The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain

Chromatin restriction by the nucleosome remodeler Mi-2β and functional interplay with lineage-specific transcription regulators control B-cell differentiation

(2019) Toshimi Yoshida et al.   GENES & DEVELOPMENT

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Sensory experience remodels genome architecture in neural circuit to drive motor learning

(2019) Tomoko Yamada et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis

(2019) Tessa Arends et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Many Roles of Cohesin in Drosophila Gene Transcription

(2019) Dale Dorsett   TRENDS IN GENETICS

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation

(2019) Adam W. Clemens et al.   MOLECULAR CELL

Regulation of neuronal connectivity in the mammalian brain by chromatin remodeling

(2019) Jared V. Goodman et al.   CURRENT OPINION IN NEUROBIOLOGY

The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression

(2018) Susanne Bornelöv et al.   MOLECULAR CELL

Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement

(2018) Antonie D. Kline et al.   NATURE REVIEWS GENETICS

Chromatin Regulation of Neuronal Maturation and Plasticity

(2018) David A. Gallegos et al.   TRENDS IN NEUROSCIENCES

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

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

CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language

(2018) Lot Snijders Blok et al.   Nature Communications

Cell-type-specific programs for activity-regulated gene expression

(2018) Jesse M Gray et al.   CURRENT OPINION IN NEUROBIOLOGY

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability

(2017) Genay O Pilarowski et al.   JOURNAL OF MEDICAL GENETICS

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration

(2017) Debbie L.C. van den Berg et al.   NEURON

De Novo Mutations in CHD4 , an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms

(2016) Karin Weiss et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome

(2016) Alexey A. Soshnev et al.   MOLECULAR CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

(2016) Alejandro Sifrim et al.   NATURE GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Chromatin remodeling inactivates activity genes and regulates neural coding

(2016) Yue Yang et al.   SCIENCE

A Functional Switch of NuRD Chromatin Remodeling Complex Subunits Regulates Mouse Cortical Development

(2016) Justyna Nitarska et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Identification of hierarchical chromatin domains

(2015) Caleb Weinreb et al.   BIOINFORMATICS

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

(2014) Tomoko Yamada et al.   NEURON

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1

(2013) Gemma L Carvill 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

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

(2012) Michael E. Talkowski et al.   CELL

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

(2012) B. J. O'Roak et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Transcriptional Regulation of Neuronal Polarity and Morphogenesis in the Mammalian Brain

(2011) Luis de la Torre-Ubieta et al.   NEURON

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE