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

Oasis: online analysis of small RNA deep sequencing data

(2015) Vincenzo Capece et al.   BIOINFORMATICS

DNA Methylation in Memory Formation

(2015) Frankie D. Heyward et al.   NEUROSCIENTIST

Labeling of active neural circuits in vivo with designed calcium integrators

(2015) B. F. Fosque et al.   SCIENCE

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

(2014) Li Shen et al.   BMC GENOMICS

From CNS stem cells to neurons and glia: Sox for everyone

(2014) Simone Reiprich et al.   CELL AND TISSUE RESEARCH

Epigenetic memory: the Lamarckian brain

(2014) A. Fischer   EMBO JOURNAL

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

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

Transcriptional and epigenetic regulation of Hebbian and non-Hebbian plasticity

(2014) Mikael C. Guzman-Karlsson et al.   NEUROPHARMACOLOGY

Early remodeling of the neocortex upon episodic memory encoding

(2014) A. W. Bero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can changes in histone acetylation contribute to memory formation?

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

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

Genome-wide analysis of H4K5 acetylation associated with fear memory in mice

(2013) C Park et al.   BMC GENOMICS

Epigenetic regulation of memory formation and maintenance

(2013) I. B. Zovkic et al.   LEARNING & MEMORY

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Histone acetylation: molecular mnemonics on the chromatin

(2013) Johannes Gräff et al.   NATURE REVIEWS NEUROSCIENCE

The Emerging Field of Neuroepigenetics

(2013) J. David Sweatt   NEURON

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain

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

Creating a False Memory in the Hippocampus

(2013) S. Ramirez et al.   SCIENCE

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Involvement of the anterior cingulate cortex in formation, consolidation, and reconsolidation of recent and remote contextual fear memory

(2012) E. O. Einarsson et al.   LEARNING & MEMORY

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

(2012) Charlotte Proudhon et al.   MOLECULAR CELL

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

Generation of a Synthetic Memory Trace

(2012) A. R. Garner et al.   SCIENCE

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

Epigenetic Mechanisms in Cognition

(2011) Jeremy J. Day et al.   NEURON

Early Tagging of Cortical Networks Is Required for the Formation of Enduring Associative Memory

(2011) E. Lesburgueres et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Histone Methylation Regulates Memory Formation

(2010) S. Gupta et al.   JOURNAL OF NEUROSCIENCE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Cortical DNA methylation maintains remote memory

(2010) Courtney A Miller et al.   NATURE NEUROSCIENCE

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice

(2010) S. Peleg et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish

(2009) José Bessa et al.   DEVELOPMENTAL DYNAMICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Long-term plasticity of excitatory inputs to granule cells in the rat olfactory bulb

(2009) Yuan Gao et al.   NATURE NEUROSCIENCE

Molecular and Cellular Approaches to Memory Allocation in Neural Circuits

(2009) A. J. Silva et al.   SCIENCE

Isolation of neuronal chromatin from brain tissue

(2008) Yan Jiang et al.   BMC NEUROSCIENCE

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY