 study of CPI-1205, a small molecule inhibitor of EZH2, combined with enzalutamide (E) or abiraterone/prednisone (A/P) in patients with metastatic castration resistant prostate cancer (mCRPC).

(2018) Mary-Ellen Taplin et al.   JOURNAL OF CLINICAL ONCOLOGY

An integrative transcriptome analysis reveals a functional role for thyroid transcription factor-1 in small cell lung cancer

(2018) Masafumi Horie et al.   JOURNAL OF PATHOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

DeTiN: overcoming tumor-in-normal contamination

(2018) Amaro Taylor-Weiner et al.   NATURE METHODS

Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts

(2018) Benjamin J. Drapkin et al.   Cancer Discovery

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage

(2018) Jung Wook Park et al.   SCIENCE

Biology and evolution of poorly differentiated neuroendocrine tumors

(2017) David S Rickman et al.   NATURE MEDICINE

LuCaP Prostate Cancer Patient-Derived Xenografts Reflect the Molecular Heterogeneity of Advanced Disease an­­d Serve as Models for Evaluating Cancer Therapeutics

(2017) Holly M. Nguyen et al.   PROSTATE

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

(2017) Sheng Yu Ku et al.   SCIENCE

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

(2017) Orly L. Wapinski et al.   Cell Reports

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis

(2017) Jingwei Cheng et al.   PLoS Pathogens

Nothing But NET: A Review of Neuroendocrine Tumors and Carcinomas

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

(2016) Qian Qin et al.   BMC BIOINFORMATICS

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

(2016) Sarah K. Denny et al.   CELL

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

BET Bromodomain Inhibitors Enhance Efficacy and Disrupt Resistance to AR Antagonists in the Treatment of Prostate Cancer

(2016) I. A. Asangani et al.   MOLECULAR CANCER RESEARCH

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

(2016) Himisha Beltran et al.   NATURE MEDICINE

ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs

(2016) Mark D. Borromeo et al.   Cell Reports

Inhibition of Pluripotency Networks by the Rb Tumor Suppressor Restricts Reprogramming and Tumorigenesis

(2015) Michael S. Kareta et al.   Cell Stem Cell

Transformation from non-small-cell lung cancer to small-cell lung cancer: molecular drivers and cells of origin

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Single-cell chromatin accessibility reveals principles of regulatory variation

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A DLL3-targeted antibody-drug conjugate eradicates high-grade pulmonary neuroendocrine tumor-initiating cells in vivo

(2015) Laura R. Saunders et al.   Science Translational Medicine

Polycomb-mediated silencing in neuroendocrine prostate cancer

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CopywriteR: DNA copy number detection from off-target sequence data

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Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer

(2014) Irfan A. Asangani et al.   NATURE

ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers

(2014) A. Augustyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GSVA: gene set variation analysis for microarray and RNA-Seq data

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Platinum-Based Chemotherapy for Variant Castrate-Resistant Prostate Cancer

(2013) A. M. Aparicio et al.   CLINICAL CANCER RESEARCH

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

(2012) Charles M Rudin et al.   NATURE GENETICS

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Pathologic Classification of Neuroendocrine Tumors

(2010) David S. Klimstra et al.   PANCREAS

Targeted Disruption of NeuroD, a Proneural Basic Helix-Loop-Helix Factor, Impairs Distal Lung Formation and Neuroendocrine Morphology in the Neonatal Lung

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