Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies

The Emerging Picture of Autism Spectrum Disorder: Genetics and Pathology

(2015) Jason A. Chen et al.   Annual Review of Pathology-Mechanisms of Disease

Specific identification and quantification of circular RNAs from sequencing data

(2015) Jun Cheng et al.   BIOINFORMATICS

A Genome-wide Association Study of Autism Using the Simons Simplex Collection: Does Reducing Phenotypic Heterogeneity in Autism Increase Genetic Homogeneity?

(2015) Pauline Chaste et al.   BIOLOGICAL PSYCHIATRY

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Recent Advances in the Genetics of Autism Spectrum Disorder

(2015) Silvia De Rubeis et al.   Current Neurology and Neuroscience Reports

Specific Regional and Age-Related Small Noncoding RNA Expression Patterns Within Superior Temporal Gyrus of Typical Human Brains Are Less Distinct in Autism Brains

(2015) Boryana Stamova et al.   JOURNAL OF CHILD NEUROLOGY

Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome

(2015) Ahmed Mahfouz et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers

(2015) T. Pramparo et al.   Molecular Systems Biology

Coexpression networks identify brain region–specific enhancer RNAs in the human brain

(2015) Pu Yao et al.   NATURE NEUROSCIENCE

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

(2015) Andrew E Jaffe 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

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

(2015) Neelroop N. Parikshak et al.   NATURE REVIEWS GENETICS

Determining the role of microRNAs in psychiatric disorders

(2015) Orna Issler et al.   NATURE REVIEWS NEUROSCIENCE

From the genetic architecture to synaptic plasticity in autism spectrum disorder

(2015) Thomas Bourgeron   NATURE REVIEWS NEUROSCIENCE

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation

(2015) Francesca Telese et al.   NEURON

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

(2015) Stephan J. Sanders et al.   NEURON

RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene

(2015) Lilach Pnueli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

(2015) Andranik Ivanov et al.   Cell Reports

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

(2015) Linda Szabo et al.   GENOME BIOLOGY

A comprehensive meta-analysis of common genetic variants in autism spectrum conditions

(2015) Varun Warrier et al.   Molecular Autism

Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders

(2014) Dalila Pinto et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

(2014) Raphael Bernier et al.   CELL

The discovery of integrated gene networks for autism and related disorders

(2014) Fereydoun Hormozdiari et al.   GENOME RESEARCH

The Familial Risk of Autism

(2014) Sven Sandin et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Detecting and characterizing circular RNAs

(2014) William R Jeck et al.   NATURE BIOTECHNOLOGY

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Most genetic risk for autism resides with common variation

(2014) Trent Gaugler et al.   NATURE GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease

(2014) T. C. Roberts et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2014) Simone Gupta et al.   Nature Communications

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

(2014) Jakub O. Westholm et al.   Cell Reports

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

(2014) Han Wu et al.   PLoS Genetics

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

Digital sorting of complex tissues for cell type-specific gene expression profiles

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

(2013) A. Jeremy Willsey et al.   CELL

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

(2013) Neelroop N. Parikshak et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue

(2013) Brooke E. Hjelm et al.   HUMAN MOLECULAR GENETICS

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Identification of differentially expressed microRNAs across the developing human brain

(2013) M N Ziats et al.   MOLECULAR PSYCHIATRY

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Epigenetics and ncRNAs in Brain Function and Disease: Mechanisms and Prospects for Therapy

(2013) Miguel A. Varela et al.   Neurotherapeutics

When Is Hub Gene Selection Better than Standard Meta-Analysis?

(2013) Peter Langfelder et al.   PLoS One

The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option

(2013) Aaron M. Wenger et al.   PLoS Genetics

Autism in DSM-5: progress and challenges

(2013) Fred R Volkmar et al.   Molecular Autism

Characterization of Enhancer Function from Genome-Wide Analyses

(2012) Glenn A. Maston et al.   Annual Review of Genomics and Human Genetics

The Pathophysiology of Fragile X (and What It Teaches Us about Synapses)

(2012) Asha L. Bhakar et al.   Annual Review of Neuroscience

Global Prevalence of Autism and Other Pervasive Developmental Disorders

(2012) Mayada Elsabbagh et al.   Autism Research

Aberrant Expression of Long Noncoding RNAs in Autistic Brain

(2012) Mark N. Ziats et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Comparative RNA editing in autistic and neurotypical cerebella

(2012) A Eran et al.   MOLECULAR PSYCHIATRY

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

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

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

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

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

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

A Noncoding RNA Antisense to Moesin at 5p14.1 in Autism

(2012) T. Kerin et al.   Science Translational Medicine

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Networks of Neuronal Genes Affected by Common and Rare Variants in Autism Spectrum Disorders

(2012) Eyal Ben-David et al.   PLoS Genetics

Common genetic variants, acting additively, are a major source of risk for autism

(2012) Lambertus Klei et al.   Molecular Autism

Genetic Heritability and Shared Environmental Factors Among Twin Pairs With Autism

(2011) Joachim Hallmayer   ARCHIVES OF GENERAL PSYCHIATRY

The Human Brain in a Dish: The Promise of iPSC-Derived Neurons

(2011) Ricardo Dolmetsch et al.   CELL

Mechanisms of neurocognitive dysfunction and therapeutic considerations in tuberous sclerosis complex

(2011) Peter Tsai et al.   CURRENT OPINION IN NEUROLOGY

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

(2011) Carlo Colantuoni et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

(2011) Brian J O'Roak et al.   NATURE GENETICS

Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain

(2011) Alexandre Kuhn et al.   NATURE METHODS

Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism

(2011) Stephan J. Sanders et al.   NEURON

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genotator: A disease-agnostic tool for genetic annotation of disease

(2010) Dennis P Wall et al.   BMC Medical Genomics

A genome-wide scan for common alleles affecting risk for autism

(2010) R. Anney et al.   HUMAN MOLECULAR GENETICS

Engineered Alterations in RNA Editing Modulate Complex Behavior inDrosophila

(2010) James E. C. Jepson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Functional impact of global rare copy number variation in autism spectrum disorders

(2010) Dalila Pinto et al.   NATURE

A genome-wide linkage and association scan reveals novel loci for autism

(2009) Lauren A. Weiss et al.   NATURE

Common genetic variants on 5p14.1 associate with autism spectrum disorders

(2009) Kai Wang et al.   NATURE

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes

(2009) Joseph T. Glessner et al.   NATURE

Structural Variation of Chromosomes in Autism Spectrum Disorder

(2008) Christian R. Marshall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Immune transcriptome alterations in the temporal cortex of subjects with autism

(2008) Krassimira Garbett et al.   NEUROBIOLOGY OF DISEASE