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

Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population

(2016) Elise B Robinson et al.   NATURE GENETICS

Advancing the understanding of autism disease mechanisms through genetics

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

Brain connectivity in normally developing children and adolescents

(2016) Budhachandra S. Khundrakpam et al.   NEUROIMAGE

Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops

(2016) Caitlin Mullins et al.   NEURON

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity

(2015) Ian Maze et al.   NEURON

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

(2015) Stephan J. Sanders et al.   NEURON

An alternative splicing event amplifies evolutionary differences between vertebrates

(2015) S. Gueroussov et al.   SCIENCE

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

FastRFunctions for Robust Correlations and Hierarchical Clustering

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

Transcriptional Consequences of 16p11.2 Deletion and Duplication in Mouse Cortex and Multiplex Autism Families

(2014) Ian Blumenthal et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2014) S. Anders et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

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

A Global Regulatory Mechanism for Activating an Exon Network Required for Neurogenesis

(2014) Bushra Raj et al.   MOLECULAR CELL

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

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

Most genetic risk for autism resides with common variation

(2014) Trent Gaugler et al.   NATURE GENETICS

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

(2014) Andrew E Jaffe et al.   NATURE NEUROSCIENCE

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

(2014) Simone Gupta et al.   Nature Communications

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

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease

(2013) Jacob Gratten et al.   NATURE GENETICS

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

(2013) Jie Wu et al.   NUCLEIC ACIDS RESEARCH

GO-Elite: a flexible solution for pathway and ontology over-representation

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

Haploinsufficiency ofSOX5at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features

(2012) Allen N. Lamb et al.   HUMAN MUTATION

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

(2012) K. A. Dittmar et al.   MOLECULAR AND CELLULAR BIOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

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

(2012) Cole Trapnell et al.   Nature Protocols

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

Age-Dependent Brain Gene Expression and Copy Number Anomalies in Autism Suggest Distinct Pathological Processes at Young Versus Mature Ages

(2012) Maggie L. Chow et al.   PLoS Genetics

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Accelerated Recruitment of New Brain Development Genes into the Human Genome

(2011) Yong E. Zhang et al.   PLOS BIOLOGY

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

The organization of the transcriptional network in specific neuronal classes

(2009) Kellen D Winden et al.   Molecular Systems Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Immune transcriptome alterations in the temporal cortex of subjects with autism

(2008) Krassimira Garbett et al.   NEUROBIOLOGY OF DISEASE

SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons

(2008) K. Y. Kwan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA