Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons

Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

(2018) Vincent Croset et al.   eLife

Honey bee foraging induces upregulation of early growth response protein 1 , hormone receptor 38 and candidate downstream genes of the ecdysteroid signalling pathway

(2017) A. S. Singh et al.   INSECT MOLECULAR BIOLOGY

RNA polymerase II primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation

(2017) Carmelo Ferrai et al.   Molecular Systems Biology

Long-term effects of maternal separation coupled with social isolation on reward seeking and changes in dopamine D1 receptor expression in the nucleus accumbens via DNA methylation in mice

(2017) Takayo Sasagawa et al.   NEUROSCIENCE LETTERS

Histone deacetylase 5 modulates the effects of social adversity in early life on cocaine-induced behavior

(2017) Alessandro Valzania et al.   PHYSIOLOGY & BEHAVIOR

Epigenetic mechanisms modulate differences inDrosophilaforaging behavior

(2017) Ina Anreiter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reduced Sleep During Social Isolation Leads to Cellular Stress and Induction of the Unfolded Protein Response

(2017) Marishka K. Brown et al.   SLEEP

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

(2017) Gozde Kar et al.   Nature Communications

The Role of Histone Deacetylase 6 in Synaptic Plasticity and Memory

(2017) Sarah Perry et al.   Cell Reports

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder

(2017) Tom S. Koemans et al.   PLoS Genetics

RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides

(2017) Katharine C. Abruzzi et al.   PLoS Genetics

Reduced Sleep During Social Isolation Leads to Cellular Stress and Induction of the Unfolded Protein Response

(2017) Marishka K. Brown et al.   SLEEP

Methyl-CpG binding domain proteins inhibit interspecies courtship and promote aggression in Drosophila

(2017) Tarun Gupta et al.   Scientific Reports

Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos

(2016) Youqiong Ye et al.   CELL DEATH AND DIFFERENTIATION

Long-Term Memory in Drosophila Is Influenced by Histone Deacetylase HDAC4 Interacting with SUMO-Conjugating Enzyme Ubc9

(2016) S. Schwartz et al.   GENETICS

A critical period of vulnerability to adolescent stress: epigenetic mediators in mesocortical dopaminergic neurons

(2016) Minae Niwa et al.   HUMAN MOLECULAR GENETICS

Operation of a homeostatic sleep switch

(2016) Diogo Pimentel et al.   NATURE

An epigenetic mechanism mediates developmental nicotine effects on neuronal structure and behavior

(2016) Yonwoo Jung et al.   NATURE NEUROSCIENCE

Genome-wide identification of neuronal activity-regulated genes in Drosophila

(2016) Xiao Chen et al.   eLife

Early stress evokes dysregulation of histone modifiers in the medial prefrontal cortex across the life span

(2015) Madhavi Pusalkar et al.   DEVELOPMENTAL PSYCHOBIOLOGY

The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing

(2015) O. Bartok et al.   EMBO JOURNAL

The Transgenic RNAi Project at Harvard Medical School: Resources and Validation

(2015) L. A. Perkins et al.   GENETICS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Solitary Confinement and Risk of Self-Harm Among Jail Inmates

(2014) Fatos Kaba et al.   AMERICAN JOURNAL OF PUBLIC HEALTH

Chromatin regulators in neurodevelopment and disease: Analysis of fly neural circuits provides insights

(2014) Hiroaki Taniguchi et al.   BIOESSAYS

Fold change rank ordering statistics: a new method for detecting differentially expressed genes

(2014) Doulaye Dembélé et al.   BMC BIOINFORMATICS

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

(2014) Li Shen et al.   BMC GENOMICS

Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT)

(2014) N. M. Amin et al.   DEVELOPMENT

Epigenetic Control of Learning and Memory in Drosophila by Tip60 HAT Action

(2014) Songjun Xu et al.   GENETICS

Analytical tools and current challenges in the modern era of neuroepigenomics

(2014) Ian Maze et al.   NATURE NEUROSCIENCE

Drosophila models of early onset cognitive disorders and their clinical applications

(2014) Monique van der Voet et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

(2014) Jian Feng et al.   GENOME BIOLOGY

Affinity-based Isolation of Tagged Nuclei from Drosophila Tissues for Gene Expression Analysis

(2014) Jingqun Ma et al.   Jove-Journal of Visualized Experiments

Sleep quality, social well-being, gender, and inflammation: an integrative analysis in a national sample

(2013) Elliot M. Friedman   Annals of the New York Academy of Sciences

Reinforcement signalling in Drosophila; dopamine does it all after all

(2013) Scott Waddell   CURRENT OPINION IN NEUROBIOLOGY

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

(2013) M. S. Enuameh et al.   GENOME RESEARCH

Increasing Tip60 HAT Levels Rescues Axonal Transport Defects and Associated Behavioral Phenotypes in a Drosophila Alzheimer's Disease Model

(2013) A. A. Johnson et al.   JOURNAL OF NEUROSCIENCE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

The Histone Deacetylase HDAC4 Regulates Long-Term Memory in Drosophila

(2013) Helen L. Fitzsimons et al.   PLoS One

Competing dopamine neurons drive oviposition choice for ethanol in Drosophila

(2013) R. Azanchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single dopaminergic neurons that modulate aggression in Drosophila

(2013) O. V. Alekseyenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adolescent Stress-Induced Epigenetic Control of Dopaminergic Neurons via Glucocorticoids

(2013) M. Niwa et al.   SCIENCE

The epigenetic effect of nicotine on dopamine D1 receptor expression in rat prefrontal cortex

(2013) Oguz Gozen et al.   SYNAPSE

Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance

(2013) Alfredo Ghezzi et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Two Dopaminergic Neurons Signal to the Dorsal Fan-Shaped Body to Promote Wakefulness in Drosophila

(2012) Qili Liu et al.   CURRENT BIOLOGY

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

(2012) F. A. Steiner et al.   GENOME RESEARCH

Nicotine induces chromatin remodelling through decreases in the methyltransferases GLP, G9a, Setdb1 and levels of H3K9me2

(2012) Kayla A. Chase et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

A subset of dopamine neurons signals reward for odour memory in Drosophila

(2012) Chang Liu et al.   NATURE

Layered reward signalling through octopamine and dopamine in Drosophila

(2012) Christopher J. Burke et al.   NATURE

Identification of a dopamine pathway that regulates sleep and arousal in Drosophila

(2012) Taro Ueno et al.   NATURE NEUROSCIENCE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Cell type–specific genomics of Drosophila neurons

(2012) Gilbert L. Henry et al.   NUCLEIC ACIDS RESEARCH

Cyber-T web server: differential analysis of high-throughput data

(2012) M. A. Kayala et al.   NUCLEIC ACIDS RESEARCH

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Activity and Nuclear Localization of Cabut, the Drosophila Ortholog of Vertebrate TGF-β-Inducible Early-Response Gene (TIEG) Proteins

(2012) Yaiza Belacortu et al.   PLoS One

High-Resolution Positional Tracking for Long-Term Analysis of Drosophila Sleep and Locomotion Using the “Tracker” Program

(2012) Nathan Donelson et al.   PLoS One

Using translational enhancers to increase transgene expression in Drosophila

(2012) B. D. Pfeiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

An integrative approach to ortholog prediction for disease-focused and other functional studies

(2011) Yanhui Hu et al.   BMC BIOINFORMATICS

NR4A Gene Expression Is Dynamically Regulated in the Ventral Tegmental Area Dopamine Neurons and Is Related to Expression of Dopamine Neurotransmission Genes

(2011) Jeffrey B. Eells et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Epigenetic Regulation of Learning and Memory by Drosophila EHMT/G9a

(2011) Jamie M. Kramer et al.   PLOS BIOLOGY

Histone demethylase JARID1B/KDM5B is a corepressor of TIEG1/KLF10

(2010) Joanna Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Epigenetic influence of social experiences across the lifespan

(2010) Frances A. Champagne   DEVELOPMENTAL PSYCHOBIOLOGY

DrosophilaSIN3 Isoforms Interact with Distinct Proteins and Have Unique Biological Functions

(2010) Marla M. Spain et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

The epigenetics of social adversity in early life: Implications for mental health outcomes

(2010) Patrick O. McGowan et al.   NEUROBIOLOGY OF DISEASE

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Nurr1 Is Required for Maintenance of Maturing and Adult Midbrain Dopamine Neurons

(2009) B. Kadkhodaei et al.   JOURNAL OF NEUROSCIENCE

Dissecting differential gene expression within the circadian neuronal circuit of Drosophila

(2009) Emi Nagoshi et al.   NATURE NEUROSCIENCE

CREB regulation of nucleus accumbens excitability mediates social isolation–induced behavioral deficits

(2009) Deanna L Wallace et al.   NATURE NEUROSCIENCE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genome-wide Analysis of Chromatin Regulation by Cocaine Reveals a Role for Sirtuins

(2009) William Renthal et al.   NEURON

MEME SUITE: tools for motif discovery and searching

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

Social Experience Modifies Pheromone Expression and Mating Behavior in Male Drosophila melanogaster

(2008) Joshua J. Krupp et al.   CURRENT BIOLOGY

Social Context Influences Chemical Communication in D. melanogaster Males

(2008) Clement Kent et al.   CURRENT BIOLOGY