Epigenomic Convergence of Neural-Immune Risk Factors in Neurodevelopmental Disorder Cortex

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

(2018) Michael J. Gandal et al.   SCIENCE

Pan-cancer deconvolution of tumour composition using DNA methylation

(2018) Ankur Chakravarthy et al.   Nature Communications

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

(2018) Quy Xiao Xuan Lin et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

(2017) Carrie V. Breton et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons

(2017) S. Jesse Lopez et al.   Epigenetics

Microglia from offspring of dams with allergic asthma exhibit epigenomic alterations in genes dysregulated in autism

(2017) Annie Vogel Ciernia et al.   GLIA

Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity

(2017) Richa Hanamsagar et al.   GLIA

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci

(2017) John F Fullard et al.   HUMAN MOLECULAR GENETICS

Understanding the functions and relationships of the glymphatic system and meningeal lymphatics

(2017) Antoine Louveau et al.   JOURNAL OF CLINICAL INVESTIGATION

Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment

(2017) D Mattei et al.   Translational Psychiatry

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules

(2016) Korinna Kochinke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome

(2016) Peijie Lin et al.   BMC GENOMICS

Histone Acetylome-wide Association Study of Autism Spectrum Disorder

(2016) Wenjie Sun et al.   CELL

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Advancing the understanding of autism disease mechanisms through genetics

(2016) Luis de la Torre-Ubieta et al.   NATURE MEDICINE

The landscape of DNA methylation amid a perfect storm of autism aetiologies

(2016) Annie Vogel Ciernia et al.   NATURE REVIEWS NEUROSCIENCE

Microglia development follows a stepwise program to regulate brain homeostasis

(2016) O. Matcovitch-Natan et al.   SCIENCE

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes

(2016) Keith W. Dunaway et al.   Cell Reports

Genome-wide characteristics of de novo mutations in autism

(2016) Ryan KC Yuen et al.   npj Genomic Medicine

Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli

(2015) James C. Cronk et al.   IMMUNITY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Host microbiota constantly control maturation and function of microglia in the CNS

(2015) Daniel Erny et al.   NATURE NEUROSCIENCE

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis

(2015) Inge R Holtman et al.   Acta Neuropathologica Communications

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

Maternal lifestyle and environmental risk factors for autism spectrum disorders

(2014) Kristen Lyall et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Bias towards large genes in autism

(2014) Shahar Shohat et al.   NATURE

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism

(2014) Simone Gupta et al.   Nature Communications

Costs of Autism Spectrum Disorders in the United Kingdom and the United States

(2014) Ariane V. S. Buescher et al.   JAMA Pediatrics

DNA methylation analysis of the autistic brain reveals multiple dysregulated biological pathways

(2014) S Nardone et al.   Translational Psychiatry

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Common DNA methylation alterations in multiple brain regions in autism

(2013) C Ladd-Acosta et al.   MOLECULAR PSYCHIATRY

The microglial sensome revealed by direct RNA sequencing

(2013) Suzanne E Hickman et al.   NATURE NEUROSCIENCE

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites

(2013) Alexey Kozlenkov et al.   NUCLEIC ACIDS RESEARCH

Epigenetic layers and players underlying neurodevelopment

(2013) Janine M. LaSalle et al.   TRENDS IN NEUROSCIENCES

Genes and pathways underlying regional and cell type changes in Alzheimer's disease

(2013) Jeremy A Miller et al.   Genome Medicine

Combined analysis of exome sequencing points toward a major role for transcription regulation during brain development in autism

(2012) E Ben-David et al.   MOLECULAR PSYCHIATRY

Wild-type microglia arrest pathology in a mouse model of Rett syndrome

(2012) Noël C. Derecki et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Rare Deletions at the Neurexin 3 Locus in Autism Spectrum Disorder

(2011) Andrea K. Vaags et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism

(2009) Simon G Gregory et al.   BMC Medicine

MECP2promoter methylation and X chromosome inactivation in autism

(2008) Raman P. Nagarajan et al.   Autism Research

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

MeCP2, a Key Contributor to Neurological Disease, Activates and Represses Transcription

(2008) M. Chahrour et al.   SCIENCE