A disordered region controls cBAF activity via condensation and partner recruitment

Interaction modules that impart specificity to disordered protein

(2023) Katerina Cermakova et al.   TRENDS IN BIOCHEMICAL SCIENCES

Phase Transitions of Associative Biomacromolecules

(2023) Rohit V. Pappu et al.   Chemical Reviews

Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection

(2023) Jin Wei et al.   NATURE GENETICS

Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders

(2023) Alfredo M. Valencia et al.   NATURE GENETICS

Sequence-dependent surface condensation of a pioneer transcription factor on DNA

(2022) Jose A. Morin et al.   Nature Physics

Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains

(2022) Max V. Staller et al.   Cell Systems

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

(2022) Xiangze Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic variation associated with condensate dysregulation in disease

(2022) Salman F. Banani et al.   DEVELOPMENTAL CELL

Sequence grammar underlying the unfolding and phase separation of globular proteins

(2022) Kiersten M. Ruff et al.   MOLECULAR CELL

SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

(2022) Roodolph St. Pierre et al.   NATURE GENETICS

Phase-separating RNA-binding proteins form heterogeneous distributions of clusters in subsaturated solutions

(2022) Mrityunjoy Kar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division

(2022) Min Kyung Shinn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations

(2022) Mina Farag et al.   Nature Communications

Mammalian SWI/SNF continuously restores local accessibility to chromatin

(2021) Mario Iurlaro et al.   NATURE GENETICS

Identifying molecular features that are associated with biological function of intrinsically disordered protein regions

(2021) Taraneh Zarin et al.   eLife

Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins

(2021) Megan C. Cohan et al.   JOURNAL OF MOLECULAR BIOLOGY

Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

(2021) Anne Bremer et al.   Nature Chemistry

Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling

(2021) Louis-Philippe Bergeron-Sandoval et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation

(2020) Jamie A. Greig et al.   MOLECULAR CELL

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Structure of nucleosome-bound human BAF complex

(2020) Shuang He et al.   SCIENCE

Cryo-EM structure of SWI/SNF complex bound to a nucleosome

(2020) Yan Han et al.   NATURE

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms

(2020) Nazar Mashtalir et al.   CELL

Nucleated transcriptional condensates amplify gene expression

(2020) Ming-Tzo Wei et al.   NATURE CELL BIOLOGY

Efficient low-cost chromatin profiling with CUT&Tag

(2020) Hatice S. Kaya-Okur et al.   Nature Protocols

MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins

(2020) Marco Necci et al.   BIOINFORMATICS

Description of neurodevelopmental phenotypes associated with 10 genetic neurodevelopmental disorders: A scoping review

(2020) Ciara Hanly et al.   CLINICAL GENETICS

MobiDB: intrinsically disordered proteins in 2021

(2020) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds

(2019) Dan Bracha et al.   CELL

In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

(2019) Valentin Iglesias et al.   Frontiers in Physiology

The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity–independent genomic targeting

(2019) Joshua Pan et al.   NATURE GENETICS

Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling

(2019) Alfredo M. Valencia et al.   CELL

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

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

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders

(2018) Caroline F Wright et al.   GENETICS IN MEDICINE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis

(2018) Gabriel J. Sandoval et al.   MOLECULAR CELL

Efficient proximity labeling in living cells and organisms with TurboID

(2018) Tess C Branon et al.   NATURE BIOTECHNOLOGY

Mutational Landscapes and Phenotypic Spectrum of SWI/SNF-Related Intellectual Disability Disorders

(2018) Nina Bögershausen et al.   Frontiers in Molecular Neuroscience

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

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

(2018) Nazar Mashtalir et al.   CELL

Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers

(2018) Julien P. N. Papillon et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

(2018) Jovylyn Gatchalian et al.   Nature Communications

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

(2017) Yuan Lin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

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

(2017) Robert T Nakayama et al.   NATURE GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor

(2017) Kathryn P. Sherry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

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

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

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A Deeper Look into Comet—Implementation and Features

(2015) Jimmy K. Eng et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

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

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

NMR contributions to structural dynamics studies of intrinsically disordered proteins

(2014) Robert Konrat   JOURNAL OF MAGNETIC RESONANCE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Coffin-Siris Syndrome and the BAF Complex: Genotype-Phenotype Study in 63 Patients

(2013) Gijs W.E. Santen et al.   HUMAN MUTATION

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

(2013) Cigall Kadoch et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

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

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

(2012) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

SWI/SNF complex in disorder

(2012) Gijs W.E. Santen et al.   Epigenetics

RNA catalysis through compartmentalization

(2012) Christopher A. Strulson et al.   Nature Chemistry

Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome

(2012) Gijs W E Santen et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Peptide–nucleotide microdroplets as a step towards a membrane-free protocell model

(2011) Shogo Koga et al.   Nature Chemistry

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY