Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

(2019) Chloe C Y Wong et al.   HUMAN MOLECULAR GENETICS

Monoallelic Gene Expression in Mammals

(2016) Andrew Chess   Annual Review of Genetics

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data

(2016) E. Y. Kang et al.   GENETICS

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

(2016) Neelroop N. Parikshak et al.   NATURE

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

(2016) Ye E Wu et al.   NATURE NEUROSCIENCE

Gene hunting in autism spectrum disorder: on the path to precision medicine

(2015) Daniel H Geschwind et al.   LANCET NEUROLOGY

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Stephan J. Sanders et al.   NEURON

dbMAE: the database of autosomal monoallelic expression

(2015) Virginia Savova et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

Allelic expression analysis in the brain suggests a role for heterogeneous insults affecting epigenetic processes in autism spectrum disorders

(2014) Eyal Ben-David et al.   HUMAN MOLECULAR GENETICS

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Monoallelic expression of the humanFOXP2speech gene

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

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues

(2014) Kimberly R. Kukurba et al.   PLoS Genetics

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

(2014) S Nardone et al.   Translational Psychiatry

Altered Gamma-Aminobutyric Acid Type B Receptor Subunit 1 Splicing In Alcoholics

(2013) Changhoon Lee et al.   BIOLOGICAL PSYCHIATRY

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

(2013) Neelroop N. Parikshak et al.   CELL

Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome

(2013) Avinash M. Veerappa et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis

(2013)   LANCET

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Global Prevalence of Autism and Other Pervasive Developmental Disorders

(2012) Mayada Elsabbagh et al.   Autism Research

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

(2012) Brian DeVeale et al.   PLoS Genetics

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   CELL

Neuron-specific impairment of inter-chromosomal pairing and transcription in a novel model of human 15q-duplication syndrome

(2011) Makiko Meguro-Horike et al.   HUMAN MOLECULAR GENETICS

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Imprinted DLK1-DIO3 region of 14q32 defines a schizophrenia-associated miRNA signature in peripheral blood mononuclear cells

(2011) E Gardiner et al.   MOLECULAR PSYCHIATRY

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

miRNA Expression in Colon Polyps Provides Evidence for a Multihit Model of Colon Cancer

(2011) Ann L. Oberg et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Increased copy number for methylated maternal 15q duplications leads to changes in gene and protein expression in human cortical samples

(2011) Haley A Scoles et al.   Molecular Autism

PLEXY: efficient target prediction for box C/D snoRNAs

(2010) Stephanie Kehr et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Allele-specific DNA methylation: beyond imprinting

(2010) B. Tycko   HUMAN MOLECULAR GENETICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex-Specific Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li 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

Genetic predisposition to human disease: allele-specific expression and low-penetrance regulatory loci

(2009) A de la Chapelle   ONCOGENE

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Copy-number variations associated with neuropsychiatric conditions

(2008) Edwin H. Cook Jr et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions

(2007) Peter S. Bazeley et al.   GENE