A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation

The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

(2018) Matthew J. McBride et al.   CANCER CELL

Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes

(2018) Aktan Alpsoy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

(2018) Joshua Pan et al.   Cell Systems

Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes

(2017) Maximilian Witzel et al.   NATURE GENETICS

SMARCB1 is required for widespread BAF complex–mediated activation of enhancers and bivalent promoters

(2017) Robert T Nakayama et al.   NATURE GENETICS

SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism

(2017) Pierre Priam et al.   NATURE GENETICS

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers

(2017) Burak H. Alver et al.   Nature Communications

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

(2016) Hye-Jung E. Chun et al.   CANCER CELL

Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor

(2016) Laetitia J. Martin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Concurrent ARID1A and ARID1B inactivation in endometrial and ovarian dedifferentiated carcinomas

(2016) Mackenzie Coatham et al.   MODERN PATHOLOGY

Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition

(2016) Anja F Hohmann et al.   Nature Chemical Biology

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

(2016) Xiaofeng Wang et al.   NATURE GENETICS

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice

(2016) Radhika Mathur et al.   NATURE GENETICS

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

(2016) D. M. Munoz et al.   Cancer Discovery

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition

(2015) Natalie H. Theodoulou et al.   JOURNAL OF MEDICINAL CHEMISTRY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Autodeubiquitination Protects the Tumor Suppressor BAP1 from Cytoplasmic Sequestration Mediated by the Atypical Ubiquitin Ligase UBE2O

(2014) Nazar Mashtalir et al.   MOLECULAR CELL

ARID1B is a specific vulnerability in ARID1A-mutant cancers

(2014) Katherine C Helming et al.   NATURE MEDICINE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

(2014) G. R. Hoffman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial Sarcoma

(2013) Cigall Kadoch et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

Kinetic Analysis of npBAF to nBAF Switching Reveals Exchange of SS18 with CREST and Integration with Neural Developmental Pathways

(2013) B. T. Staahl et al.   JOURNAL OF NEUROSCIENCE

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers

(2013) A. Hunter Shain et al.   PLoS One

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

MicroRNA-mediated conversion of human fibroblasts to neurons

(2011) Andrew S. Yoo et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Spectrum of SMARCB1/INI1 mutations in familial and sporadic rhabdoid tumors

(2010) Katherine W. Eaton et al.   PEDIATRIC BLOOD & CANCER

Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma

(2010) Siân Jones et al.   SCIENCE

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Oncogenesis Caused by Loss of the SNF5 Tumor Suppressor Is Dependent on Activity of BRG1, the ATPase of the SWI/SNF Chromatin Remodeling Complex

(2009) X. Wang et al.   CANCER RESEARCH

MicroRNA-mediated switching of chromatin-remodelling complexes in neural development

(2009) Andrew S. Yoo et al.   NATURE

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BRD7, a Novel PBAF-specific SWI/SNF Subunit, Is Required for Target Gene Activation and Repression in Embryonic Stem Cells

(2008) Matthias D. Kaeser et al.   JOURNAL OF BIOLOGICAL CHEMISTRY