KDM6A epigenetically regulates subtype plasticity in small cell lung cancer

Genomic and transcriptomic analysis of a library of small cell lung cancer patient-derived xenografts

(2022) Rebecca Caeser et al.   Nature Communications

Heterogeneity of neuroendocrine transcriptional states in metastatic small cell lung cancers and patient-derived models

(2022) Delphine Lissa et al.   Nature Communications

POU2F3 in SCLC: Clinicopathologic and Genomic Analysis With a Focus on Its Diagnostic Utility in Neuroendocrine-Low SCLC

(2022) Marina K. Baine et al.   Journal of Thoracic Oncology

Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities

(2021) Carl M. Gay et al.   CANCER CELL

Small-cell lung cancer

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Intrinsic immunogenicity of small cell lung carcinoma revealed by its cellular plasticity

(2021) Navin R. Mahadevan et al.   Cancer Discovery

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Molecular Subtypes of Primary Small Cell Lung Cancer Tumors and Their Associations with Neuroendocrine and Therapeutic Markers

(2021) Song Qu et al.   Journal of Thoracic Oncology

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

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

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer

(2021) Joseph M. Chan et al.   CANCER CELL

Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

(2021) Deli Hong et al.   CANCER RESEARCH

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

(2021) Paloma Cejas et al.   Nature Communications

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

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

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer

(2020) Mark Kalisz et al.   EMBO JOURNAL

Lysine demethylase KDM6A in differentiation, development and cancer

(2020) Nhien Tran et al.   MOLECULAR AND CELLULAR BIOLOGY

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Small Cell Lung Carcinoma Subtypes Defined by ASCL1, NEUROD1, POU2F3 and YAP1: Comprehensive Immunohistochemical and Histopathologic Characterization

(2020) Marina K. Baine et al.   Journal of Thoracic Oncology

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate

(2019) Abhishek A. Chakraborty et al.   SCIENCE

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

UTX Mutations in Human Cancer

(2019) Lu Wang et al.   CANCER CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

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

The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis

(2019) Matthew G. Oser et al.   GENES & DEVELOPMENT

A Menin-MLL Inhibitor Induces Specific Chromatin Changes and Eradicates Disease in Models of MLL-Rearranged Leukemia

(2019) Andrei V. Krivtsov et al.   CANCER CELL

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

(2018) MacIntosh Cornwell et al.   BMC BIOINFORMATICS

Loss of KDM6A Activates Super-Enhancers to Induce Gender-Specific Squamous-like Pancreatic Cancer and Confers Sensitivity to BET Inhibitors

(2018) Jaclyn Andricovich et al.   CANCER CELL

POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer

(2018) Yu-Han Huang et al.   GENES & DEVELOPMENT

UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

(2018) Malgorzata Gozdecka et al.   NATURE GENETICS

Kabuki syndrome: international consensus diagnostic criteria

(2018) Margaret P Adam et al.   JOURNAL OF MEDICAL GENETICS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Small Cell Lung Cancer Exhibits Frequent Inactivating Mutations in the Histone Methyltransferase KMT2D/MLL2 : CALGB 151111 (Alliance)

(2017) Arnaud Augert et al.   Journal of Thoracic Oncology

A UTX-MLL4-p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription

(2017) Shu-Ping Wang et al.   MOLECULAR CELL

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts

(2017) Lingjian Yang et al.   Oncotarget

Small Cell Lung Cancer

(2017) Gregory P. Kalemkerian et al.   Journal of the National Comprehensive Cancer Network

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

UTX demethylase activity is required for satellite cell–mediated muscle regeneration

(2016) Hervé Faralli et al.   JOURNAL OF CLINICAL INVESTIGATION

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

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

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Comprehensive genomic profiles of small cell lung cancer

(2015) Julie George et al.   NATURE

UTX and MLL4 Coordinately Regulate Transcriptional Programs for Cell Proliferation and Invasiveness in Breast Cancer Cells

(2014) Jae-Hwan Kim et al.   CANCER RESEARCH

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Identification of KMT2D and KDM6A mutations by exome sequencing in Korean patients with Kabuki syndrome

(2014) Chong Kun Cheon et al.   JOURNAL OF HUMAN GENETICS

Cancer Epigenetics: Tumor Heterogeneity, Plasticity of Stem-like States, and Drug Resistance

(2014) Hariharan Easwaran et al.   MOLECULAR CELL

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

(2013) D. R. Zerbino et al.   BIOINFORMATICS

Utx Is Required for Proper Induction of Ectoderm and Mesoderm during Differentiation of Embryonic Stem Cells

(2013) Cristina Morales Torres et al.   PLoS One

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang 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

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Charles M Rudin et al.   NATURE GENETICS

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

(2012) Martin Peifer et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Loss of p130 Accelerates Tumor Development in a Mouse Model for Human Small-Cell Lung Carcinoma

(2010) B. E. Schaffer et al.   CANCER RESEARCH

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase

(2009) Michel DuPage et al.   Nature Protocols

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

(2009) Yair Benita et al.   NUCLEIC ACIDS RESEARCH

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY