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

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

(2018) Douglas M. Ruderfer et al.   CELL

The human noncoding genome defined by genetic diversity

(2018) Julia di Iulio et al.   NATURE GENETICS

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Genetic identification of brain cell types underlying schizophrenia

(2018) Nathan G. Skene et al.   NATURE GENETICS

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

(2018) Antonio F. Pardiñas et al.   NATURE GENETICS

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

(2018) Andrew E. Jaffe et al.   NATURE NEUROSCIENCE

Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1

(2018) Celine K. Vuong et al.   NEURON

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

(2018) Michael J. Gandal et al.   SCIENCE

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Investigating the neuroimmunogenic architecture of schizophrenia

(2017) R Birnbaum et al.   MOLECULAR PSYCHIATRY

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Sex-specific transcriptional signatures in human depression

(2017) Benoit Labonté et al.   NATURE MEDICINE

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

(2017) Priit Pruunsild et al.   Cell Reports

Post-mortem molecular profiling of three psychiatric disorders

(2017) Ryne C. Ramaker et al.   Genome Medicine

Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

(2017) Hoang T. Nguyen et al.   Genome Medicine

Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

(2017)   Molecular Autism

Systematic analysis of gene expression patterns associated with postmortem interval in human tissues

(2017) Yizhang Zhu et al.   Scientific Reports

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

(2016) Endre Sebestyén et al.   GENOME RESEARCH

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

(2016) Mathieu Quesnel-Vallières et al.   MOLECULAR CELL

Transcriptome sequencing implicates dorsal striatum-specific gene network, immune response and energy metabolism pathways in bipolar disorder

(2016) R Pacifico et al.   MOLECULAR PSYCHIATRY

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

(2016) Neelroop N. Parikshak et al.   NATURE

Genome-wide association study identifies 74 loci associated with educational attainment

(2016) Aysu Okbay et al.   NATURE

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

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

(2016) Monkol Lek et al.   NATURE

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

(2016) Michael I Love et al.   NATURE BIOTECHNOLOGY

Genetic variants associated with subjective well-being, depressive symptoms and neuroticism identified through genome-wide analyses

(2016) Aysu Okbay et al.   NATURE GENETICS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Origin, fate and dynamics of macrophages at central nervous system interfaces

(2016) Tobias Goldmann et al.   NATURE IMMUNOLOGY

Advancing the understanding of autism disease mechanisms through genetics

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

The road to precision psychiatry: translating genetics into disease mechanisms

(2016) Michael J Gandal et al.   NATURE NEUROSCIENCE

Gene expression elucidates functional impact of polygenic risk for schizophrenia

(2016) Menachem Fromer et al.   NATURE NEUROSCIENCE

Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

(2016) Giulio Genovese et al.   NATURE NEUROSCIENCE

The neurogenetics of alternative splicing

(2016) Celine K. Vuong et al.   NATURE REVIEWS NEUROSCIENCE

Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes

(2016) Ji-Ann Lee et al.   NEURON

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

The ExAC browser: displaying reference data information from over 60 000 exomes

(2016) Konrad J. Karczewski et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia

(2016) S E Ellis et al.   Translational Psychiatry

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

(2015) Bjarni J. Vilhjálmsson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Functional genomics bridges the gap between quantitative genetics and molecular biology

(2015) Tuuli Lappalainen   GENOME RESEARCH

Inflammation as a neurobiological substrate of cognitive impairment in bipolar disorder: Evidence, pathophysiology and treatment implications

(2015) Joshua D. Rosenblat et al.   JOURNAL OF AFFECTIVE DISORDERS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

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

Immune mediators in the brain and peripheral tissues in autism spectrum disorder

(2015) Myka L. Estes et al.   NATURE REVIEWS NEUROSCIENCE

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

(2015) Stephan J. Sanders et al.   NEURON

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Low load for disruptive mutations in autism genes and their biased transmission

(2015) Ivan Iossifov 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

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

The autism-associated gene chromodomain helicase DNA-binding protein 8 (CHD8) regulates noncoding RNAs and autism-related genes

(2015) B Wilkinson et al.   Translational Psychiatry

The Global Burden of Mental, Neurological and Substance Use Disorders: An Analysis from the Global Burden of Disease Study 2010

(2015) Harvey A. Whiteford et al.   PLoS One

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

(2014) Manuel Irimia et al.   CELL

RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder

(2014) N Akula et al.   MOLECULAR PSYCHIATRY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing

(2014) Barbara Treutlein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Simone Gupta et al.   Nature Communications

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

(2013) Neelroop N. Parikshak et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

(2013) G Barry et al.   MOLECULAR PSYCHIATRY

Development, maintenance and disruption of the blood-brain barrier

(2013) Birgit Obermeier et al.   NATURE MEDICINE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

(2013) Sara Mostafavi et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development

(2012) Brent L. Fogel et al.   HUMAN MOLECULAR GENETICS

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Increased inflammatory markers identified in the dorsolateral prefrontal cortex of individuals with schizophrenia

(2012) S G Fillman et al.   MOLECULAR PSYCHIATRY

Two gene co-expression modules differentiate psychotics and controls

(2012) C Chen et al.   MOLECULAR PSYCHIATRY

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

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

(2012)   NATURE GENETICS

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

(2012) Irina Rusinova et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Excess of De Novo Deleterious Mutations in Genes Associated with Glutamatergic Systems in Nonsyndromic Intellectual Disability

(2011) Fadi F. Hamdan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Jennifer C. Darnell et al.   CELL

Truncating mutations in NRXN2 and NRXN1 in autism spectrum disorders and schizophrenia

(2011) Julie Gauthier et al.   HUMAN 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

The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain

(2011) Lauren T Gehman et al.   NATURE GENETICS

Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4

(2011)   NATURE GENETICS

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Schizophrenia and Autism: Both Shared and Disorder-Specific Pathogenesis Via Perinatal Inflammation?

(2011) URS MEYER et al.   PEDIATRIC RESEARCH

Evaluating genetic markers and neurobiochemical analytes for fluoxetine response using a panel of mouse inbred strains

(2011) Cristina S. Benton et al.   PSYCHOPHARMACOLOGY

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

(2011) A. E. West et al.   Cold Spring Harbor Perspectives in Biology

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

The Mouse Blood-Brain Barrier Transcriptome: A New Resource for Understanding the Development and Function of Brain Endothelial Cells

(2010) Richard Daneman et al.   PLoS One

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

(2009) Mike J Mason et al.   BMC GENOMICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Involvement of SMARCA2/BRM in the SWI/SNF chromatin-remodeling complex in schizophrenia

(2009) Minori Koga et al.   HUMAN MOLECULAR GENETICS

Increased excitotoxicity and neuroinflammatory markers in postmortem frontal cortex from bipolar disorder patients

(2009) J S Rao et al.   MOLECULAR PSYCHIATRY

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development

(2009) P. P. Amaral et al.   RNA

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging

(2008) J. A. Miller et al.   JOURNAL OF NEUROSCIENCE

Evolutionary toggling of the MAPT 17q21.31 inversion region

(2008) Michael C Zody et al.   NATURE GENETICS

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA