Massively parallel techniques for cataloguing the regulome of the human brain

Integrating CRISPR Engineering and hiPSC-Derived 2D Disease Modeling Systems

(2020) Kristina Rehbach et al.   JOURNAL OF NEUROSCIENCE

Studying Human Neurodevelopment and Diseases Using 3D Brain Organoids

(2020) Ai Tian et al.   JOURNAL OF NEUROSCIENCE

ASCL1- and DLX2-induced GABAergic neurons from hiPSC-derived NPCs

(2020) Natalie Barretto et al.   JOURNAL OF NEUROSCIENCE METHODS

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

(2020) Emily E. Burke et al.   Nature Communications

Transcriptional Programming of Human Mechanosensory Neuron Subtypes from Pluripotent Stem Cells

(2020) Alec R. Nickolls et al.   Cell Reports

Modeling the complex genetic architectures of brain disease

(2020) Michael B. Fernando et al.   NATURE GENETICS

A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles

(2020) Nancy Y. A. Sey et al.   NATURE NEUROSCIENCE

Transcriptomic Landscape and Functional Characterization of Induced Pluripotent Stem Cell–Derived Cerebral Organoids in Schizophrenia

(2020) Annie Kathuria et al.   JAMA Psychiatry

Using human pluripotent stem cell models to study autism in the era of big data

(2020) Ralda Nehme et al.   Molecular Autism

A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes

(2020) Gustav Y. Cederquist et al.   Cell Stem Cell

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

(2020) M. Grace Gordon et al.   Nature Protocols

Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants

(2020) Siwei Zhang et al.   SCIENCE

Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts

(2020) Laura M. Huckins et al.   Cell Reports

Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism

(2020) Michael S. Breen et al.   Molecular Autism

High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation

(2020) Matthew A. Lalli et al.   GENOME RESEARCH

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

(2020) Jason C. Klein et al.   NATURE METHODS

Cell type–specific genetic regulation of gene expression across human tissues

(2020) Sarah Kim-Hellmuth et al.   SCIENCE

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

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

(2019) Molly Gasperini et al.   CELL

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Genome-Scale CRISPRa Screen Identifies Novel Factors for Cellular Reprogramming

(2019) Jian Yang et al.   Stem Cell Reports

SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons

(2019) Kirill Zaslavsky et al.   NATURE NEUROSCIENCE

Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions

(2019) David M. Howard et al.   NATURE NEUROSCIENCE

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

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

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

(2019) Laura M. Huckins et al.   NATURE GENETICS

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Interrogating the Genetic Determinants of Tourette’s Syndrome and Other Tic Disorders Through Genome-Wide Association Studies

(2019) Dongmei Yu et al.   AMERICAN JOURNAL OF PSYCHIATRY

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Development of Human in vitro Brain-blood Barrier Model from Induced Pluripotent Stem Cell-derived Endothelial Cells to Predict the in vivo Permeability of Drugs

(2019) Yuan Li et al.   Neuroscience Bulletin

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa

(2019) Hunna J. Watson et al.   NATURE GENETICS

A screen of 1,049 schizophrenia and 30 Alzheimer's‐associated variants for regulatory potential

(2019) Leslie Myint et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Synergistic effects of common schizophrenia risk variants

(2019) Nadine Schrode et al.   NATURE GENETICS

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

(2019) Fumitaka Inoue et al.   Cell Stem Cell

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Mapping and predicting gene–enhancer interactions

(2019) Daniel J. Gaffney   NATURE GENETICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

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

(2019) Alexi Nott et al.   SCIENCE

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

(2019) Martin Kircher et al.   Nature Communications

Genome‐wide association study of shared liability to anxiety disorders in Army STARRS

(2019) John M. Hettema et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

(2019) Phil H. Lee et al.   CELL

Spatial genome exploration in the context of cognitive and neurological disease

(2019) Prashanth Rajarajan et al.   CURRENT OPINION IN NEUROBIOLOGY

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

(2019) Carl G. de Boer et al.   NATURE BIOTECHNOLOGY

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS

(2018) Amanda Dobbyn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Bayesian framework for multiple trait colocalization from summary association statistics

(2018) Claudia Giambartolomei et al.   BIOINFORMATICS

Genetic identification of brain cell types underlying schizophrenia

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

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

(2018) Alvaro N. Barbeira et al.   Nature Communications

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

(2018) Yanxia Liu et al.   Cell Stem Cell

Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder

(2018) Ditte Demontis et al.   NATURE GENETICS

Complete Disruption of Autism-Susceptibility Genes by Gene Editing Predominantly Reduces Functional Connectivity of Isogenic Human Neurons

(2018) Eric Deneault et al.   Stem Cell Reports

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

High-Throughput Approaches to Pinpoint Function within the Noncoding Genome

(2017) Antonino Montalbano et al.   MOLECULAR CELL

Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability

(2017) L E Duncan et al.   MOLECULAR PSYCHIATRY

Revealing the complex genetic architecture of obsessive–compulsive disorder using meta-analysis

(2017) Paul D Arnold et al.   MOLECULAR PSYCHIATRY

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

(2017) Rebecca Sims et al.   NATURE GENETICS

Generation of pure GABAergic neurons by transcription factor programming

(2017) Nan Yang et al.   NATURE METHODS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

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

(2017) Edsel M. Abud et al.   NEURON

Rapid and efficient generation of oligodendrocytes from human induced pluripotent stem cells using transcription factors

(2017) Marc Ehrlich 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

Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes

(2017) Seok-Man Ho et al.   Stem Cell Reports

An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells

(2017) Julia TCW et al.   Stem Cell Reports

FINEMAP: efficient variable selection using summary data from genome-wide association studies

(2016) Christian Benner et al.   BIOINFORMATICS

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

(2016) Jacob C. Ulirsch et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

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

(2016) Ryan Tewhey et al.   CELL

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

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Detection and interpretation of shared genetic influences on 42 human traits

(2016) Joseph K Pickrell 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

Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment

(2016) Nathan G. Skene et al.   Frontiers in Neuroscience

Generation of functional human serotonergic neurons from fibroblasts

(2015) K C Vadodaria et al.   MOLECULAR PSYCHIATRY

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

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

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

(2015) Eric R Gamazon et al.   NATURE GENETICS

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

(2015) Anca M Paşca et al.   NATURE METHODS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Conditionally Stabilized dCas9 Activator for Controlling Gene Expression in Human Cell Reprogramming and Differentiation

(2015) Diego Balboa et al.   Stem Cell Reports

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation

(2014) Ramon Y. Birnbaum et al.   PLoS Genetics

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Functional Maturation of hPSC-Derived Forebrain Interneurons Requires an Extended Timeline and Mimics Human Neural Development

(2013) Cory R. Nicholas et al.   Cell Stem Cell

Statistical Testing of Shared Genetic Control for Potentially Related Traits

(2013) Chris Wallace   GENETIC EPIDEMIOLOGY

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

Rapid Generation of Functional Dopaminergic Neurons From Human Induced Pluripotent Stem Cells Through a Single-Step Procedure Using Cell Lineage Transcription Factors

(2013) Ilda Theka et al.   Stem Cells Translational Medicine

SHANK3 haploinsufficiency: a “common” but underdiagnosed highly penetrant monogenic cause of autism spectrum disorders

(2013) Catalina Betancur et al.   Molecular Autism

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Use of Postmortem Human Dura Mater and Scalp for Deriving Human Fibroblast Cultures

(2012) Lindsay A. Bliss et al.   PLoS One

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

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13

(2008) Vincent Plagnol et al.   BIOSTATISTICS