Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes

Coexistent ARID1A–PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling

(2015) Ronald L. Chandler et al.   Nature Communications

Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics

(2015) C. Kadoch et al.   Science Advances

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

(2014) S. Anders et al.   BIOINFORMATICS

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis

(2014) C. Attanasio et al.   GENOME RESEARCH

ARID1B is a specific vulnerability in ARID1A-mutant cancers

(2014) Katherine C Helming et al.   NATURE MEDICINE

A rationale to target the SWI/SNF complex for cancer therapy

(2014) Anja F. Hohmann et al.   TRENDS IN GENETICS

Transcriptional Repression by the BRG1-SWI/SNF Complex Affects the Pluripotency of Human Embryonic Stem Cells

(2014) Xiaoli Zhang et al.   Stem Cell Reports

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

(2013) Cigall Kadoch 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

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

(2013) Austin M Dulak et al.   NATURE GENETICS

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

(2013) Cigall Kadoch et al.   NATURE GENETICS

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters

(2013) M. Y. Tolstorukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAX Inactivation in Small Cell Lung Cancer Disrupts MYC-SWI/SNF Programs and Is Synthetic Lethal with BRG1

(2013) O. A. Romero et al.   Cancer Discovery

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

ARID1a-DNA Interactions Are Required for Promoter Occupancy by SWI/SNF

(2012) R. L. Chandler et al.   MOLECULAR AND CELLULAR BIOLOGY

NOTCH1 Nuclear Interactome Reveals Key Regulators of Its Transcriptional Activity and Oncogenic Function

(2012) Ahmad Yatim et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma

(2012) Jian Huang et al.   NATURE GENETICS

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

(2012) Cécile Guichard et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

Essential Role of ARID2 Protein-containing SWI/SNF Complex in Tissue-specific Gene Expression

(2011) Fuhua Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma

(2011) Meng Li et al.   NATURE GENETICS

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

(2011) Ghia M. Euskirchen et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

ARID1AMutations in Endometriosis-Associated Ovarian Carcinomas

(2010) Kimberly C. Wiegand et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Antagonistic Roles for BRM and BRG1 SWI/SNF Complexes in Differentiation

(2009) Stephen Flowers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Variations in the composition of mammalian SWI/SNF chromatin remodelling complexes

(2009) Jessica Ryme et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

The SWI/SNF complex and cancer

(2009) D Reisman et al.   ONCOGENE

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY