Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes

Molecular phenotypes associated with antipsychotic drugs in the human caudate nucleus

(2022) Kira A. Perzel Mandell et al.   MOLECULAR PSYCHIATRY

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

(2022) Vassily Trubetskoy et al.   NATURE

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain

(2021) Matthew N. Tran et al.   NEURON

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

PhenomeXcan: Mapping the genome to the phenome through the transcriptome

(2020) Milton Pividori et al.   Science Advances

Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia

(2019) Leonardo Collado-Torres et al.   NEURON

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder

(2019) Gabriel E. Hoffman et al.   Scientific Data

Genetic identification of brain cell types underlying schizophrenia

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

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

(2018) Alexander Gusev 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

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

(2018) Michael J. Gandal et al.   SCIENCE

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations

(2017) Eden R. Martin et al.   GENETIC EPIDEMIOLOGY

Comparative genomic evidence for the involvement of schizophrenia risk genes in antipsychotic effects

(2017) Y Kim et al.   MOLECULAR PSYCHIATRY

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

qSVA framework for RNA quality correction in differential expression analysis

(2017) Andrew E. Jaffe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

(2017) Xiaoquan Wen et al.   PLoS Genetics

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors

(2016) Xiaoquan Wen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das 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

Gene expression elucidates functional impact of polygenic risk for schizophrenia

(2016) Menachem Fromer et al.   NATURE NEUROSCIENCE

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Schizophrenia

(2015) René S. Kahn et al.   Nature Reviews Disease Primers

Using theRPackagecrlmmfor Genotyping and Copy Number Estimation

(2015) Robert B. Scharpf et al.   Journal of Statistical Software

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Schizophrenia

(2014) Anissa Abi-Dargham   JOURNAL OF CLINICAL PSYCHIATRY

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs

(2013) Michal Korostynski et al.   BMC GENOMICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Striatal Presynaptic Dopamine in Schizophrenia, Part II: Meta-Analysis of [18F/11C]-DOPA PET Studies

(2012) Paolo Fusar-Poli et al.   SCHIZOPHRENIA BULLETIN

A multilevel model to address batch effects in copy number estimation using SNP arrays

(2010) R. B. Scharpf et al.   BIOSTATISTICS

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

(2009) M. E. Ritchie et al.   BIOINFORMATICS

Quantifying uncertainty in genotype calls

(2009) Benilton S. Carvalho et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS