Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus

CBP and SRF co-regulate dendritic growth and synaptic maturation

(2019) Beatriz del Blanco et al.   CELL DEATH AND DIFFERENTIATION

A translational silencing function of MCPIP1/Regnase-1 specified by the target site context

(2018) Gesine Behrens et al.   NUCLEIC ACIDS RESEARCH

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior

(2018) Ee-Lynn Yap et al.   NEURON

The Expanding Toolkit of Translating Ribosome Affinity Purification

(2017) Joseph D. Dougherty   JOURNAL OF NEUROSCIENCE

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

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

Lineage divergence of activity-driven transcription and evolution of cognitive ability

(2017) Giles E. Hardingham et al.   NATURE REVIEWS NEUROSCIENCE

Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons

(2017) Marilyn Scandaglia et al.   Cell Reports

NPTX2 and cognitive dysfunction in Alzheimer’s Disease

(2017) Mei-Fang Xiao et al.   eLife

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

(2016) Núria Queralt-Rosinach et al.   BIOINFORMATICS

Hyperphosphorylated tau in patients with refractory epilepsy correlates with cognitive decline: a study of temporal lobe resections

(2016) Xin You Tai et al.   BRAIN

Mechanisms of homeostatic plasticity in the excitatory synapse

(2016) Dominique Fernandes et al.   JOURNAL OF NEUROCHEMISTRY

Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity

(2016) Oriane Mauger et al.   NEURON

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Role of hippocampal activity-induced transcription in memory consolidation

(2016) Andrew L. Eagle et al.   REVIEWS IN THE NEUROSCIENCES

Extra-coding RNAs regulate neuronal DNA methylation dynamics

(2016) Katherine E. Savell et al.   Nature Communications

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

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

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

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness

(2015) Anna Fiorenza et al.   CEREBRAL CORTEX

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

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

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

(2015) Rashi Halder et al.   NATURE NEUROSCIENCE

Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

(2015) Xintian You et al.   NATURE NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Multiple repressive mechanisms in the hippocampus during memory formation

(2015) J. Cho et al.   SCIENCE

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

(2014) Suhas S.P. Rao et al.   CELL

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

The Neuronal Activity-Driven Transcriptome

(2014) Eva Benito et al.   MOLECULAR NEUROBIOLOGY

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP)

(2014) Myriam Heiman et al.   Nature Protocols

Can changes in histone acetylation contribute to memory formation?

(2014) Jose P. Lopez-Atalaya et al.   TRENDS IN GENETICS

Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation

(2014) Johanna Schott et al.   PLoS Genetics

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Profiling of Glucose-Sensing Neurons Reveals that GHRH Neurons Are Activated by Hypoglycemia

(2013) Sarah Stanley et al.   Cell Metabolism

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 neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory

(2013) Annie Vogel-Ciernia et al.   NATURE NEUROSCIENCE

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

The Emerging Field of Neuroepigenetics

(2013) J. David Sweatt   NEURON

Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition

(2013) Jose P. Lopez-Atalaya et al.   NUCLEIC ACIDS RESEARCH

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories

(2013) Luca Crepaldi et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II

(2011) Ramendra N Saha et al.   NATURE NEUROSCIENCE

Triptolide (TPL) Inhibits Global Transcription by Inducing Proteasome-Dependent Degradation of RNA Polymerase II (Pol II)

(2011) Ying Wang et al.   PLoS One

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

(2011) A. E. West et al.   Cold Spring Harbor Perspectives in Biology

DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks

(2010) Anna Bauer-Mehren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

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

A physiological role for gene loops in yeast

(2009) Jean-Philippe Lainé et al.   GENES & DEVELOPMENT

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY