PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids

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

(2020) F. Kyle Satterstrom et al.   CELL

Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma

(2020) Aparna Bhaduri et al.   Cell Stem Cell

Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids

(2020) Jason Dang et al.   MOLECULAR PSYCHIATRY

Decoding the development of the human hippocampus

(2020) Suijuan Zhong et al.   NATURE

Cell stress in cortical organoids impairs molecular subtype specification

(2020) Aparna Bhaduri et al.   NATURE

Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain

(2020) Yoshiaki Tanaka et al.   Cell Reports

Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation

(2020) Xuyu Qian et al.   Cell Stem Cell

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Human cognition involves the dynamic integration of neural activity and neuromodulatory systems

(2019) James M. Shine et al.   NATURE NEUROSCIENCE

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes

(2019) Andrew R. Field et al.   Stem Cell Reports

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex

(2019) Simone Mayer et al.   NEURON

Cerebral organoids at the air–liquid interface generate diverse nerve tracts with functional output

(2019) Stefano L. Giandomenico et al.   NATURE NEUROSCIENCE

Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures

(2019) Rebecca M. Marton et al.   NATURE NEUROSCIENCE

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Altered human oligodendrocyte heterogeneity in multiple sclerosis

(2019) Sarah Jäkel et al.   NATURE

hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids

(2019) Yangfei Xiang et al.   Cell Stem Cell

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

(2019) Alex A. Pollen et al.   CELL

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Specification of positional identity in forebrain organoids

(2019) Gustav Y. Cederquist et al.   NATURE BIOTECHNOLOGY

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

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

(2019) Dmitry Velmeshev et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

(2019) Silvia Velasco et al.   NATURE

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation

(2019) Damon Polioudakis et al.   NEURON

Functionalization of Brain Region-specific Spheroids with Isogenic Microglia-like Cells

(2019) Liqing Song et al.   Scientific Reports

New insights into the development of the human cerebral cortex

(2019) Zoltán Molnár et al.   JOURNAL OF ANATOMY

Single-cell multimodal transcriptomics to study neuronal diversity in human stem cell-derived brain tissue and organoid models

(2019) Mark van den Hurk et al.   JOURNAL OF NEUROSCIENCE METHODS

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

(2019) Fumitaka Inoue et al.   Cell Stem Cell

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development

(2019) Cleber A. Trujillo et al.   Cell Stem Cell

Organoid single-cell genomic atlas uncovers human-specific features of brain development

(2019) Sabina Kanton et al.   NATURE

Engineering of human brain organoids with a functional vascular-like system

(2019) Bilal Cakir et al.   NATURE METHODS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

ClinVar: improvements to accessing data

(2019) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Generation of complex human organoid models including vascular networks by incorporation of mesodermal progenitor cells

(2019) Philipp Wörsdörfer et al.   Scientific Reports

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Orchestrating single-cell analysis with Bioconductor

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

Identifying Novel Enhancer Elements with CRISPR-Based Screens

(2018) Jason C. Klein et al.   ACS Chemical Biology

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

(2018) Xiaoying Fan et al.   CELL RESEARCH

Neurovascular Communication during CNS Development

(2018) Isidora Paredes et al.   DEVELOPMENTAL CELL

Brain transcriptome databases: a user's guide

(2018) Jason M. Keil et al.   JOURNAL OF NEUROSCIENCE

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

An in vivo model of functional and vascularized human brain organoids

(2018) Abed AlFatah Mansour et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Induction of myelinating oligodendrocytes in human cortical spheroids

(2018) Mayur Madhavan et al.   NATURE METHODS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity

(2018) Bradley P. Coe et al.   NATURE GENETICS

Reliability of human cortical organoid generation

(2018) Se-Jin Yoon et al.   NATURE METHODS

Somatic mosaicism and neurodevelopmental disease

(2018) Alissa M. D’Gama et al.   NATURE NEUROSCIENCE

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

(2018) Michael J. Gandal et al.   SCIENCE

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

Microglia innately develop within cerebral organoids

(2018) Paul R. Ormel et al.   Nature Communications

Microglia Increase Inflammatory Responses in iPSC-Derived Human BrainSpheres

(2018) Celina Monteiro Abreu et al.   Frontiers in Microbiology

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

(2018) Suhn K. Rhie et al.   Science Advances

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

Erratum: Genetic effects on gene expression across human tissues

(2017)   NATURE

Assembly of functionally integrated human forebrain spheroids

(2017) Fikri Birey et al.   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Guided self-organization and cortical plate formation in human brain organoids

(2017) Madeline A Lancaster 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

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

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

(2017) Naomi Habib et al.   NATURE METHODS

iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases

(2017) Edsel M. Abud et al.   NEURON

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

(2017) Steven A. Sloan et al.   NEURON

Systematic dissection of genomic features determining transcription factor binding and enhancer function

(2017) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

(2017) Michael J. McConnell et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells

(2017) Anna S. Monzel et al.   Stem Cell Reports

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

(2016) Xuyu Qian et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Altered proliferation and networks in neural cells derived from idiopathic autistic individuals

(2016) M C Marchetto et al.   MOLECULAR PSYCHIATRY

A comprehensive transcriptional map of primate brain development

(2016) Trygve E. Bakken et al.   NATURE

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

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

(2016) Monkol Lek et al.   NATURE

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

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

Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development

(2016) Tomasz J. Nowakowski 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

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

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

(2016) B. B. Lake et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

(2016) Felipe Mora-Bermúdez et al.   eLife

Large-Scale Production of Mature Neurons from Human Pluripotent Stem Cells in a Three-Dimensional Suspension Culture System

(2016) Alessandra Rigamonti et al.   Stem Cell Reports

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

(2015) Jessica Mariani et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

(2015) Anthony A. Philippakis et al.   HUMAN MUTATION

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq

(2015) Cathryn R Cadwell et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

(2015) Anca M Paşca et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp 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

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

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

(2015) et al.   SCIENCE

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue

(2015) Hideya Sakaguchi et al.   Nature Communications

Self-Organization of Polarized Cerebellar Tissue in 3D Culture of Human Pluripotent Stem Cells

(2015) Keiko Muguruma et al.   Cell Reports

Pathogenetic mechanisms of focal cortical dysplasia

(2014) Isaac Marin-Valencia et al.   EPILEPSIA

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

(2014) Nicola H. Dryden et al.   GENOME RESEARCH

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Non-epithelial stem cells and cortical interneuron production in the human ganglionic eminences

(2013) David V Hansen et al.   NATURE NEUROSCIENCE

Subcortical origins of human and monkey neocortical interneurons

(2013) Tong Ma et al.   NATURE NEUROSCIENCE

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex

(2013) T. Kadoshima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

(2012) Michael E. Talkowski et al.   CELL

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

(2012) Jeong Ho Lee et al.   NATURE GENETICS

Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations

(2012) Annapurna Poduri et al.   NEURON

Modeling human cortical development in vitro using induced pluripotent stem cells

(2012) J. Mariani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dorsal Radial Glial Cells Have the Potential to Generate Cortical Interneurons in Human But Not in Mouse Brain

(2011) X. Yu et al.   JOURNAL OF NEUROSCIENCE

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Modelling schizophrenia using human induced pluripotent stem cells

(2011) Kristen J. Brennand et al.   NATURE

Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

(2011) Sergiu P Paşca et al.   NATURE MEDICINE

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing

(2011) A. E. Ayoub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells

(2010) Maria C.N. Marchetto et al.   CELL

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

(2009) Helen V. Firth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

(2009) Matthew B. Johnson et al.   NEURON

Gradients in the Brain: The Control of the Development of Form and Function in the Cerebral Cortex

(2009) S. N. Sansom et al.   Cold Spring Harbor Perspectives in Biology

Self-Organized Formation of Polarized Cortical Tissues from ESCs and Its Active Manipulation by Extrinsic Signals

(2008) Mototsugu Eiraku et al.   Cell Stem Cell

A framework for interpreting genome-wide association studies of psychiatric disorders

(2008)   MOLECULAR PSYCHIATRY