Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers

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

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

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

(2018) Brittany C. Michel et al.   NATURE CELL BIOLOGY

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

(2018) James M. McFarland et al.   Nature Communications

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

(2017) Robin M Meyers et al.   NATURE GENETICS

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Composition and Function of Mutant Swi/Snf Complexes

(2017) Arnob Dutta et al.   Cell Reports

Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex

(2017) Payel Sen et al.   Cell Reports

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers

(2017) Timothy W R Kelso et al.   eLife

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

The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer

(2016) Courtney Hodges et al.   Cold Spring Harbor Perspectives in Medicine

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

Pharmacological inhibition of Polo-like kinase 1 (PLK1) by BI-2536 decreases the viability and survival of hamartin and tuberin deficient cells via induction of apoptosis and attenuation of autophagy

(2015) Matthildi Valianou et al.   CELL CYCLE

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Molecular Targeting of the Oncoprotein PLK1 in Pediatric Acute Myeloid Leukemia: RO3280, a Novel PLK1 Inhibitor, Induces Apoptosis in Leukemia Cells

(2015) Na-Na Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pharmacogenomic agreement between two cancer cell line data sets

(2015) Nicolas Stransky et al.   NATURE

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

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

(2015) Jesse R. Raab et al.   PLoS Genetics

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

(2015) C. Kadoch et al.   Science Advances

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Residual Complexes Containing SMARCA2 (BRM) Underlie the Oncogenic Drive of SMARCA4 (BRG1) Mutation

(2014) B. G. Wilson et al.   MOLECULAR AND CELLULAR BIOLOGY

ARID1B is a specific vulnerability in ARID1A-mutant cancers

(2014) Katherine C Helming et al.   NATURE MEDICINE

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom 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

A Synthetic Lethality-Based Strategy to Treat Cancers Harboring a Genetic Deficiency in the Chromatin Remodeling Factor BRG1

(2013) T. Oike et al.   CANCER RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

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

(2013) Cigall Kadoch et al.   NATURE GENETICS

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

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

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

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

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

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY