Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in amyotrophic lateral sclerosis

(2020) J. M. Gregory et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk

(2020) Andrew E. Jaffe et al.   NATURE NEUROSCIENCE

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

(2020) Kristen R Maynard et al.   NUCLEIC ACIDS RESEARCH

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

(2020) Helena L. Crowell et al.   Nature Communications

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

(2019) Lindsay F. Rizzardi et al.   NATURE NEUROSCIENCE

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Genome-wide association study identifies 30 loci associated with bipolar disorder

(2019) Eli A. Stahl et al.   NATURE GENETICS

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments

(2019) Anne-Sophie Hafner et al.   SCIENCE

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

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

Local translation in neuronal processes

(2019) Anne Biever et al.   CURRENT OPINION IN NEUROBIOLOGY

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

(2018) Xiao Dong et al.   Epigenetics

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

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

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

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

Layer- and Cell Type-Specific Modulation of Excitatory Neuronal Activity in the Neocortex

(2018) Gabriele Radnikow et al.   Frontiers in Neuroanatomy

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

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

(2018) Michael J. Gandal et al.   SCIENCE

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

(2017) Peng Hu et al.   MOLECULAR CELL

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

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

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques

(2017) Zhisong He et al.   NATURE NEUROSCIENCE

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Cell Type-Specific Structural Organization of the Six Layers in Rat Barrel Cortex

(2017) Rajeevan T. Narayanan et al.   Frontiers in Neuroanatomy

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

Down Syndrome Developmental Brain Transcriptome Reveals Defective Oligodendrocyte Differentiation and Myelination

(2016) Jose Luis Olmos-Serrano et al.   NEURON

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) B. B. Lake et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

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

The neocortical circuit: themes and variations

(2015) Kenneth D Harris et al.   NATURE NEUROSCIENCE

Dendritic spine alterations in schizophrenia

(2015) Caitlin E. Moyer et al.   NEUROSCIENCE LETTERS

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

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

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

MAGMA: Generalized Gene-Set Analysis of GWAS Data

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

Prenatal Expression Patterns of Genes Associated With Neuropsychiatric Disorders

(2014) Rebecca Birnbaum et al.   AMERICAN JOURNAL OF PSYCHIATRY

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs)

(2013) Brett S Abrahams et al.   Molecular Autism

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

(2012) Hongkui Zeng et al.   CELL

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Synaptic Energy Use and Supply

(2012) Julia J. Harris et al.   NEURON